PDB2PQR 2.0 which is now available from http://www.poissonboltzmann.org/docs/downloads/.

PDB2PKA as an alternative to PROPKA for calculating pH values used to protonate residues. This feature is EXPERIMENTAL. The libraries to make this feature available are included in the binary releases. They are NOT included in the source code and are not compiled with the rest of PDB2PQR. Improved web interface. NEW FEATURES

• Improved look of web interface
• Option to automatically drop water from pdb file before processing.
• Integration of PDB2PKA into PDB2PQR as an alternative to PROPKA.
• Support for compiling with VS2008 in Windows.
• Option to build with debug headers.
• PDB2PKA now detects and reports non Henderson-Hasselbalch behavior.
• PDB2PKA can be instructed whether or not to start from scratch with –pdb2pka-resume
• Can now specify output directory for PDB2PKA.
• Improved error regarding backbone in some cases.
• Changed time format on querystatus page
• Improved error catching on web interface.

OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit.

For more information see APBS & PDB2PQR: Electrostatic and solvation properties from complex molecules.

 

Just got this email.

A major update of ASObjC Explorer, version 4.1, is now available, just in time for the holiday season. This version incorporates a new and improved logging engine, incorporating extended AppleScript syntax styling and now resolving Cocoa objects -- no more will you have to deal with «class ocid» id «data optr000...» entries. ASObjC Explorer is the editor for Mavericks and Yosemite users wishing to write ASObjC code. You can read more here: http://www.macosxautomation.com/applescript/apps/explorer.html. You can also download it and try it out free for 30 days. To celebrate, you can use the coupon code NEWLOG to receive a $US10 discount between now and the end of January. Ho, ho.

 

I'm a long time BBEdit user but I still enjoy reading tips for making your use of BBEdit more efficient.

This blog post offers some tips for the various "Find" options within BBEdit.

I'd certainly agree with the final comment.

Text editors with limited capabilities keep you at a beginner level, no matter how long you've been using them. Serious text editors have a depth that rewards their users.

 

The Medicinal Chemistry Toolkit app is a suite of resources to support the day to day work of a medicinal chemist. Based on the experiences of medicinal chemistry experts, we developed otherwise difficult-to-access tools in a portable format for use in meetings, on the move and in the lab. The app is optimised for iPad and contains calculator functions designed to ease the process of calculating values of: Cheng-Prusoff; Dose to man; Gibbs free energy to binding constant; Maximum absorbable dose calculator; Potency shift due to plasma protein binding; Log D vs pH curves; Attrition Modeller, Drug-drug interactions.

What's New in Version 1.1 New (December 2014): Three additional functions: LogD vs pH curves, Attrition modeller and Drug-drug interactions.

 

The molecular modelling platform MOE 2014.09 has been updated, some of the new features in MOE include:

• MOE Project for Organizing SBDD Data
• Focused Protein and Antibody Libraries - Virtual Phage Display
• Quantum Mechanical Refinement of Conformations and Energy Minimization
• Template Forced Docking and Molecular Superposition
• Non-natural Amino Acid Support for Protein and Peptide Design
• Specialized Protein Family Databases and Search Interface

MOE is a software system designed to support Cheminformatics, Molecular Modelling, Bioinformatics, Virtual Screening, Structure-based-design and can be used to build new applications based on SVL (Scientific Vector Language).

There are several reviews of the previous versions of MOE here

 

I just noticed that an update to CodeRunner has been released. CodeRunner 2 is a complete overhaul of the original app and in addition to a host of new features also brings support for Yosemite. CodeRunner can run code in 20 languages out-of-the-box, and can be easily extended to run code in any other language. Adding a language is as easy as entering its terminal command.

 

Previously known as StarVue, the latest release of Ocura, version 6.0, is now available. This latest release will enable you to open and view files from the latest releases of StarDrop 6.0 and Sentira 1.0.

Ocura is a desktop application is specifically designed for scientists who want a simple way to load a set of molecule structures and easily browse through the data.

The Keyboard Extension Chemistry Keyboard has been updated.

What's New in Version 1.0.1
• Landscape keyboard now has a lower case Greek character map.
• Moved Grid of Elements to bottom of keyboard and improved its gesture handling
• Dark Keyboard had been blanking out the element grid.
• Search results were sometimes mislabeling temperatures as °C instead of K.
• Search results would occasionally include garbage strings.

There are many more apps for iOS on the Mobile Science site

 

The extremely popular reference management application Papers has been updated.

New Features

• Keyboard shortcuts: Adds "Add Review" & "Add Keywords" menu items (keyboard shortcuts ⇧⌘R and ⇧⌘K respectively) under the "Paper" menu, previously available in Papers 2.

Performance & Stability

• Paper management: Choosing "New Paper → From Reference…" when viewing a paper in the Reader no longer results in a crash.
• Reduces the likelihood of app crashes in rare circumstances, for example when editing note annotations.
• Papers Online: Changes to star rating, color labels or general notes for papers in Papers Online collections are now shown consistently.
• Library Search: Complete library metadata is now available when using the Search tab and "Papers Library" as the search engine.
• Papers Online: Improvements to error handling when signed in to Papers Online.
• Multiple authors or keywords can now be added or deleted without the "Add Author" & "Add Keyword" pop-over views being dismissed automatically.
• Library Export: All exporters now respect currently-selected papers regardless of which tab is selected, rather than only exporting any previously-selected papers in the Library tab.
• Dragging a metadata file onto the Overview inspector for a paper will now correctly offers the ability to replace the paper's metadata.
• Citekeys are now unlocked when they are deleted, reverting back to a universal citekey. Previously, blank citekeys would be exported.
• Spotlight Indexing: When switching to a different library, the Spotlight Search Index is automatically re-built if one does not exist.
• When closing the last paper in the Reader tab, the app will now return to the previously open tab before entering the Reader.
• QuickLook improvements: More filetypes are now compatible for previewing via QuickLook within Papers 3 for Mac.
• Improved handling of non-roman characters that require multiple keystrokes to type (such as Chinese, Japanese or Korean characters).
• Improved Library search bar typing responsiveness on OS X 10.10 Yosemite.
• Minor UI tweaks to menus & layout.

 

I just got this email

ChemDoodle 7, released in September, continues to receive great reviews and an ever increasing userbase in over 80 countries. We are working hard on many new features and continue to improve the massive number of features already available. We want to let you know that introductory pricing ends on December 31st, 2014. If you have friends or colleagues who are considering purchasing ChemDoodle, please tell them to purchase by the end of this year to take advantage of these low prices, and save as much as 50% off the regular price.

You can buy ChemDoodle here: http://www.chemdoodle.com/buy-now

There is a review of ChemDoodle here.

 

As part of the Computer Science Education Week (Dec 8-14th) Apple are hosting workshops in their retails stores.

Join us on December 11 for the Hour of Code, a free one-hour introduction to the basics of computer programming.

 

I've just added Plot2 to the list of data analysis tools available for Mac OS X.

This project started in 1993 with SciPlot on NeXTStep and was updated at the end of November 2014. Plot2 is designed for everyday plotting, it is easy to use, it creates high quality plots, and it allows easy and powerful manipulations and calculations of data.

 

Typed is the latest addition to the growing list of Markdown editors, designed from the ground up for clutter and distraction free writing.

 

The Mobile Science website continues to attract additional views. November has turned out to be the most popular yet with over 3,000 page views.

ChemDoodle, Elemental and Wolfram|Alpha continue to be the most popular.

 

I've continued to update the Scientific Applications under Yosemite we are now up to the 18th update. Many thanks for the people who have contributed.

With over 5,000 people viewing the page it is clearly pretty useful.

 

The excellent mixpanel continue to monitor iOS8 uptake among other things. iOS adoption is now over 60% with the steady decline in iOS7 continuing.

 

I must admit I’m a big fan of BBEdit for all my text editing, Markdown and python programming but I still keep an eye out for interesting alternatives. I was recently sent a link to PyCharm a Python IDE. PyCharm's code editor provides support for Python, JavaScript, CoffeeScript, TypeScript, CSS, and a number of other languages. What caught my eye was the recently added support for iPython notebooks, with PyCharm 4 you can perform all the usual IPython Notebook actions with *.ipynb files. Everything you're used to doing with the ordinary IPython Notebook is now supported inside PyCharm.

Another very useful features for scientific programming is the NumPy array viewer to easily get a graphical view of a NumPy array and support for matplotlib.

There is a really comprehensive support section that includes demos and screencasts .

 

With iOS 8 Apple now support third party custom keyboards

A custom keyboard replaces the system keyboard for users who want capabilities such as a novel text input method or the ability to enter text in a language not otherwise supported in iOS.

The Chemistry Keyboard allows users to enter chemical formulae, equations etc without having to struggle entering subscripts etc. Whilst the chemistry keyboard is an app in itself it also allows you to use the custom keyboard with other applications

You can read more details here.

 

I've just added Papers 3 for teams to the mobile science site. This app has been designed for teams, departments, companies and institutions to offer the same flexibility and easy management of Papers 3 to users with iOS devices as there is with desktop volume licenses.

 

Whenever I get a late night call I always fear the worst, I guess it is one of the unexplained features of being a parent. This night it was a very despondent child “My laptop has been stolen”. After confirming that they were OK and that nothing irreplaceable had been stolen I immediately logged into the Undercover website and logged the laptop as stolen and waited…

I think I first met Peter Schols the developer at WWDC in 2005 and heard about his idea for an application to trace stolen Macs, when the application became available I installed it on all my families machines. As time has gone on we have replaced machines and upgraded the software without any need to actually activate it until now.

The machine was stolen on a friday night from typical university accommodation, always people around, but you can never be sure if anyone has a copy of a key. We got an automated email from Orbicule saying the they were sorry to hear about the laptop and that they would inform me when the laptop was next online. They also asked me to fill in a form with the police incident information and contact details for the officer in charge of the case.

Nothing happened for several days and we were beginning to think the machine was lost for good when suddenly I got an email saying the machine was online. I quickly logged onto the Undercover website and within a short while we had the location, IP address, together with a series of photographs of the user. The police officer went around but unfortunately the culprit was out, over the next few days it was possible to build up a picture of the culprit’s working routine and to get screenshots of their bank account, ebay activities and much more personal information. Orbicule were then able to provide with a detailed evidence package to the police and they were able to target a time when the culprit would be at home.

The police were then able to arrest the culprit and recover the laptop!

The police were stunned by the detailed evidence that Orbicule were able to provide, I don't think they had ever seen such a comprehensive evidence package.

As I said I've had Undercover installed for years and it will be the first thing that is installed on any new machine.

 

Computable has been updated.

What's New in Version 1.1.1

• Fixed input cell text field scrolling issue on iOS 8
• Fixed issue with info button positioning on iOS 8
• Fix crash when showing info button
• Fix crash when presenting code completions
• Fixed welcome tour layout on iOS 8
• Fixed completions table view layout on iOS 8

Computable is a full-featured IPython system. Create, edit, and run IPython notebooks on your iPad

 

I just added Topspin from Bruker to the list of spectroscopy applications.

Topspin is capable of data processing of 1D and higher dimensional NMR datasets including Fourier transform, window functions, baseline and phase correction, peak picking, integration, line shape analysis (Gauss/Lorentz, dynamic NMR, solids), relaxation and multiplet analysis, spectrum and Fid simulation, printing/plotting, quantification, AU/Python/Macro programming. Optionally NUS processing and small molecule structure elucidation (demo licenses available). For Mac systems the CPU must be capable of executing 64bit-instructions according to “Intel Core 2 Duo” processor type or newer.

 

a href="http://www.biosolveit.de/SeeSAR/">SeeSAR version 1.6 has been released. It covers:

The ability to change the charge of an Atom (+/-) and to protect such change against ProToss (this is the automated protonation/tautomerism to optimize the overall H-bonding network) overwrite

Improved table: pM affinity, in/exclude multiple columns, the pose-specific context-menu, quick-find molecules including a 2D popup rendering, this can be very useful when trying to work out the structure from a 3D conformation.

There is a review of an early version of the software here

 

Papers for iOS has been updated. This is a substantial update and includes a number of new features together with significant improvements to performance.

• Library Filtering: You can now filter your library by a particular color label, as well as by all colors at once as in previous versions.
• Library Sorting: You can now sort in ascending or descending order when using any of the filters in the Library view or Federated Search.
• Sync Settings: The library sync settings section has been redesigned to give you more control over your sync settings and manual syncing.
• Notes: It is now possible to add General Notes to a paper on both iPad and iPhone, or edit existing notes.
• Support: Improvements to the "Help" section in the sidebar to include a completely redesigned support website and a direct link if you need to open a support request.
• Reading List: Improved interactions with the Papers Online Reading List.
• Linking to a Papers library on Dropbox now automatically starts an initial sync.
• Improves the "Add Keywords" screen to make it clearer which keywords are currently selected for the paper in question.
• Reduces the delay before the pop-up bottom menu bar appears on iPhone for better user experience.
• Adds a clear button to the Federated Search text bar to quickly clear a previous search query.

Performance & Stability:

• Authors are now added to a paper when using the "Match" functionality.
• User-added keywords are no longer removed when using the "Match" functionality.
• The correct PDF is now displayed when attempting to view a supplementary PDF that had been attached to a paper.
• An imported paper is now also opened automatically (as well as being imported) in the Reader when using the "Open in Papers 3" Safari functionality.
• Remaining issues with the "Open in Papers" Safari bookmarklet have been resolved.
• The "Automatic File Downloads" setting within Sync Settings will now download all available primary and supplementary files on a user's Dropbox for all papers in the library.
• The "Download All Files" functionality will now correctly download PDF files instead of associated webpages in all cases (except when PDFs can't be downloaded because they are behind a pay-wall).
• Using the Federated Search after unlinking from a library on Dropbox and deleting all local library data now returns search results.
• When choosing "Sort by Author", the Library is now sorted by surname first, and prioritizes papers with at least one author.
• Download progress bars now appear correctly for library items on iPhone as well as iPad.
• The token field bar now appears correctly on the Federated Search keyboard when using Papers 3 for iOS on iOS 8 devices.
• The color of a highlight annotation can now be changed once it has been added to a paper.
• Improved stability during initial app launch.
• Reductions to disk space usage by ensuring redundant PDF thumbnail cached data is removed when the app is launched.
• The Reading List contents are now refreshed after moving items from it to the Trash.
• Addresses some UI issues with the library screen when using Papers 3 for iOS on the iPhone 6 or 6 Plus.
• Prevents viewing the paper metadata inspector in landscape on iPhone to avoid UI issues.

 

A new production release of UCSF Chimera (version 1.10) is available.

Platforms: Windows, Mac OS X (including Yosemite), Linux. This will be the last release to support OS X 10.6 and 10.7.

New since version 1.9: Protein contact maps color-coded by distance, PDB biounit and CATH domain web fetch, plotting all-atom and backbone RMSDs along sequence alignments (previously only alpha-carbon RMSDs), update to AmberTools 14, "vop scale" density map normalization, Modeller dialog allows specifying distance restraints, further implementation of the MultiDomain Assembler homology-modeling pipeline.

More details are given below; see release notes for the full list: http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.10.html.

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.

 

The Electronic LabNotebook Findings has been updated

1.1.1, build 2396,
New psychology field, subscription to beta updates, and small fixes and improvements.
Release notes for version 1.1.1:
New: psychology field and subfields in the protocol library, as well as additional subcategories for the cookery "field".
New: subscription to pre-release versions of Findings. To be notified of beta versions, check the corresponding box in Preferences > Options.
Improvement: multiple spaces can be inserted, instead of being collapsed into one.
Improvement: native full-screen window button in Yosemite.
Improvement: displaying the year for dates outside the current year in the experiment cards.
Fix: typing composed characters using special keyboard input (Japanese, Korean, Chinese, etc) could lead to extra "fantom" characters.
Fix: undo not working when deleting an attachment while the selection includes part of the legend.
Fix: now showing styled text for the next task in experiment cards, instead of exposing the ugly and confusing markup.
Fix: experiment cards scrolling area not properly aligned with the window borders.
Fix: removing unused menu items that would only lead to confusion.
Fix: unsightly baseline changes when applying subscript or superscript.
Fix: the window would sometimes remain blank after exiting the welcome guide or the store.
Fix: rare issue where Dropbox sync could not be started because of an attachment with an extension starting with 'fd'.
Fix: library would not load when using Dropbox and the OS X account name is different from the home folder name.

 

ChEMBL is a manually curated chemical database of bioactive molecules . It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory (EMBL), based at the Wellcome Trust Genome Campus, Hinxton, UK. The database currently contains over 1.4 million unique structures with the associated activity at 10,579 different targets. It also acts as a repository for Open Access primary screening and medicinal chemistry data directed at neglected diseases.

Whilst the database can be downloaded, the data can also be accessed via a web interface (shown below) and a series of web services, these Vortex scripts show how it is possible to pull data from ChEMBL into Vortex.

As usual I’ve written it as a tutorial to try and offer some explanation how the script works, Scripting Vortex 23:- Accessing ChEMBL using Web Services

I think this rather nicely shows the power of web services and json.

There is a list of other Vortex scripts on the Hints and Tutorials page

 

I was recently sent details of a new website Chemplore the aim is to provide an modern, interactive and easy way to visualize small molecules and macromolecules in the browser. It's built using many modern web technologies and tools including WebGL, SVG and Go.

It pulls data from a variety of sources including PubChem and PDB, and provides interactive 2D and 3D viewers plus a variety of chemical information.

It is currently beta and the developers are looking for feedback

 

The iOS scientific calculator PhySyCalc has been updated. PhySyCalc 2.0 is now universal in supporting both iPhone and iPad, there is now a swipe up for keyboard and swipe down for quantities. Plus Numerous improvements to the calculator engine.

PhySyCalc reinvents the calculator. More intuitive than conventional calculator apps, PhySyCalc lets you do full calculations with units. For example, you drive 250 miles on a full 12 gallon tank of gas and want to calculate your mileage. In PhySyCalc you can skip all the unit conversions and just enter 250 mi/12 gal. PhySyCalc gives you the answer in mi/gal. Or, if you like, km/L or L/100 km, all in a few touches of your finger.

 

I was very much struck by this blog post on the Cryptogenomicon blog, in particular the comment that biologists need to be able to script.

The most important thing I want you to take away from this talk tonight is that writing scripts in Perl or Python is both essential and easy, like learning to pipette. Writing a script is not software programming. To write scripts, you do not need to take courses in computer science or computer engineering. Any biologist can write a Perl script. A Perl or Python script is not much different from writing a protocol for yourself. The way you get started is that someone gives you one that works, and you learn how to tweak it to do more of what you need. After a while, you'll find you're writing your own scripts from scratch.

I'd probably expand that to say that in most scientific disciplines being able to script is extremely useful. Whilst Perl has been (and maybe still is) a preferred scripting language for biologists I suspect that python is now the “lingua franca” for scientific scripting. I've given a couple of talks recently on the use of open source tools for drug discovery and I asked the audience for a show of hands for different programming/scripting languages and Python seems to be by far the most widespread. Indeed one of the key features that determines the selection of a program is that it provides a scripting interface that allows it to be integrated into a scientific workflow.

I'd also add that scripting does not have to result in some major software program, often the most useful scripts are those that do very simple things that just make life easier. The most popular download on this site is the applescript that simply prints the clipboard, it allows you select a piece of text from a page, copy, then print, no opening another application to paste it into.

Another example of everyday scripts are the Safari extensions, not sure what the structure of a named drug on a web page is, select the name and right click (or control click) and an option appears to search for the highlighted drug on ChemSpider and as if by magic a small window opens displaying the structure. Pretty neat and the beauty is that it only involves a small amount of javascript programming, all the heavy lifting has been done by Apple who provide the Safari extension framework and the ChemSpider folks who provide the database and web service.

Similarly the Chemical Identifier Resolver script makes use of the Chemical Identifier Resolver (CIR) by the CADD Group at the NCI/NIH to convert a huge variety of chemical identifiers into a structure.

I’d also echo the view that you don’t need to have attended a computer science course, I very firmly believe in “cut and paste” school of programming. Take an existing script and modify it to see how it works, then customise it to solve a problem that you have.

In addition to the Applescripts section the “Hints and Tutorials” section of this site includes many more scripts that use Python, Python, javascript etc., you are free to use any as starting points, if you feel they maybe generally useful I’d be happy to add them to the site.

 

Apple has released the Darwin source code for OS X 10.10 here.

 

I’ve just added Peppermint to the list of Markdown Editors, Peppermint is a sophisticated text editor that has dozens of plugins/extensions for everything you need: live preview your HTML, convert LESS or Markdown, beautify CSS/JS/HTML, complete FTP/SFTP support, Regex Editor. Well worth a look.

 

Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Given that this seems to be such a major upgrade I thought I’d set up a spare machine to test applications before I update my main machine. I’ll update the list regularly and feel free to send in information.

I have a number of applications/libraries/toolkits installed using Homebrew and installed in usr/local, this is known to cause extended installation times for Yosemite. So don’t worry if it appears the install is stuck at 1 min remaining.

If you do use Homebrew then it is worth updating

brew update
brew upgrade

Aabel 3 appears to be working fine

BBEdit version 10.5.13 and newer are compatible with Yosemite

Beaker all seems OK

ChemBioDraw versions 12, 13 and 14 all function as before.

ChemDoodle all seems to work fine

Chimera aka UCSF Chimera versions 1.10 and higher are working on Yosemite.

Conquest and  Mercury from CCDC works fine but you may need to reinstall Quartz (see below)

Cresset report that after testing that Torch, Spark, Forge and Blaze appear to be compatible with Yosemite, the only cosmetic issues are due to a couple of as yet unresolved bugs in QT here.

Cytoscape 3.1.1 seems to be working fine

DataWarrior no issues

EndNote X7.2 works well with Yosemite.

Findings Electronic Notebook no issues, only small issue is that the ‘+’ button of the window does not trigger full-screen, though it can still be done via the Window menu.

IDL 8.2 and earlier gags on a missing reference in libPng.dyld, but IDL 8.3 and later is OK

Igor Pro version 6.3.5.5 works fine

iNMR no problems reported

MacVector 13.0.6 No significant issues reported

Marvin Marvin, Instant JChem, and JChem suite all work but require Java 7 (available here http://support.apple.com/kb/DL1572

Mathematica no issues reported

Matlab 2014b works fine, 2012a thru 2014a need patching (directions available from Mathworks support site. Older versions will not run at all..

MOE works fine but you may need to reinstall Quartz (see below)

OpenBabel no issues so far

Opsin all works fine

OSRA no issues

Papers Current version is compatible but not optimised, they hope to have a beta out of a substantially redesigned version next week.

Pro Fit 6.2 appears to work fine.

Pybel no issues reported

PyCharm works fine

Pymol All these are confirmed to work:

• MacPyMOL 1.7.2.3
• MacPyMOLX11Hybrid 1.7.2.3 after XQuartz reinstall (see below)
• Open-Source PyMOL with homebrew

Known issues with MacPyMOL: - Movie export broken. Edu-only-PyMOL (free Student version) Does not work.(Now updated to work with Yosemite)
No reports so far about about - Other legacy versions (0.99 etc.) Apparently progam will not open - Open-Source PyMOL with fink or macports

PyRx 0.8 for docking works fine

RDkit no issues reported

SeeSAR all seems to be working fine

Sente 6.7.8 seems to run fine, except that it cannot open a reference library from the File > Open... dialog box. Workaround is to open from Finder.

Spartan 14 does not work because the Sentinel drivers are broken in Yosemite. The problem is NOT with Spartan, it is with the SafeNet developed Sentinel Run-Time Environment driver (the license manager). SafeNet has not given a definitive date when they will release an updated driver with Yosemite compatibility, but they are working on this. Best advice is to not upgrade but if you have to then contact support@wavefun.com for a temporary alternative license procedure.

Torch no issues

VarSeq no issues

Vortex Upgraded when the developer preview came out.  All works fine

The VVI products work well enough on Yosemite, but I'd like to achieve a higher level of quality for Yosemite (and iOS/iPad). There is an ongoing beta program for this product: https://itunes.apple.com/us/app/graph-ide/id904733611?mt=8 which is Graph Builder reincarnated on the iPad. There is also a beta program ramping for Graph Builder on Yosemite: https://itunes.apple.com/us/app/graph-builder/id470597599?mt=12 but a last minute interaction bug with Yosemite has delayed that for perhaps a few days. Please feel free to broadcast this information as you see fit. Beta program participation should be directed to support@vvi.com

VMD no issues reported

Wizard Pro is fully Yosemite compatible

XQuartz it seems the Yosemite installer deleted the symlink between /opt/X11 and /usr/X11; you can either reinstall Quartz or try "ln -s /opt/X11 /usr/X11"

Updated 30 October 2014

 

I’ve been asked if I could include some biology/bioinformatics tools in the alphabetical listing, and I’m happy to add any that are sent to me, this week I’ve added.

CellDesigner

Cytoscape 3.1.1

GenomeBrowse

VarSeq

 

The hugely popular Wolfram|Alpha has been updated.

With Wolfram|Alpha on your iPhone or iPod touch, you can explore a vast world of knowledge through an app adapted for your ever-changing, on-the-go lifestyle. Use Wolfram|Alpha to discover new information about the world and to deliver expert knowledge into any facet of your mobile life. The Wolfram|Alpha App plugs directly into the Wolfram|Alpha supercomputing cloud, computing answers to your questions quickly, efficiently, and without draining your battery.

 

New version for Yosemite and Mavericks users

ASObjC Explorer 4 is a script editor built to take full advantage of AppleScript’s ability to call Cocoa methods. With AppleScriptObjC-based libraries available in Mavericks and Yosemite, and now direct access to AppleScriptObjC code in Yosemite, ASObjC Explorer 4 can help you write and debug your code more quickly, more effortlessly, and more efficiently. It also makes a great external editor for those developing in Xcode.

ASObjC Explorer lets you write your code, write separate testing code, step through your code, log what happened, and even add scripting terminology — all in one document window. When you have finished, you can use your document as a script or library, or export to your favorite format, including Mavericks-compatible applets with embedded script libraries.

Full details are here.

 

My favourite text editor has just been updated!

BBEdit 11 has been released, with improved syntax colouring, a sophisticated text clippings manager, updated “Find Differences” and dialog boxes, floating palettes, and many internal subsystems have been rewritten or updated to support new features, improve performance, add refinement, and make future enhancements possible.

In all, BBEdit 11 contains over two hundred additions, changes, and refinements. The detailed change notes contain complete information.

Always worth a read, I particularly liked

Worked around a bunch of antisocial behaviors in the OS that would cause floating windows to end up all over the place after disconnecting and then reconnecting a display (typically an external display connected to the laptop). Now, the OS may still make your palettes dance around like they're on "The Price Is Right", but once you put them where you want them, the application will remember their positions more reliably.

Check the website for upgrade pricing.

 

Findings LabNotebook for iOS has been released. This comes with Dropbox sync.

There is a review of the MacOSX version here.

 

In addition to the Swift Blog there is now a dedicated Swift website

Swift is an innovative new programming language for Cocoa and Cocoa Touch. Writing code is interactive and fun, the syntax is concise yet expressive, and apps run lightning-fast. Swift is ready for your next iOS and OS X project — or for addition into your current app — because Swift code works side-by-side with Objective-C.

The latest entry on the Swift blog deals with “Failable Initialisers” a new feature in Swift 1.1 part of Xcode 6.1.

 

There have a few new additions to the Mobile Science site taking the total number of apps up to 350.

These include the Chemical Engineering App Suite for iPad and iPhone, and a series of apps from Wavefunction, Inc that cover molecular structure and bonding called the ODYSSEY applications.

 

Yosemite catches up to 'Everyday AppleScriptObjC'

Myriad Communications pleased to announce the availability of the second edition of 'Everyday AppleScriptObjC', updated for both Yosemite and Mavericks.

Yosemite confirms AppleScriptObjC's position as an important component of AppleScript, giving access to the Cocoa frameworks and their functionality wherever scripts are run. It is now truly an "everyday" option.

'Everyday AppleScriptObjC', Second Edition, provides an introduction to using the Cocoa frameworks from a scripter's point of view. It covers writing the code, in both Mavericks and Yosemite, as well as deployment issues.

The book has been updated to cover Yosemite, as well as to expand coverage in other areas. It is full of usable code snippets, which are also provided in file form in both Mavericks and Yosemite formats.

'Everyday AppleScriptObjC', Second Edition, is by Shane Stanley, author of 'AppleScript Explored', the guide to using AppleScriptObjC in Xcode. You can find out more here:<http://www.macosxautomation.com/applescript/apps/everyday_book.html>. It is available now for $US14.95.

 

I was just glancing at the chart on Mixpanel and I see that iOS8 is now the major iOS version. With iOS8 and iOS7 comprising over 96% of the market share it certainly makes it easier for developers to maintain compatibility.

 

OpenEye have announced the release of VIDA v4.3. This is a major update with many new features and enhancements, including improvements to depiction, 2D alignment, list manager manipulation, surface selection and display, default colouring schemes, both visual and list-driven atom subset selection, cluster viewing, colouring by SD property and extension management.

One feature I’m sure will be very popular is the new advanced depiction options, including atom property maps from the Grapheme TK, substructure highlighting, and 2D structure alignment, are available for depiction in the 2D window and spreadsheet

Support for Mac OS X 10.8 and 10.9 was added
Mac OS X 10.6 is no longer supported

 

Mestrelab Research have just announced the release of the NMR application Mnova 9.1.0. This release fixes several bugs and incorporates many new features on NMR, MS, the Molecule Editor and the GUI.

This new version also includes the release of the Mnova Screen plugin, an automatic tool for the analysis of ligand screening NMR data.

It also includes a long list of bug fixes

 

The NIH 3D Print Exchange now has over 460 models available for printing, ranging from small molecules to proteins and macromolecular assemblies to anatomical models. There are also an increasing selection of lab ware, including small flasks and racks.

There are more resources details here.

 

OpenEye ihave announce the release of POSIT v3.1, the component of the OEDocking suite devoted to pose prediction.

This update includes:

• The HYBRID and FRED algorithms have been incorporated into POSIT, the appropriate method is determined by analyzing the ligand to pose against the input receptors.
• Multiprocessing has been enabled through the use of MPI, to speed calculations.
• POSIT now supports a list of receptors files or .lst file as input. This overcomes command-line limitations for the number of receptors that can be used simultaneously.
• Added a MEDIOCRE result rating for results between 33% and 50% probability.
• Command line parameters have been simplified and updated to be compatible with the OEDocking Suite of tools.

POSIT is designed for the posing problem in lead optimization, i.e. how best to leverage project information from previous protein-ligand structures to predict the pose of a new ligand. It does this by assessing the similarity of the new ligand to known bound structures. Performance degrades as similarity decreases and so at some point it is worth searching more exhaustively.

 

Several more apps have been updated recently.

ElementalDB has been updated to use ChEMBL 19.

ChemSearch has more pricing info and now uses ChemDoodle web components 6.0.1

Chemistry by Design has been updated for iOS8.

 

I’ve had a couple of people mention that they have not updated to iOS8 because they don’t have enough space on their iPhone/iPad, well the good people at MacWorld have released a step by step video that shows how to use iTunes on your Mac to do the update.

http://www.macworld.co.uk/how-to/iosapps/how-update-iphone-ipad-ios-8-without-deleting-3451992/

 

One of the really neat features of the latest version of Vortex (> build 29622) is the ability to script multiple sub-structure searches using SMARTS. There are many occasions when this sort of feature is useful, if you want to flag molecules that contain reactive functional groups, toxicophores, or PAINS functional groups that have been shown to interfere with a variety of screens. Alternatively if you have a drug discovery project with multiple chemotypes you might want to tag particular groups of compounds as belonging to a named series to aid analysis.

The latest Vortex tutorial/script shows how to do this.

 

SeeSAR 1.5 has been released. SeeSAR it is intended as an interactive tool for designing/improving ligands for drug discovery.

The latest release covers two major topics: 1. A series of features that make the editing more swift and easier. To this end they introduced hot-keys, context menus and drawing a bond by drag&drop. 2. Often times people use SeeSAR for visual inspection e.g. after docking. Now normally you'll have multiple poses per compound. For a better overview the Table now allows you to collapse all poses to just one line per compound.

Furthermore you can set a bookmark to indicate what you like and export only the ones on the wish list.

There is a review of SeeSAR here.

 

If you have needed to write a manuscript with co-workers on different sites you will know what a pain it can be to keep track of the latest version as everyone makes additions and changes. There is a very useful article in Nature 514, 127–128 (02 October 2014) doi, describing several browser-based collaborative writing tools.

Four tools are described, writeLaTeX, shareLaTeX, Fidus Writer, Authorea, whilst you can also use something like Google docs these tools are aimed squarely at those writing technical articles, with support for building bibliographies and incorporating references from reference managers. For a great introduction to drawing chemical structures in Latex have a look at https://www.sharelatex.com/learn/Chemistry_formulae and http://chimpsky.uwaterloo.ca/mol2chemfig/

 

ChemSpider has been updated with additional advanced filtering options (e.g. log P, density, rule of fives violations, etc.). Also a minor UI tweaks and bugfixes.

A new addition to the mobile science site 3D Molecules Edit & Test,

FEATURES:

• Building molecule model of any organic or inorganic compound using most of periodic table elements.
• “Test yourself” mode to build the target chemical compounds.
• Support of single, double and triple bonds.
• Building molecule models of cyclic compounds.
• Hints which provide information about what's going wrong with the builded molecule.
• Visualization of Wireframe style, Stick style, Ball and Stick, Spacefill (CPK) models.
• Visualization of atomic orbitals and electron effects.
• T-shaped and «seesaw» molecular geometries support.
• Availability of information about the bond length and chemical element symbols in the molecule.
• Bond-angle optimization.
• Saving and sending the created model by e-mail.
• Loading, editing and saving molecule in SDF file format.
• Loading, editing and saving molecule in PDB file format.
• Creating, sending and opening molecule verification file.
• Export to VRML format for builded molecule.
• Opening the molecule file attachments directly from Mail.
• Opening and saving created molecules in cloud services and third-party applications.

 

When I created the Mobile Science site I did wonder how popular it would be. I occasionally check the page views and September has proved to be the busiest month to date with over 2400 page views.

As you might expect the three most recent additions generated the most page views with Computable a iPython system for the iPad topped the list, closely followed by the Medicinal Chemistry Toolkit an app designed to help drug designers. In third place was Chemical Valence a teaching aid to learn about chemical bonding.

In fourth place was ChemDoodle Mobile this is the iPhone and iPad companion to the popular chemical publishing desktop application, this app has also proved to be the most popular upvoted on the mobile science site. Two apps tied for fifth place Elemental and ChemDraw for iPad.

I’ve tagged each of the applications in order to make searching a little easier and the most popular tag is Chemical Drawing, closely followed by Molecule Viewer.

There are now 340 entries spanning a diverse area of science, if anyone knows of any that I’ve missed feel free to send me the App Store link.

 

The popular reference management application Papers has been updated.

Freehand annotations that were added using Papers 3 for iOS are now synched and displayed on Papers 3 for Mac! (Freehand annotation editing on Papers 3 for Mac will be added in a future update). Dragging one or more papers from your library into a note annotation will now add the citekey references to that note. Scripting API: It's now possible to set a publication's authors or editors via a string of person names:

tell application "Papers"
    set selectedPapers to selected publications of front library window
    set author names of first item of selectedPapers to "Griekspoor, A.C.; Neefjes, J.J.; Groothuis, T.A.M."
end tell

I’m delighted to see that they are already addressing bugs that have arisen in OS X 10.10 (Yosemite).

 

I just got this email

Thank you for your collaboration in helping us to test the beta version of the FORECASTER Suite 2014. From your feedback and bug reports, we have now released the final version of the Suite. The files were updated and posted on the download page. Please send us any bugs that you might have not yet reported.

The FITTED docking tool was initially been developed as a suite of three programs: SMART (used to prepare the small molecules for docking), PROCESS (used to prepare the protein files for docking) and the docking program FITTED. More recently, these three programs together with several others have been integrated into a single package, namely FORECASTER.

More information can be found here http://fitted.ca/download.html#forecaster

 

Caleydo is an open source visual analysis framework targeted at biomolecular data. It has been described in a number of publications and I noticed that a recent project ConTour included chemical structures.

Large scale data analysis is nowadays a crucial part of drug discovery. Biologists and chemists need to quickly explore and evaluate potentially effective yet safe compounds based on many datasets that are in relationship with each other. However, there is a is a lack of tools that support them in these processes. To remedy this, we developed ConTour, an interactive visual analytics technique that enables the exploration of these complex, multi-relational datasets.

Christian Partl, Alexander Lex, Marc Streit, Hendrik Strobelt, Anne-Mai Wassermann, Hanspeter Pfister, Dieter Schmalstieg ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery IEEE Transactions on Visualization and Computer Graphics (VAST '14), to appear, 2014.

I’ve added Caleydo to the listing of data analysis tools.

 

Swift is a new programming language from Apple for iOS and OS X apps that builds on the best of C and Objective-C, without the constraints of C compatibility. I’m delighted to hear that people are starting to explore it’s use in scientific applications. Dr. Alex M. Clark has posted his early impressions on the Cheminformatics blog, well worth a read.

There is also the Swift blog for more interesting tips.

 

A interesting page monitoring iPhone 6 and iOS 8 adoption/usage rates.

 

ChemDoodle is now firmly established as one of the key chemical drawing packages that offers an inexpensive alternative to some of the increasingly expensive drawing packages. It also has the advantage in that it supports Mac, Linux and Windows and offers access to ChemDoodle Web Components. I’ve written a review of the latest update.

 

Since I added the new MacPro to my network I’ve decided I need a network file server and improved backup strategy. After reading a number of reviews I’ve narrowed the choice to Synology DS213J 2 Bay DiskStation Desktop NAS (Amazon link) which seems ideal for a small office environment.

I was slightly surprised to find that the enclosure with 8TB storage Synology DS213J 8TB (2 x 4TB WD Red) 2 Bay DiskStation Desktop NAS is pretty similarly priced to buying the enclosure and drives separately.

Any comments or suggestion?

 

The ADF modeling suite consists of the GUI, the powerful DFT codes ADF (molecules) and BAND (surfaces, bulk), the semi-empirical DFTB and MOPAC2012 modules, ReaxFF, and COSMO-RS. The binaries for the entire suite work out of the box, in parallel, on all popular platforms (Windows, Mac, Linux).

A summary of new features and improvements in the 2014 release:

• lower-memory, better parallel SCF in ADF
• significant speed-ups in DFTB and the periodic DFT code BAND (AO-based)
• many-body dispersion functionals (Tkatchenko et al.)
• conformer search, support for multiple configurations, spectra averaging
• TD-DFTB and DFTB-NEGF, with electronic parameters for 87 elements
• ReaxFF force field optimizer, Grand Canonical Monte Carlo
• COSMO-SAC 2013-ADF parameters

 

You might want to have a look at a new website that I’ve just been sent details of.

CHARMMing contains an integrated set of tools for uploading structures, performing simulations, and viewing the results. In order to provide the best possible user experience, it incorporates a number of freely available tools such as JSmol for visualization and an automatic residue topology file (RTF) generator (GENRTF) which generates the necessary information for atoms and residues that are currently not supported by the CHARMM force fields. Below is a partial list of functionality that currently is incorporated into charmming.org:

• A CHARMM tutorial that has been specifically designed for novice CHARMM users
• PDB/CRD reader and input script generator
• Integrated molecular graphics
• Integrated simulation tools (i.e. minimization, solvation, dynamics)
• Automatic topology generation

 

Findings is a Mac electronic lab notebook designed for scientists that aims to replace the paper lab notebook still in use in most research labs. I did have a look at Findings when it came out but it did not seem well suited to a chemist so I thought I’d wait and see what the reaction was from other disciplines. Findings app has very distinguished roots, it was founded by Alexander Griekspoor (author of the Apple design award winning Papers and EnzymeX) and Charles Parnot (of Xgrid@Stanford fame), an ex-scientist metamorphosed into a software developer.

A reader sent me this initial view of Findings and I thought I’d share it since it nicely showcases the application:

Here is an interesting article highlighting the current status of WebGL. WebGL is finally available by default in all browsers on all platforms and on both desktop and mobile devices.

Scientific applications now have the ability to creatively communicate information in both 2D and 3D through HTML5 across all platforms and can be distributed freely over the internet. We have been making sure that WebGL support in the ChemDoodle Web Components remain compliant and thorough throughout its development. So no worries if you have not yet learned WebGL, as you can take advantage of this powerful 3D graphics technology for free under the GPL license through the ChemDoodle Web Components, joining hundreds of other projects that currently use our library to create the most stunning scientific web and mobile apps.

There is a demo of what can be done with ChemDoodle Web components in the hints and tutorials.

 

I just got this email

iScienceSearch, the Internet search engine for chemists is now completely free! Please click http://isciencesearch.com/iss to start the application. There is nothing to download. This application will run in your browser.

I’ve previously reviewed iScienceSearch and it seem to have been updated considerably since then.

iScienceSearch is a meta search engine that searches over 100 different databases, The search engine is intelligent and will search using any synonyms or chemical structures of your search query to extend the search to data sources that might not include the original query text.

• Search the Internet by drawing a structure.
• Type a name or identifier and you get the structure.
• Find suppliers for lab and research chemicals
• Search the AKosSamples database by substructure

 

The latest incarnation of iOS is a major change and the most comprehensive review I’ve seen to date is the Ars Technica iOS8 Review

One feature that may be of particular interest is iCloud Drive, iCloud Drive keeps the concept of application-specific folders for data, but it allows users (and other applications) to see the filesystem and access data stored in multiple app folders. This means that you can open a molecular data file with the applecation of your choice.

BUT

In iOS 8, you'll be given the opportunity to upgrade from standard iCloud to iCloud Drive once you sign into your account, but you should tread lightly here—converting your account to use iCloud Drive is a one-time deal and it can't be reversed. iOS 8 still supports "Documents & Data" sync, the old-style iCloud syncing method that will continue to work with Mavericks and older iOS versions.

If you still use Macs running OS X 10.9 or older or if you have an iPhone you can’t upgrade to iOS8 and you want to sync data between them, don't turn iCloud Drive on.

 

ChemSpider Mobile has been updated.

Version 2 has a completely redesigned user interface, with powerful new functionality for previewing search results, saving compounds, and exporting to other apps and webservices. The new look incorporates the latest graphical art from the Royal Society of Chemistry, and the style conventions of iOS 7.

 

The CLC Drug Discovery Workbench has been updated to version 1.5.

The new features are described on the updates page and in a video.

 

George Papadatos, from the ChEMBL group, has produced a superb iPython notebook tutorial demonstrating the use of RDkit.

 

I’ve updated the page of clipboard managers, correcting a couple of broken links and adding a few new apps that readers have sent me details of.

 

It has just been announced that Swift has reached 1.0.

Today is the GM date for Swift on iOS. We have one more GM date to go for Mac. Swift for OS X currently requires the SDK for OS X Yosemite, and when Yosemite ships later this fall, Swift will also be GM on the Mac. In the meantime, you can keep developing your Mac apps with Swift by downloading the beta of Xcode 6.1.

Swift is an innovative new programming language for Cocoa and Cocoa Touch. Writing code is interactive and fun, the syntax is concise yet expressive, and apps run lightning-fast. Swift is ready for your next iOS and OS X project — or for addition into your current app — because Swift code works side-by-side with Objective-C.

 

ComputableUpdated

• Added Python code completions and inline documentation

• Added a Welcome Tour for new users

• Dropbox sync fixes

• Fixed a bug with incorrect initial caret position in the Python editor

• No longer hiding the navigation bar in landscape mode to keep the navigation bar buttons available

Computable is a full-featured IPython system that allows users to create, edit, and run IPython notebooks on the iPad

 

The latest issue of J Cheminformatics has an article entitled “A document classifier for medicinal chemistry publications trained on the ChEMBL corpus”, Journal of Cheminformatics 2014, 6:40 doi:.

The large increase in the number of scientific publications has fuelled a need for semi- and fully automated text mining approaches in order to assist in the triage process, both for individual scientists and also for larger-scale data extraction and curation into public databases. Here, we introduce a document classifier, which is able to successfully distinguish between publications that are ‘ChEMBL-like’ (i.e. related to small molecule drug discovery and likely to contain quantitative bioactivity data) and those that are not. The unprecedented size of the medicinal chemistry literature collection, coupled with the advantage of manual curation and mapping to chemistry and biology make the ChEMBL corpus a unique resource for text mining.

The models, workflows and tools are freely available for download. https://github.com/chembl/chemblliteratureclassifier

 

CheS-Mapper has been updated to version 2.4.

New Features Add Moss as new structural fragment mining algorithm Show the number of distinct 3D positions (at the top right, alongside other dataset info) Mapping warnings are now acessible within the viewer (Menu: Help > Show mapping warnings) Add hint for multiselection of compounds via 'control'-key (is shown when zooming into compounds for the first 3 times) More Changes The viewer no longer zooms out when changing component size or spread Add log conversion of feature values, by adding a new feature, instead of log-highlighting (gives better overview of log-distributed values, e.g. within the chart) Multiple selected compounds are now highlighted within the chart for nominal features (was only possible for numerical features) Fix Fix error that showed strucutural fragment values as '1'/'0' instead of 'match'/'no-match'

CheS-Mapper (Chemical Space Mapper) is a open source 3D-viewer for chemical datasets of small molecules, a publication in the Journal of Chemiformatics describes an early version of the application DOI: 10.1186/1758-2946-4-7, and there is a review here.

 

There is a recent publication “How Mobile Devices and Apps for Green Chemistry can bring value to scientists” DOI nicely illustrates how much mobile devices have become part of our working lives.

We made the American Chemical Society Green Chemistry Institute (ACS GCI) Pharmaceutical Roundtable Solvent Selection Guide more accessible and have increased its visibility by creating a free mobile app for the Apple iOS platform called Green Solvents. We have also used this content for molecular similarity calculations using additional solvents to predict potential environmental and health categories, which could help in solvent selection.

Green Solvents is a reference card for chemical solvents, with data regarding their "greenness": safety, health and environmental effects.

There is a full listing of mobil iOS apps on the MobileScience Website

 

An interesting meeting for anyone who is interested the storing, exchange of chemicals, names or identifiers.

What’s in a Name:  Terminology and Nomenclature the unsung heroes of open innovation

21st October 2014
CICAG and ITaaU one Day Meeting
RSC, Burlington House, London

Introduction & Keynote
10.00 Registration and tea/coffee
10.30 Welcome. Representative from the Royal Society of Chemistry
10.40 Introduction. Jeremy Frey, University of Southampton

10.45 Keynote presentation: What's in a Name? Possibly Death and Taxes! Richard Hartshorn, University of Canterbury, Christchurch, New Zealand; Past President, IUPAC Division of Chemical Nomenclature and Structure Representation

Nomenclature Challenges for the 21st Century
11.25 Extended Structures, Crystallography and Polymers – Challenges. Clare Tovee, Cambridge Crystallographic Data Centre
11.45 Naming Polymers – Buy One Get One Free. Richard Jones, Emeritus Professor of Polymer Science, University of Kent; UK National Representative, IUPAC Polymer Division
12.05 The Importance of Chemical Identifier Standards in the Pharmaceutical Industry. Colin Wood, Enterprise Information Architect, R&D IT, GlaxoSmithKline
12.25 Discussion
12.45 Lunch

The Impact of Computers and the Web
13.30 The Web – What is the Issue? Egon Willighagen, Department of Bioinformatics, Maastricht University
13.50 Health and Safety and the Semantic Web. Mark Borkum, Department of Chemistry, University of Southampton
14.10 Defining Chemical Classes in OWL-based English for ChEBI. Janna Hastings, EBI
14.30 The IUPAC Green Book – Unit's Dictators Source Book? Jürgen Stohner, Zürich University of Applied Sciences; IUPAC Commission on Physicochemical Symbols, Terminology, and Units (Comm. I.1)
14.50 Reaction InChI – Distilling the Essence of a Chemical Transformation. Jonathan Goodman, University of Cambridge and Jeremy Frey, University of Southampton
15.10 Discussion
15.30 Tea/coffee

15.50 Keynote presentation: From Chaos Comes Order – Managing Data in Open Source Drug Discovery. Matthew Todd, University of Sydney

16.30 Discussion and RSC/CICAG Role
16.50 Meeting closes

 

I use markdown extensively on my website and so I tend to keep an eye out for new developments and editors.

Markdown is a text-to-HTML conversion tool for web writers. Markdown allows you to write using an easy-to-read, easy-to-write plain text format, then convert it to structurally valid XHTML (or HTML).

Whilst beautifully simple initial implementation as it has grown in popularity it has evolved and with no unambiguous specification has become fragmented, however I’m delighted to hear that there is now a standard markdown specification in development. There is more information on the website http://standardmarkdown.com.

 

The latest update to the hugely popular chemical drawing package ChemDoodle has just been announced.

Some of the new features in ChemDoodle 7:

• A new and improved interface based on the feedback from the last 6 years. The new interface is focused on the content and allows you to maximize your drawing areas. Widgets are now floating and can be individually enabled and disabled.
• ChemDoodle 3D. A new application for creating 3D graphics and more for the sciences. You have full control over the 3D graphics and animations, including text. Distance, angle and torsion measurements are provided. Also a corresponding builder for 3D ChemDoodle Web Components. There is so much more.
• Full multipage document support. Create lists of pages or grids. Draw between all pages and print them out.
• BioArt. Large, full color, libraries of new art for use in biological figures, including animals, organs and organelles.
• A set of 48 safety symbols included in the glassware set.
• Significant performance improvements, in many cases 20x faster than v6. ChemDoodle will now load faster, work faster and respond faster.
• New drawing features: collapse fragments to labels, incrementing list attributes (to quickly number or designate parts of structures), new TLC options, rotate atom labels if only a single atom is selected (as opposed to the global option), and more visual specifications among others.
• Twitter integration.
• Integration with the LabArchives ELN.
• Support for both Java 6 and 7 on Mac OS X.
• Dozens more improvements and additions.

If you want to find out more about ChemDoodle 7 there are a series of Webinars that describe it in detail

I hope to write a review later this week.

 

The OpenPhacts API has been updated to include two new data sets and the corresponding API calls.

1) DisGeNet target-disease associations These API calls use URIs inputs that correspond to either diseases or targets (proteins or genes). The disease identifiers correspond to UMLS CUIs, Mesh ids or ConceptWiki and can use several namespaces, e.g. http://linkedlifedata.com/resource/umls/id/C0004238, http://purl.bioontology.org/ontology/MSH/D001281, or http://www.conceptwiki.org/concept/index/095cb66f-76ef-41b5-a8ae-c39352e6007e

2) neXtProt nanopublications for tissue expression (PREVIEW mode) These API calls use URIs that correspond to either tissues or targets. The tissue identifiers correspond to the Caloha tissue ontology from neXtProt. These identifiers can use either the namespace from the neXtProt database (e.g. http://www.nextprot.org/db/term/TS-0564, will be operational next week) or the Caloha ontology (ftp://ftp.nextprot.org/pub/currentrelease/controlledvocabularies/caloha.obo#TS-0564, operational now).

To reduce the barriers to drug discovery in industry, academia and for small businesses, the Open PHACTS Discovery Platform provides tools and services to interact with multiple integrated and publicly available data sources. To integrate this data, extensive cross-referencing of scientific concepts is needed across all databases.

 

Sage is a Python based free open-source mathematics software system licensed under the GPL. It builds on top of nearly 100 open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R to provide a common unified interface, either as a notebook in a web browser or the command line.

In addition to a local installation it is also possible to use SageMathCloud a free service with support from the University of Washington.

I’ve added Sage to the list of data analysis tools for Mac OS X.

 

The Medicinal Chemistry Toolkit app is a suite of resources to support the day to day work of a medicinal chemist. Based on the experiences of medicinal chemistry experts, we developed otherwise difficult-to-access tools in a portable format for use in meetings, on the move and in the lab. The app is optimised for iPad and contains calculator functions designed to ease the process of calculating values of: Cheng-Prusoff; Dose to man; Gibbs free energy to binding constant; Maximum absorbable dose calculator; Potency shift due to plasma protein binding.

The app has been designed in collaboration with the editors of the forthcoming book, The Handbook of Medicinal Chemistry: Principles and Practice, which will be published in November 2014 providing a comprehensive, everyday resource for a practicing medicinal chemist throughout the drug development process and is an ideal companion for the biannual MedChem Summer school run by the RSC.

 

I’ve just added Computable to the mobile science site. Computable brings iPython and SciPy to the iPad allowing to create, edit and run iPython notebooks on your iPad. Computable comes with full-featured SciPy stack, Numpy, SciPy, SymPy, Pandas, Matplotlib. The free download includes a series of 32 example notebooks and lectures that allow you to evaluate the application. To create or edit your own notebooks you will have to make an in app purchase to unlock the full feature set ($9.99).

 

Everybody’s favourite text editor have been updated BBEdit 10.5.11 release consists entirely of fixes for reported issues, and contains no new features.

I also saw this note about future Yosemite support.

OS X Yosemite (10.10) We cannot fully support the use of our products on beta versions of OS X. If you encounter difficulty when using the latest version of BBEdit, TextWrangler, or Yojimbo on any pre-release version of OS X Yosemite, please first verify whether the problem also occurs when running on the latest public release of OS X Mavericks (10.9); and then file a bug report with Apple using an appropriate feedback channel. They will contact us as necessary.

 

The Apple Design Award winning application EnzymeX has been updated. EnzymeX is a beautifully designed DNA sequence editor that Comes with numerous helpful tools and calculators, and includes handy reference data like codon tables and amino acid tables.

Talking to the developers they have fixed some 10.8/10.9 bugs, added gatekeeper support, and then reviewed the entire enzyme list and made quite a lot of changes as things had been updated throughout the years. In the process adding about 100 new enzymes, there is now Restriction enzyme information for almost 700 commercially available enzymes

 

KiSThelP is a cross-platform free open-source program developed to estimate molecular and reaction properties from electronic structure data. To date, three computational chemistry software formats are supported (Gaussian, GAMESS, NWChem). Some key features are:

• gas-phase molecular thermodynamic properties (offering hindered rotor treatment)
• thermal equilibrium constants
• transition state theory rate coefficients (TST, VTST) including one-dimensional tunnelling effects (Wigner and Eckart)
• RRKM rate constants, for elementary reactions with well-defined barriers.

KiSThelP is intended as a working tool both for the general public and also for more expert users. It provides graphical front-end capabilities designed to facilitate calculations and interpreting results. KiSThelP enables to change input data and simulation parameters directly through the GUI and to visually probe how it affects results. Users can access results in the form of graphs and tables. The graphical tool offers customizing of 2D-plots, exporting images and data files.

 

SeeSAR from BioSolve-it has just been updated, SeeSAR is intended as an interactive tool for designing/improving ligands for drug discovery. This update includes an option to highlight the neighbouring atoms that lead to a particular hyde-score, in the example below the carbon in the ring that gets a pretty big red (unfavourable) score, can be explained by the Receptor desolvation penalty ascribed to the carbonyl oxygen. stereo hardware support (as a first step supporting the polarized-glass-type only), a screen shot feature, an option to move labels out of the way for a better view.

There is a review of SeeSAR here

 

An interesting paper from George Whitesides et al “Universal mobile electrochemical detector designed for use in resource-limited applications” in PNAS DOI. It describes an inexpensive, handheld device that couples the most common forms of electrochemical analysis directly to “the cloud” using a mobile phone.

Several electroanalytical techniques (chronoamperometry, cyclic voltammetry, differential pulse voltammetry, square wave voltammetry, and potentiometry) are described and demonstrated.

Four applications demonstrate the analytical performance of the device: these involve the detection of (i) glucose in the blood for personal health, (ii) trace heavy metals (lead, cadmium, and zinc) in water for in-field environmental monitoring, (iii) sodium in urine for clinical analysis, and (iv) a malarial antigen (Plasmodium falciparum histidine-rich protein 2) for clinical research.

Full technical details are included in the supporting information.

 

A little while ago I suggested on Twitter that it might be useful if all chemistry undergraduates conduct a LogP or pKa determination as part of their practical classes. These results could then be stored in an open access database that would grow into a fantastic resource.

Sven Kochmann has now fleshed that initial idea out into a detailed proposal. Well worth reading and I’d encourage people to participate.

 

Open Drug Discovery Teams has been updated to add Ebola a disease topic.

The Open Drug Discovery Teams (ODDT) project is a crowd-sourced content aggregator for chemical topics.

Features:

Magazine-like interface for browsing topics, which include rare and neglected diseases, and precompetitive initiatives like green chemistry. Back-end server which harvests links from Twitter, based on topic hashtags. App integration with Twitter, allowing users to influence content by crowd-sourced ranking. Chemically-aware recognition of content: browsing and integration with other apps.

 

The latest beta of CLC Drug Discovery Workbench v1.5 beta 4 is available for download. The workbench provides an integrated environment for drug discovery providing tools to explore visualise protein targets and ligands binding to them

MOLECULE STRUCTURE VISUALIZATION

• Molecule 3D structure import: Mol2, SDF, PDB
• Direct download of PDB structures from NCBI
• Quick-style options including ball-n-sticks and molecular surfaces
• Custom visualization applied to selected atoms
• Save molecule visualizations on data
• Molecule tables with 2D depiction of molecules

CHEMICAL AWARENESS

• Generate molecule 3D structure from SMILES or 2D representation*
• Automatic assignment of atom and bond properties
• Automatic binding site setup
• Chemical consistency check
• Lipinski’s rule of five check

STRUCTURE BASED DRUG DISCOVERY

• Binding pocket finder
• Easy, graphical protein target setup
• Fast track molecular docking
• Optimize ligand interactions in binding site
• Virtual screening
• Ligand binding inspection
• Calculate molecular properties
• Protein structure and binding site alignment

 

Molecular Materials Informatics, Inc. have been updating and expanding their portfolio of iOS apps, the latest addition is Green Lab Notebook, this looks like an interesting application for managing chemical reactions on a handheld device.

There are now nearly 350 mobile science apps on the Mobile Science website.

 

Sean Ekins gave a talk on TB Mobile at the recent ACS in San Francisco.

The presentation entitled “New target prediction and vizualization tools incorporating open source molecular fingerprints for TB Mobile version 2” is now on slideshare. Well worth a read. Also a recent publication New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0

There are now nearly 350 mobile science apps on the Mobile Science website.

 

The developers of Findings are looking for people to test the latest features.

Findings Sync can already be enabled in the version 1.0.6 of Findings for Mac. First, make sure you have the latest version using the menu Findings > Check for Updates. After restarting the app, you can enable Dropbox sync in the 'Library' tab in your preferences (accessed via the menu Findings). Note that because of OS X security, you will need to give access to your Dropbox folder by selecting its location on disk (typically the Dropbox folder in your home folder). Do the same on all your Macs, and have all your experiments and protocols in Dropbox, available everywhere! Please let us know if you have any question or problem: send us an email using the Help menu in Findings

 

The latest post on the Swift developers blog concerns Value and Reference Types

Types in Swift fall into one of two categories: first, “value types”, where each instance keeps a unique copy of its data, usually defined as a struct, enum, or tuple. The second, “reference types”, where instances share a single copy of the data, and the type is usually defined as a class. In this post we explore the merits of value and reference types, and how to choose between them.

 

There was an interesting presentation at the 248 ACS Meeting Accessing 3D Printable Structures Online Vincent F. Scalfani, Antony J. Williams, Robert M. Hanson, Jason E. Bara, Aileen Day, and Valery Tkachenko Science and Engineering Librarian, The University of Alabama vfscalfani@ua.edu 248th ACS National Meeting San Francisco, CA August 13, 2014 slideshare describing the construction of the RSC Crystal Data Repository of crystal structures all of which can be downloaded in a format suitable for 3D printing.

Currently contains: the entire Crystallography Open Database (COD) of 289,395 .cif and 48,022 .hkl files of molecules and extended solids; 3D Printable Files – 31,239 .wrl files (color printing) and 11,732 .stl files. 3 Still in beta mode, can manually browse through files. Repository will soon have user interface that is fully searchable (name, structure, formula, SMILES, InChI, and others) with deposition and crowd-source curation/ annotation platform.

I’ve also updated the 3D printing page to include several new resources.

 

CheS-Mapper has been updated, CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets with small compounds.

The tool can be used to analyze the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. CheS-Mapper embedds a dataset into 3D space, such that compounds that have similar feature values are close to each other. It can compute a range of descriptors and supports clustering and 3D alignment.

There is a review of Ches-Mapper here

 

Whilst R is a very comprehensive statistical and data analysis package it does have a very steep learning curve.

R Instructor is an iPhone, iPad and iPod Touch application that uses plain, non-technical language and over 30 videos to explain how to make and modify plots, manage data and conduct both parametric and non-parametric statistical tests.

R-Instructor for iOS

Now added to the mobile science site.

 

I just noticed that R was updated last month to version 3.1.1 ((Sock it to Me).

R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms.

I’ve also updated the list of Data Analysis packages for Mac OSX.

 

Sentira is a new chemical data visualisation tool from Optibrium. The focus is on ease of use data visualisation and as such is probably targeted at the bench scientist rather than a specialist computational scientist. It supports a selection of plotting and SAR tools.

I’ve written a review of my first impressions.

There is also a list of data visualisation applications here.

 

According to a report at the ACS Yield101 and Reaction101 are now available for free.

 

I’ve been approached a couple of times by people asking me if I know of any software to organise the workflow, instrument booking in a science lab. I’ve seen a couple but they seem rather expensive and focussed on proprietary platforms.

I just read an interesting article describing a FileMaker-based software project generated by a NHS histopathology laboratory describing their work on a laboratory workflow tool used to capture information.

Many histopathology laboratories are using antiquated reporting software. Upgrading to a more modern system is expensive. Even the more modern systems often lack the technology needed for pathologists to efficiently report complex cases allowing workflow to be visually managed and supporting the use of customisable templates and proformas. They are often difficult to use across multiple sites. We have developed web based reporting software that overcomes these difficulties. This has been used to report thousands of cases; many complex tumour cases requiring key data element capture.

There is an online demo, and you can download the software to try it out using the 30-day demo license from FileMaker.

They are now near to completing a much more sophisticated version of the software written specifically for Filemaker 13, and exploiting the the improved functionality of the HTML5 based WebDirect browser access, and access via the FileMaker Go app on iPad and iPhone. This version of the software is also being adapted for use in other areas of clinical medicine, including breast surgery. This version works beautifully on mobile devices, together with web browsers, PCs and Macs.

 

An update on the swift blog

Many people have asked about the Balloons playground we demonstrated when introducing Swift at WWDC. Balloons shows that writing code can be interactive and fun, while presenting several great features of playgrounds. Now you can learn how the special effects were done with this tutorial version of ‘Balloons.playground’, which includes documentation and suggestions for experimentation.

This playground uses new features of SpriteKit and requires the latest beta versions of Xcode 6 and OS X Yosemite

 

One of the most popular pages on the site is the listing of clipboard managers with over 10,000 page views so I thought I’d spent a little time tidying up the page. I’ve added a couple of new entries and updated a couple of broken links.

 

Asteris has been updated. Asteris is an iOS app that arose from a collaboration between Optibrium and Integrated Chemistry Design that allows medicinal chemists to design new molecules on their iPad and then calculate a range of physiochemical and ADME properties.

What's New in Version 1.0.2 Add sulfoxide support, using either double bond, or separated charges, Add multiple ring creation with one gesture if atoms are selected. Permit scaling with selected atoms and bonds. Add wavy bonds if Single bond tapped a second time. Add Presentation Mode.

There is a review of version one here

 

Workflow tools are becoming increasingly common in science and this publication by Wendy Warr gives an excellent comparison of the leading alternatives, Scientific workflow systems: Pipeline Pilot and KNIME DOI.

Really well worth a read.

 

ChemSearch is an iPad app that gives you access to the Acros Chemicals catalog. It uses the ChemDoodle Web components as a front end to structure-based searching.

You can then look at all the chemical property and safety information by selecting a particular molecule.

 

I was recently asked about compiling an algorithm, plane of best fit (PBF), to quantify and characterize the 3D character of molecules as described in Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules, Nicholas C. Firth, Nathan Brown, and Julian Blagg, Journal of Chemical Information and Modeling 2012 52 (10), 2516-252 DOI. The source code is all available from the rdkit repository https://github.com/rdkit/rdkit/tree/master/Contrib/PBF.

The compilation had a slight glitch but full details are here.

 

It seems that Python is becoming the preferred language for scripting in science and I wrote a getting started page for Chemists and several people have pointed out a couple of resources that may be useful in particular Roaslind.

Rosalind is a platform for learning bioinformatics and programming through problem solving.

I looks like an excellent starting point for newcomers and more experienced programmers, whilst focussed on bioinformatics the exercises are useful for all disciplines.

For chemists chempython looks to be a very useful resource.

 

DataWarrior is a data analysis tool that understands chemistry, it provides an efficient way to search, sort and analyse structure-activity data. DataWarrior was developed at Actelion and it is highly integrated into the drug discovery platform, in 2014 it was decided to release DataWarrior without the integration layer as a stand-alone tool to the public. DataWarrior is a Java application and thus is cross platform.

I’ve written a review on my initial impressions.

 

I suspect most scientists are now finding that they are storing data in SQL databases and I noticed that Impathic have released a series of tools to access a variety of SQL databases from your iOS device, so whether you are using MySQL, Oracle, Access etc there is probably a dataglass app to give you access.

 

Gigawiz have just announced the release of an updated version of Aabel.

Aabel™ NG is the result of a 5-year special project and massive development effort, rewriting millions lines of code to transform the Gigawiz flagship product into an icon of power and simplicity for professional users.

The update includes:

• Modernization and optimization of the main processing code
• A total redesign of the user interface, adding power with modeless simplicity
• Complete Carbon (32-bit)-to-Cocoa (64-bit) transformation
• Minimizing overhead between the user interface and the main processing code (a crucial step for sustainability and future development)
• Replacement of high-level Cocoa classes with Aabel NG-specific code, a key alteration for any part of the application that requires high performance with large data sets
• Addition of numerous new features

The transformation to 64-bit should enable much larger data sets to be handled, and there are a host of new statistical methods however I’m not familiar enough with the area to comment on how useful they are.

Interactive graphing means that you no longer have to manually update a plot to see how the changes look, the enhanced exploratory analytics could be really useful when working with large data-sets.

A Mac OS X Mavericks; Intel- based Mac and a colour monitor with a minimum resolution of 1440 x 900 is required. There are also a couple of issues with backward compatibility.

Aabel v3/v2 are 32-bit applications; Aabel NG (v4) is 64-bit and hence cannot use Apple data structures and formats that have not been ported to 64-bit. In summary, the implications are as follows: A feature of Aabel v3/v2, called database metaphor (i.e., a container that refers to a collection of worksheets), due to its dependency on Apple 32-bit subsystems, is not available in the 64-bit version. While Aabel NG (v4) reads the worksheet files of Aabel v3/v2, it will NOT be able to read their viewer files, because the latter files have contents that require Apple 32-bit subsystems (which are unavailable in 64-bit). In Aabel v3/v2, the System Alias Manager manages the connections between the graphs and their source worksheets. The Alias Manager has unresolved issues making the continuation of its use not sustainable. In Aabel NG (v4), the saved graphs will be hot-linked to their source worksheets along paths defined at the time their pipelines are created.

The price of the new version is $1250 (academic $750) and there are reduced pricing for upgrades.

I’m using Aabel 3 at the moment and I’m very happy with it, I’d be very interested to hear from anyone who upgrades.

 

The Crystallographic Information File (CIF) is the internationally agreed standard file format for information exchange in crystallography. The CIF standard is supported, maintained and developed by the International Union of Crystallography (IUCr) and most major journals require electronic data depositions in CIF format. enCIFer enables users to validate CIFs and ensure their files are format-compliant for deposition with journals and databases or for storage in laboratory archives. enCIFer should also be used to add information safely to CIFs without corrupting the strict syntax. enCIFer operates on single or multi-block CIFs allowing you to:

• Identify and correct syntax/format violations
• Safely edit information to your CIF without corrupting the strict syntax, for both single data items and data loops
• Supplement the data in your CIF via two data entry wizards, one for publication details and the other for chemical, physical and crystallographic properties
• Select from a choice of CIF dictionaries and check against a user-customisable list of mandatory data items
• Visualise structure(s) in a CIF, including displacement ellipsoids

Requires Mac OS X: 10.6, 10.7, 10.8, 10.9

 

I’m delighted to report DataDesk 7 has been released, this update requires a Macintosh computer running Mac OS X 10.6, 10.7, 10.8, or 10.9 and Intel processor and 2 GB RAM.

Data Desk brings fast, easy-to-use visual analysis to your desktop. It provides interactive graphical tools for exploring and understanding your data—for finding the patterns, relationships, and exceptions. While it implements many traditional statistics techniques suitable for data from planned experiments and sample surveys, Data Desk’s true strength is its powerful tools for data exploration. Its insightful graphic displays simplify intuitive investigation of your data.

DataDesk can handle very large datasets (up to 2 billion cases), it supports a wide variety of statistical techniques and supports linked plots so that selections in one plot are highlighted in another so you get multiple views of your data. They have supported the Mac since the mid 1980’s and I suspect it is now the oldest commercial application for the Mac. A series of continuous updates have kept DataDesk at the forefront of data analysis. The accompanying manual also serves as an invaluable resource for learning statistical analysis.

I’ve updated the list of data analysis tools available for the Mac.

 

I’ve been asked a couple of times what application I use to create screen capture movies, I actually use Screenflow and I’d certainly recommend it to anyone who is planning create regular screen recordings. However if it is a one off movie than you can use QuickTime Player, go to the File menu and select “New Screen Recording”.

A small widget appears that offers a couple of options and is used to start the recording.

Once finished stop the recording and you can use Quicktime to do any minor edits or you can use iMovie to do more substantial editing.

 

I was recently sent a link to an interesting publication.

The Multiple Sclerosis Performance Test (MSPT): An iPad-Based Disability Assessment Tool DOI

As someone who has known a number of MS patients I was very much aware of the difficulties in accurately assessing the progress of the disease. The MSPT application uses the iPad as a data collection platform to assess balance, walking speed, manual dexterity, visual function, and cognition. It also provides an objective analysis and comparison with a reference population.

 

Calca is a powerful symbolic calculator that updates as you type giving you instant answers. It solves equations and simplifies complex expressions. It's also a rich Markdown text editor so that you can explain your ideas alongside your calculations. This looks like a really interesting application,

Calculation Features:

• Variables x = 42
• Functions f(c) = 9/5*c + 32 and even recursive functions
• Units 42 mph in kmph and currency ¥599 in $
• Solves equations (x + 2x + 4x = 42, what is x?)
• Matrices with inverses so you can solve linear equations
• Sum, prod, map, and reduce operations on lists, matrices, and ranges
• Trigonometry and complex numbers
• Derivatives of functions
• Logic operations and if statements
• Binary math (& and |) and support for binary and hex number (0xA9 and 0b1010)
• Keeps track of units (m, s, m/s, m/s^2, etc.) so you can verify your equations as you compute

There is a comprehensive reference page that gives more details.

There is a MacOSX version and an iOS version for your iPad or iPhone.

The nice thing is you can use Markdown to format the calculation and add an explanation.

There is a listing of Markdown Editors for Mac OSX here,

 

X11 2.7.7 has been released

The XQuartz project is an open-source effort to develop a version of the ​X.org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

Installation

Download XQuartz-2.7.7_rc1.dmg, and open it with OS X's Installer.

Important Notices

OS X Requirements

OS X 10.6.3 or later is required to install this package.

Default X11 Server

If this is your first time installing XQuartz, you may wish to logout and log back in. This will update your DISPLAY environment variable to point to XQuartz.app rather than X11.app. If you would prefer to keep using X11.app as your default server (you can still launch XQuartz.app manually), you'll want to disable /Library/LaunchAgents/org.macosforge.xquartz.startx.plist using ​launchctl(1).

Changes in 2.7.7

All changes in 2.7.6 plus: app: ​xcursorgen 1.0.6 ​xscope 1.4.1 ​xterm 309 lib: ​libICE 1.0.9 ​libXft 2.3.2 ​libXi 1.7.4 ​pixman 0.32.6 ​xcb-util-renderutil 0.3.9 proto: glproto 1.4.17 ​inputproto 2.3.1 server: ​xorg-server 1.15.2 plus ​other patches Fixes multimonitor support on Mavericks (#832) Fix Xephyr "failed to create root window" bug (#822)

 

OEToolkits 2014.Jun This release of the OpenEye toolkits is focused on stability and new platform support. The last release, 2014.Feb, was a major feature release introducing numerous new features. This release focused on fixing many bugs and improving the overall stability of the OpenEye toolkits.

There is still a major new feature being added in this release:

FreeForm API added to Szybki TK

Mac Users should note this release will be the last release to support OSX 10.7.

 

I saw an interesting bog post from ChemBark. On experiences using an iPad to present organic chemistry lectures.

How to Use an iPad for Orgo Lectures…and Embarrass Yourself, the involves connecting the iPad to the projector through a lightning-to-VGA adapter and a VGA cable and then using Notability to write/draw on top of the document and screencast everything through the projector.

However we have Keynote and Powerpoint for iPad and I saw this tutorial, and I was wondering how many people were using their iPad for presentations?

 

I’ve just been sent links to a selection of iOS apps related to space exploration.

The NASA Visualization Explorer, the coolest way to get stories about advanced space-based research delivered right to your iOS device. The NASA app allows you to explore with NASA and discover the latest images, videos, mission information, news, feature stories, tweets, NASA TV and featured content. There is also the NASA TV for live feeds. Portal to the Universe a news aggregator for space news.

The ESO Top 100 Images, which brings users a selection of the best astronomy images taken by a suite of the world’s most advanced ground-based telescopes from the Atacama Desert in Chile. Whilst the ESA/Hubble Top 100 Images, which brings users the best Hubble pictures from ESA. Looks like an ideal place to browse for new desktop pictures.

Finally if you want to explore the Science Museum in London from the comfort of your sun lounger, with Journeys of Invention you can study, rotate and even operate some of the most revolutionary scientific inventions of all time.

 

I don’t use regular expressions often enough to become an expert but I do use them often enough to know how valuable they are. I always seem to spend more time than I’d like sorting out the regular expression and I often feel that I’ve done something similar before.

I came across an application that I think will make my life a lots easier, RegExRX is a regular expression development tool.

A complete regular expression development tool meant for novices and professionals alike, this editor has many features designed to help in the development and storage of regular expressions. Based on the PCRE library, RegExRX will allow a user to craft patterns that are compatible with most regular expression flavors and will let them easily copy those patterns to other languages like Objective-C, Perl, Ruby, PHP and Xojo.

 

The electronic notebook Findings has been updated

1.0.5, build 2264
New: display completed experiment as a list
Release notes for version 1.0.5:
New: display experiment as a list (menu Findings > Preferences > General).
Improvement: file preview update when modified externally (for instance after updating an Excel file).
Improvement: day editing and insertion of a day before the first day.
Bug fix: high CPU usage and memory build-up triggered when adding a present or future date to an experiment previously marked as completed.
Bug fix: parts of an experiment could have a wrong completion status (wrongly grayed out).
Bug fix: PDF export menu stays disabled after canceling.
Bug fix: memory leak in PDF export.
Bug fix: inconsistent button labels in embedded license store.

 

I’ve written several Vortex scripts that use external tools to calculate physicochemical properties including the use of ChemAxon (e.g. charge, pKa, logP, logD). However I often need to simply classify molecules as acid, base, neutral or zwitterion, so I’ve updated the script to create another column containing a text annotation.

 

Applescript has had to take a bit of a back seat in recent years but there have been a couple of posts recently that will be of significant interest to all scripters.

Papers is a multi-award winning reference management application that hugely popular with scientists. I saw a very interesting entry on their blog.

The latest beta version of Papers for Mac adds support for scripting. This allows you to automate tasks or fetch and manipulate data in your Papers library by using AppleScript, or JavaScipt in Yosemite. Papers 3 features extensive AppleScript support that allows data to be fetched from a Papers library. You can also execute commands, like import and export. You can even create new data and set its most important properties. Some parts of the UI can be automated as well: the current selection can be changed, as well as the current view mode.

The importance of adding Applescript support to applications is nicely illustrated in an article by Brent Simmons, Making Your Mac App’s Data Scriptable.

Scripting isn’t a matter of automating button clicks; it’s about exposing the model layer to people who could use your app in their workflows.

There have been many concerns that the introduction of “sandboxing” will compromise the ability of applescripts to automate complex multi application workflows. There has been a recent article that shows the current best practices for controlling another app using AppleScript, Scripting from a Sandbox.

This comment sums things up nicely

While that’s usually a small minority of users (who use applescript), they’re power users — the kind of people who recommend apps to friends and family. They blog and tweet about apps, and people listen to them. They can be your app’s biggest evangelists.

And of course it is easy to share applescripts. I’ve added the links to the Applescript Resources page.

 

Core Informatics have announced the release of it’s new chemistry app for Platform for Science. The newly developed Core ELN (Electronic Lab Notebook) Chemistry application is designed to help chemists document research activities and compound registration in the cloud.

The Core ELN Chemistry app, developed through a partnership with ChemAxon, streamlines daily documentation responsibilities of research chemists across all R&D disciplines including analytical, medicinal, process, & CRO. It provides a chemically intelligent and flexible environment which allows scientists to manage synthetic transformations, capture experimental details and analytical results supporting internal and contract syntheses.  Compound registration is augmented by powerful search capabilities that span reagents, compounds, experiments, instruments, collaborators, and synthetic campaigns.

 

Copies allows clipboard sharing between Mac OSX and iOS using device specific versions, it uses iCloud for data sync, there's no other setup needed. File copy maximum file size is 20MB, and file transferring uses HTTPS with the developers server powered by Linode.

There is a listing of clipboard managers here.

 

Apple have started a new blog to help developers interested in Swift, Swift is a new programming language for Cocoa and Cocoa Touch.

Get started with Swift by downloading Xcode 6 beta, now available to all Registered Apple Developers for free. The Swift Resources tab has a ton of great links to videos, documentation, books, and sample code to help you become one of the world's first Swift experts. There's never been a better time to get coding!

The first blog entry deals with the issue of compatibility, and how to ensure your app will continue to function as the language evolves.

 

The have been a couple of new additions to the mobile science database of scientific applications for iOS.

StatsMate is a calculator designed to make statistical analysis easier.

Bio Flowchart Lite is a collection of biological clip art.

Chemist Virtual Chemistry Lab is a fun app for undertaking chemistry experiments, Try mixing chemicals by pouring them into beakers or test tubes. You can also heat the chemicals with a bunsen burner, or put a piece of cesium into water.

 

I recently wrote a review of SeeSAR and one of my comments was:-

Unfortunately there is no 2D display of ligands in the ligand list so sometimes it can be difficult to keep track of modifications.

Well, in keeping with the “fast and agile” release plan a update is now available that includes a 2D display.

More information

 

Last month I compiled a page of Fortran resources for the Mac. At the time I was hoping it would be a useful resource but thought it would draw a limited audience. In fact it turned out to very popular, the page has been accessed nearly 1000 times with readers spending between 3 and 4 minutes on the page. I've also been contacted by a couple of fortran developers who have suggested additional resources and tips for compiling.

 

Nvidia have released CUDA driver 6.0.51 which is required for CUDA support on Mac OS X 10.9 Mavericks. Note: Quadro FX for Mac or GeForce for Mac must be installed prior to CUDA 6.0.51 installation

An alternative method to download the latest CUDA driver is within Mac OS environment.  Access the latest driver through System Preferences > Other > CUDA.  Click 'Install CUDA Update'.

There are a number of GPU-accelerated science applications described on the GPU Science Page.

 

I use Markdown extensively on my sites and I keep an eye out for useful tools to make life a little easier. I keep a list of markdown editors and I thought I’d mention The Markdown Service Tools .

The Markdown Service Tools are a collection of OS X Services designed to make creating Markdown-formatted text that much easier. Services work in any OS X Cocoa based application.

For those who are new to markdown this getting started guide is well worth reading

 

Chargemol program performs atomic population analysis to determine DDEC net atomic charges, atomic spin moments, and effective bond orders. Because the DDEC net atomic charges are simultaneously optimized to reproduce atomic chemical states and the electrostatic potential surrounding a material, they are well-suited for constructing force-fields used in atomistic simulations (e.g., classical molecular dynamics or monte carlo simulations) and for quantifying electron transfer between atoms in complex materials and during chemical reactions

The DDEC method is described in the following publication and references therein.

Thomas A. Manz and David S. Sholl, "Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Non-Periodic Materials", J. Chem. Theory Comput., Vol. 8 (2012) 2844-2867. DOI

The program can be run using either Matlab or Fortran source codes, which yield identical numbers. The Fortran code is parallelized with OpenMP and runs much faster than the Matlab code.

 

I’ve just added the 300th iOS app to the mobile science website. The honour goes to Predictive Tools for Breast Cancer this is a tool for risk prediction of additional axillary metastases after Tumor-Positive sentinel node biopsy, described in a recent publication.

I also found a number of other iOS applications that might be of interest to those working in the area of Onclogy.

The Roche Oncology Pipeline app is a comprehensive guide to all oncology molecules currently under investigation in Roche/Genentech clinical trials. Similarly the [Lilly Oncology Pipeline app] (http://www.macinchem.org/mobilescience/biology,medical/lilly-oncology-pipeline/) gives access to the Lilly oncology pipeline. Genetech also provide the HER2 testing roadmap an iPad application that details the steps required for accurate HER2 testing for breast cancer. The BRisk Breast Cancer Risk Assessment is intended to provide a means of assessing age-specific risk of breast cancer for women with a family history of breast and/or ovarian cancer. The Breast Cancer @Point of Care™ is a clinical support platform that provides comprehensive information on the diagnosis, treatment, and management of Breast Cancer, made up of a progressive series of chapters and other learning tools. HER2 Reader is a simple clinical decision support app developed primarily for pathologists and oncologists who perform predictive marker testing for breast cancer.

 

DataWarrior is a data analysis tool that understands chemistry.

DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns. Chemical descriptors encode various aspects of chemical structures, e.g. the chemical graph, chemical functionality from a synthetic chemist’s point of view or 3-dimensional pharmacophore features. These allow for fundamentally different types of molecular similarity measures, which can be applied for many purposes including row filtering and the customization of graphical views. DataWarrior supports the enumeration of combinatorial libraries as the creation of evolutionary libraries. Compounds can be clustered and diverse subsets can be picked. Calculated compound similarities can be used for multidimensional scaling methods, e.g. Kohonen nets. Physicochemical properties can be calculated, structure activity relationship tables can be created and activity cliffs be visualized.

 

PureFluids calculates the Helmholtz free energy for various pure fluids using equations of state (EOS) collected from the scientific literature. Derivatives of the Helmholtz free energy with respect to density and temperature allows the calculation of the following thermodynamic properties

Inner energy, enthalpy, Helmholtz free energy, Gibbs free energy, entropy, heat capacity at constant V and P, ideal heat capacity at constant P, speed of sound, isobaric expansion coefficient, relative pressure coefficient, isothermal compressibility, Joule Thompson coefficient, isentropic temperature-pressure coefficient, isothermal throttling coefficient, isothermal stress coefficient, second virial and third coefficient, fugacity and fugacity coefficient, compressibility factor.

The program allows the calculation of the thermodynamic properties at arbitrary temperature and density or pressure conditions (List), tables with even spaced increments of temperature and density/volume (Table), or properties at the vapor saturation curve (Saturation). All these results are listed in Report tab which can be printed. The Plot tab allows the graphical representation of the thermodynamic properties for various conditions and includes the calculation of isopleths. These plots can be also printed. The Unit tab allows the user to choose the appropriate units for the individual thermodynamic properties.

By default the thermodynamic values for the inner energy, the enthalpy, the entropy, the Helmholtz free energy, and the Gibbs free energy are calculated as reported by the respective EOS. If required, the values for these properties can be corrected for an ideal gas with H = 0 and S = 0 at respective reference conditions (typically 298.15 K and 0.1 MPa). The reference conditions, however, can be chosen by the user.

 

I’ve just been sent details of two more clipboard managers, Paster is a clip board manager for both Mac and iPhone with Cloud-based synching usinging https rather than Wifi or bluetooth. It has searchable history and keyword filtering. Colective will remember: Text, images, PDFs, movies, URLs, appointments, files etc. When Collective is running, a "C" will appear in the top-right of your menu bar. Pressing ⌘-Shift-V will show Collective's history of what you have copied (alternatively, you can click the "C" in the menu bar). Clicking on any item will add it back to your clipboard, so you can paste it again. No synching between devices.

There is a list and short description of 21 different clipboard managers here. As they say choice is good.

 

The popular iOS molecule viewer iMolView lite has been updated with the ability to draw a structure in 2D and then convert to 3D.

There are also several new additions to the Mobile Science site medicinal-plants-pro a guide to 150 common species of medicinal plants. Molar is an educational tool and reference for students with features such as periodic table, triangle solver, and chemical equation balancer. TB Mobile makes available a set of molecules with activity against Mycobacterium Tuberculosis, and known targets available in CDD. Stephen Hawking’s Snapshots of the Universe explains the principles that control our universe through simple and fun experiments

 

Findings 1.0.4 is out!

New: ongoing/completed state of experiments, experiment vignette, and other improvements

 

Well things can change quickly at times, in the last tutorial I wrote..

Vortex has a limited capacity to render HTML, it is however a very limited ability so there is no support for javascript or CSS but you can introduce a number of useful extra features.

If you download the latest daily build of Vortex from the Dotmatics Support site there is a version that comes bundles with Java 8, if you download this version are a host of new options for displaying plots. In particular you can now display web pages, follow links on pages, and there is support for javascript.

In Scripting Vortex 21 there is a demonstration of this feature and an example script that uses SMARTCyp to predict sites of metabolism.

There are many more scripts on the Hints and Tutorials Page.

 

I’ve just updated the list of clipboard managers to include Copy’em Paste a clipboard history application it supports text, images, links, HTML, code, PDFs, files and you access the clippings via menubar or keyboard shortcut (e.g., ⌘-Shift-V). You can search, delete or edit clippings and blacklist applications (not save clippings from them).

 

I was recently sent details of another electronic lab notebook (ELN), Labarchives appears to be a web-based system that supports all major platforms any time you are connected to the Internet. This includes any Windows, Mac, or Linux system using Internet Explorer, Firefox, Chrome, and Safari, as well as on the iPad.

The Professional version is priced for academic institutions and non-profits at $99 per user per year (which includes 100 GB of storage per user), representing a 50% discount off of pricing for commercial organisations.

Special departmental and site license pricing is also available as well as quantity discounts.

LabArchives can also be installed on a local server.

 

The secret of a good iOS app is often finding a niche that is both useful but does not require lots of functionality or screen real estate. Chemical Names Spell Checker ticks both boxes nicely.

The Chemical Names Spell Checker provides chemical name spell checking and chemical name synonym look-up. Data are provided by the ChemSpell service that contains more than 1.3 million chemical names related to organic, inorganic, pharmaceutical, toxicological, and environmental health topics.

Once checked the name can be copied to the clipboard for use in another application.

The ChemSpell Web Service API is free of charge. Neither registration or licensing is required. This app nicely underlines the power of chemistry web services.

Well worth all chemists having on their iPhone or iPad.

 

The very popular NMR processing tool iNMR has been updated

The new versions 5.3.7 (for Mac) and 2.3.7 (for Windows), both available since June 20, add Covariance NMR to the processing toolbox. This technique creates a symmetric square matrix, starting from any 2-D matrix. The result can look completely different from the starting spectrum, though the information contained is necessarily the same. An example is hsqc-tocy (a kind of hetero-correlation experiment). After normal processing, it has two different axes: a 1-H axis and a 13-C axes. Starting from here you can apply two different kinds of Covariance. The so-called Direct Covariance creates a symmetric H-H matrix. The so-called Indirect Covariance creates a symmetric C-C matrix. Both are homo-correlation plots.

A more detailed description is available here:

http://nmr-analysis.blogspot.it/2008/10/introduction-to-covariance-nmr.html

This link leads to the pioneer of the method:

https://research.chemistry.ohio-state.edu/bruschweiler/web-servers/370-2/

There are more spectroscopy applications for Mac OSX here

 

An interesting news snippet.

Wiley acquired SimBioSys, a scientific software provider of tools used in the drug discovery process. Chemists use these tools, including the ARChem - Route Designer, to perform organic synthesis (designing synthetic routes for target molecules). ARChem’s organic chemistry system is derived from databases such as Wiley’s ChemInform Reaction Library (CIRX). The Canada-based company is privately held, and terms of its agreement with Wiley were not disclosed.

“By combining our traditional published content and databases with machine learning algorithms, we can support chemists in innovative research as they advance world knowledge” while using Wiley Science Solutions, says Steve Miron, Wiley’s SVP of global research.

I can see that logic behind acquiring ARChem since it allows them to better leverage their reaction databases, but I wonder what this means for some of the other Symbiosis tools in particular things like eHits?

 

SeeSAR is an interesting new product from BioSolve-it, it is intended as an interactive tool for designing/improving ligands for drug discovery. I’ve written a brief review that you can read here.

This is a really interesting application, it seems a little rough around the edges but the developers have released it early are very keen to get feedback. I found them very responsive and enthusiastic about getting the views of users involved in how the application evolves. I would certainly encourage people to download it and use the free trial period to give it a go, and provide them with feedback.

There are more software reviews here.

 

Vortex has a limited capacity to render HTML, it is however a very limited ability so there is no support for javascript or CSS but you can introduce a number of useful extra features.

Im the latest tutorial you can find out how to use this to add images, plots and graphs to the molecular worksheet.

Scripting Vortex 20:-Adding images to Vortex

 

The popular molecule viewer for iOS Chem3D has been updated, the release notes suggest no new functionality just bug fixes.

There is a page of molecule viewers for iOS here

 

Findings electronic LabNotebook has just been updated.

Findings 1.0.3 just released: improved support for pasting files or images, and misc bug fixes (menu Findings > Check for Updates)

Great to see the app evolving so rapidly, and the roadmap gives an idea of things to come.

My favourite text editor BBEdit has been updated, this release consists entirely of fixes for reported issues, and contains no new features.

• Fixed crash which would occur occasionally (depending on the shape of memory) when trying to balance delimiters and the selection start was at the beginning of the document.

• Worked around bug on 10.8.x which broke running-browser detection (and thus the "Markup => Preview in => All Running Browsers" command).

• Worked around an elusive OS behavior in which the application would receive spurious change notifications for folders that it wasn't actually watching, which in turn triggered inappropriate refreshes of the Scripts, Text Filters, Stationery, and/or Clippings menus.

• Fixed crash which would happen when reloading ctags data in response to the tags files being changed on disk.

• Fixed crash which would occur when using "Save as Styled HTML" after using the expert preference to turn off inline CSS generation.

• Made further changes to the Dropbox check, since the on-disk format of ~/.dropbox/ has changed yet again. Now, the existence of that directory is enough to prove installation of Dropbox and trigger discovery of ~/Dropbox for application support content.

• Fixed likely cause of an occasional crash at startup.

I use Markdown on my site and I’m seeing it used regularly in documents so I was interested to see this in the latest DEVONthink update, and there is a list of Markdown Editors here.

Markdown has become a popular way for adding simple formatting to text without relying on platform-specific file formats. DEVONthink already supported plain Markdown. Starting with version 2.7.5 it now renders MultiMarkdown, too. For DEVONagent 3.8 we have updated almost all plugins and made many of them language-aware.

To get DEVONthink to render a Markdown file

Show the Markdown file in DEVONthink, then choose View > Best Alternative.

 

ChemAxon have just announced the release of version 6.3.

This release includes several new features including the ability to draw and analyze complex patent Markush structures, display Markush hierarchy, work with R-Groups and enumerate Markush structures.

A new Solubility Predictor, the aqueous solubility predictor is based on the topology of the input molecules, but also calculates the pH dependence and the solubility at a desired pH level.

IUPAC name conversion supports now Japanese names as well as the existing English and Chinese names even if mixed in the same document so you can extract all the chemistry from documents in these languages.

There are also updates for Marvin JS 6.3, Standardizer & Structure Checker 6.3, Instant JChem 6.3, and Compound Registration 6.3.

 

The excellent ChemDoodle Web Components have been updated.

This is a bugfix update to the ChemDoodle Web Components, fixing all the issues brought to our attention. Fixes

• WebGL based components now work in IE11.
• iChemLabs Cloud services now work based on a queue, so all requests will proceed in the order requested, and you will no longer see a message to wait for the previous request to finish.
• Added a iChemLabs.useHTTPS() function for websites that want only to use HTTPS.
• Optimize zone now provides better placement when drawing triple bonds or higher.
• Optimize zone now avoids placing substituents inside of rings.
• Removed code calling jQuery.browser which was removed in jQuery 1.9. This code is only helpful for detecting when to use Google Chrome Frame. Note that Google Chrome Frame support (and therefore support in IE6-8) will be removed soon.
• Fixed issue where clicking on the help button in some browsers would lock the component into a drag gesture.
• Fixed bug where rendering atoms in 2D surrounded with a circle would error out.
• Improved and simplified shaders.
• Picking in 3D is now object aware, and will exclude objects if not selectable. So picking atoms for measurements is now much more responsive.
• Fixed issue where measurements were not working in the Editor3D canvas on Android.
• Help button now works in the Editor3DCanvas on Android.
• Measurement values now render with a forward z-index of 1 Ångstrom to be placed on top of any objects in the immediate vacinity.
• Minor syntax and lexical fixes.

There is a quick tutorial here, and many more on the ChemDoodle Web Components website

 

ChemDoodle has been updated to version 6.0.1, this is a free update to fix a couple of bugs.

• A new EXE is built for Windows. This EXE will now use either the 64 bit or 32 bit JRE if available. If both are available, the new executable defaults to the 64 bit JRE.
• iChemLabs Updater has been updated to work in mixed Java environments on Mac OS X. Those with both Java 1.7 and 1.6 installed on Mac OS X will notice that ChemDoodle will not automatically open after the update. Ignore this, as this new updater corrects this issue.
• Fixed IUPAC naming issue where locants were not correct in ring blocks for stereocenters.
• Fixed IUPAC naming where a double dash could occur.
• Fixed bug where groups would not always resize all their contents.
• Fixed crash if non-recognized colors were present in ChemDoodle Documents.
• Colors in groups and reaction area text are now stored correctly in ChemDoodle Documents.
• Limited the size of files previewed by the Quicklook plugin to 200MB.

 

This is another Vortex script, this one is used to implement a central nervous system penetration (CNS) algorithm described in the literature.

It is clear from many publications that a number of physicochemical properties influence central nervous system (CNS) penetration and it is often possible to play off one property against another in an effort to improve CNS penetration. An interesting paper from Wagner et al Moving beyond Rules: The Development of a Central Nervous System Multiparameter Optimization (CNS MPO) Approach To Enable Alignment of Druglike Properties describes an algorithm to score compounds with respect to CNS penetration.

The CNS MPO score was built based on six fundamental physicochemical properties: ClogP, ClogD, MW, TPSA, HBD, and pKa each weighted from 0 to 1.0

Update

One of the popular features in Vortex is to colour code columns, this is done automatically but sometimes you want to customise the colouring. For example in one set of values smaller values might be better, in another columns (perhaps an off-target activity) larger numbers might be better. Chatting to Sune Askjær, the author of the Unichem Script, it seemed that this might be a nice addition to this script.

The updated script is here.

 

I’ve just added Panoply to the list of data analysis applications. Panoply is an application from NASA that plots geo-gridded and other arrays from netCDF, HDF, GRIB, and other datasets. You can:-

• Slice and plot geo-gridded latitude-longitude, latitude-vertical, longitude-vertical, or time-latitude arrays from larger multidimensional variables.
• Slice and plot "generic" 2D arrays from larger multidimensional variables.
• Slice 1D arrays from larger multidimensional variables and create line plots.
• Combine two geo-gridded arrays in one plot by differencing, summing or averaging.
• Plot lon-lat data on a global or regional map using any of over 100 map projections or make a zonal average line plot.
• Overlay continent outlines or masks on lon-lat map plots.
• Use any of numerous color tables for the scale colorbar, or apply your own custom ACT, CPT, or RGB color table.
• Save plots to disk GIF, JPEG, PNG or TIFF bitmap images or as PDF or PostScript graphics files.
• Export lon-lat map plots in KMZ format.
• Export animations as AVI or MOV video or as a collection of individual frame images.
• Explore remote THREDDS and OpenDAP catalogs and open datasets served from them.

 

ASObjC Explorer for Mavericks

Changes from version 3.2.0 to 3.2.2

Code-completion enhancements. Code-completion has been enhanced for relevance. As part of this, Explorer supports new variable-naming conventions. Please read the section entitled 'Contextual Completion' in the Help file for more details.

Bug fix. Choosing 'Look Up in AppKiDo' from the contetual menu in the Library Pane erroneously entered the resulting script in the log. This no longer happens.

Sparkle update. A newer version of the Sparkle update framework is included. If you choose automatic updates, they should now happen automatically.

Updated scripts and user shortcuts. You can extract these from the application's bundle, or remove the existing ones and relaunch the application to have them instlled automatically.

Updated example scripts. These have been updated to reflect the new variable naming conventions

 

DOT is a software package for docking macromolecules, including proteins, DNA, and RNA. DOT performs a systematic, rigid-body search of one molecule translated and rotated about a second molecule. The intermolecular energies for all configurations generated by this search are calculated as the sum of electrostatic and van der Waals energies. These energy terms are evaluated as correlation functions, which are computed efficiently with Fast Fourier Transforms. In a typical run, energies for about 108 billion configurations of two molecules can be calculated in a few hours on a few desktop workstations working in parallel.

Roberts, Victoria A. and Thompson, Elaine E. and Pique, Michael E. and Perez, Martin S. and Ten Eyck, L. F., (2013) "DOT2: Macromolecular docking with improved biophysical models" Journal of Computational Chemistry, Volume 34, Issue 20, pages 1743-1758, 30 July 2013 DOI:

 

MongoDB (from "humongous") is an open-source object orientated document database.

Classified as a NoSQL database, MongoDB eschews the traditional table-based relational database structure in favor of JSON-like documents with dynamic schemas (MongoDB calls the format BSON), making the integration of data in certain types of applications easier and faster.

As you might expect chemical searching is not something that is traditionally supported, but there have been a couple of blog articles describing initial efforts, and there is now a detailed step by step description available. The post described implementation of chemical similarity searching using MongoDB and RDKit fingerprints it also has some initial comparisons with the more traditional SQL implementation using the RDKit PostgreSQL cartridge.

 

RCSB PDB the official molecule viewer for the RCSB PDB has been updated to include the latest molecule of the month.

There are many more science applications for iOS here

 

First let me say I’m not a big Fortran user but any blog posts about Fortran always seem to be very popular, and I do get asked regularly about how to compile Fortran applications. So I’ve put together a page summarising all the resources that I’m aware of, together with some installation instructions.

If you know of anything I’ve missed feel free to email me or add them to the comments.

 

Quantum Expresso 5.1 is available for download.

QUANTUM ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modelling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

 

The reference management software Bookends has been updated. The update includes

• New PDF viewer with search, markup, and annotation

• Tight integration between PDF notes and the Bookends note stream

• Move groups between folders with a hierarchical menu

• Watch folders work when the default attachment folder is not on the boot HD

• Use AppleScripts to set the contents of a field

• Bibliography generation is faster

• Set text output style (e.g. Styled Text, BibTeX, HTML, etc.) in Preferences, Scan & Bib tab

• Worked around a Mendeley XML incompatibility with EndNote XML so that reference Types are imported correctly

• The keyboard shortcut for Autofill From Internet has been changed to Shift-Command-A

• If Bookends can't find an assigned attachment folder, the factory default folder will be used

• JSTOR search and Autocomplete Paper were updated to deal with changes made by JSTOR

• The number of references you can import from Google Scholar at once has been reduced from 50 to 20

• Updated Google Scholar parsing to deal with changes made by Google

• Existing font styles will be preserved when pasting decomposed Unicode text into a text field

• Smarter handling of Title Case

There is a comprehensive listing of reference management software for Mac OSX here.

 

This is another Vortex script, this one is used to implement a central nervous system penetration (CNS) algorithm described in the literature.

It is clear from many publications that a number of physicochemical properties influence central nervous system (CNS) penetration and it is often possible to play off one property against another in an effort to improve CNS penetration. An interesting paper from Wagner et al Moving beyond Rules: The Development of a Central Nervous System Multiparameter Optimization (CNS MPO) Approach To Enable Alignment of Druglike Properties describes an algorithm to score compounds with respect to CNS penetration.

The CNS MPO score was built based on six fundamental physicochemical properties: ClogP, ClogD, MW, TPSA, HBD, and pKa each weighted from 0 to 1.0 full details of the script are here.

 

McQSAR:  A Multiconformational Quantitative Structure−Activity Relationship Engine Driven by Genetic Algorithms

McQSAR, an extension to the traditional GA approach to derive QSARs. McQSAR is able to use descriptors for multiple representations per compound, such as different conformers, tautomers, or protonation forms. Test runs show that the algorithm converges to a set of representations that describe the binding mode of the set of input molecules to a reasonable resolution provided that suitable descriptors based on the three-dimensional structure are used.

Mikko J. Vainio and Mark S. Johnson (2005) McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms. J. Chem. Inf. Model. 45, 1953-1961 DOI.

The recently updated Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and confomer ensembles using a multi-objective genetic algorithm. The input can be SMILES, SDF or MOL2 format. Output is SDF or MOL2. Flexibility of aliphatic rings and stereochemistry about double bonds and tetrahedral chiral atoms is handled.

 

ChemBioDraw 14 was released recently and I thought I’d download the demo version and have a quick look at it. I’ve written my first impressions here.

 

In late 2012 Robert Bruns and Ian Watson published a paper entitled Rules for Identifying Potentially Reactive or Promiscuous Compounds. These 275 rules encapsulated 18 years of Drug Discovery experience and are used to identify potentially troublesome molecules.

The code to implement these rules was kindly made available by Ian Watson on GitHub unfortunately my initial attempts to compile this failed, but Matt was able to provide a patch to compile under Mac OSX (Mavericks) using Clang. Whilst this would be sufficient he then went the extra step and made it available via HomeBrew.

You can read more here.

 

Many journals now provide a reader so that you can access the journal on your mobile device. I’ve been adding them to the Mobile Science site, currently there are 34 different journal readers available.

You can see them all here.

There are many more science applications for iOS on the Mobile Science site.

 

IDdx: Infectious Disease Queries Users can find lists of matching infectious diseases by picking disease search criteria (103 signs & symptoms, 39 epidemiological factors, and 16 regions of the world). The user can see all the symptoms associated with a disease or see all the diseases associated with a symptom.

Infectious Diseases in Clinical Practice From HIV care delivery to Hepatitis C virus testing…travel and tropical medicine…and infection surveillance, prevention, and control, Infectious Diseases in Clinical Practice delivers the vital information needed to optimally prevent and treat infectious diseases.

ECG Guide for iPad Full reference text that includes in-depth information on topics such as: Approach to ECG Interpretation, Analysis of rate, rhythm, axis, P wave, QRS complex, ST segment, T wave and QT interval, Ventricular hypertrophy and atrial enlargement and much more.

There are many more science applications for iOS here

 

Today saw the release of Findings an electronic LabNotebook.

In my very brief look at it I’d said it was aimed at the molecular biology/biochemistry scientist. It seems to be very well thought through in terms of workflow, and it is looks beautiful. Already in the works is an iOS version and they are actively seeking feedback.

With your feedback, we plan to iterate quickly, add more features and expand the scope of the app. Here are a few things planned for the future of Findings. Maybe this is just what you need?

Well worth a download of the trial version.

 

I’ve just added a list of applications to the mobile science site, these are all anatomy reference applications. For those who remember Gray's Anatomy before it became a TV series these mobile apps offer the opportunity to explore and interact in 3D at a fraction of the weight of the book!

There are many more science applications for iOS here

 

Version 2.7.6 of XQuartz has been released. This release requires Mac OSX 10.6.3 or later.

The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

 

I’ve just been sent details of a couple of mobile apps that may be of interest to the medical profession.

MediMath puts 144 of the most important medical calculators and scoring tools on your iPad, iPhone, or iPod Touch.

MedScape Medscape is the leading medical resource most used by over 4 million physicians, medical students, nurses and other healthcare professionals for clinical information. - Medical News: - Drug Information and Tools: - Disease & Condition Information: - Medical Calculators

Micromedex-drug-reference Comprehensive drug information.

There are many more science applications for iOS here

 

One of the advantages of using a Mac for science is that you can often make use of the UNIX underpinnings of Mac OSX to access programs written for Linux.

A recent publication in Journal of Cheminformatics caught my eye, screening of molecules using electrostatics is usually a very time-consuming process, but this publication describes an interesting and very quick way to screen molecules.

A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening Francois Berenger, Arnout Voet, Xiao Yin Lee and Kam YJ Zhang Journal of Cheminformatics 2014, 6:23 doi

I’ve written instructions for how to install ACPC under Mac OSX.

 

iMOLView has been updated, this update optimises the app for iOS7.

Several apps have also been recently added MacroMole is a molecule viewer/teaching aid. Biochemistry Refence is a self-contained 350 page series of articles for a wide range of biochemistry topics. The comprehensive medical reference The Merck Manual is available for iOS.

Apple have also brought out iOS Human Interface Guidelines.

 

Version 1.9 of UCSF Chimera has been released.

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.

This looks to be an extensive update,

New features include

Multiple sequence alignment using Clustal Omega or MUSCLE web services. Building double-helical nucleic acids,"colorkey" command, "struts" command to reinforce structures for 3D printing, "vseries" volume series playback and processing options,more efficient save/restore of coordinates in sessions, Dynameomics amino acid rotamer library, WMV2 movie output, COLLADA export.

 

I’ve just been sent details of this webinar.

An Overview of AMBER 14 - Creating the World's Fastest Molecular Dynamics Software Package Tuesday, May 13, 2014 9:00 AM - 10:00 AM PDT

This webinar will provide an overview of the AMBER Molecular Dynamics Software package with focus on what is new with regards to GPU acceleration in the recently released version 14. This includes details of peer-to-peer support and optimizations, which have resulted in version 14 being the fastest MD software package on commodity hardware. Benchmarks will be provided, along with recommended hardware choices. In addition, an overview of the new GPU centric features in AMBER 14 will be covered, including support for multi-dimensional replica exchange MD, hydrogen mass repartitioning, accelerated MD, Scaled MD, and support-as-a-service on Amazon Web Services. This is a joint webinar by Ross C. Walker, University of California San Diego, Scott Le Grand, Amazon Web Services, and Adrian Roitberg, University of Florida.

 

I’ve just been sent details of two more Science apps for iOS.

X-ray utilities looks like a handy app for crystallographers. Real-time PCR is an iOS Application from Life Technologies, a collection of easy-to-use real-time PCR resources, and a comprehensive reference.

There are many more science applications for iOS here

 

RCSB PDB Mobile has been updated to include the May Molecule of the Month.

Aquaporin, May 2014 Molecule of the Month by David Goodsell 1fqy

There many more science applications for iOS here

 

Whenever I post anything about Fortran there is a noticeable uptick to page views so I thought I’d post a link to this review on Ars Technica

Scientific computing’s future: Can any coding language top a 1950s behemoth?. This is a very interesting review and discussion on scientific programming and it is no surprise that for the more computationally intensive number crunching applications Fortran still rules.

“I don't know what the language of the year 2000 will look like, but I know it will be called Fortran.” —Tony Hoare, winner of the 1980 Turing Award, in 1982.

 

I’ve just added to two applications to the spectroscopy page.

LSD (Logic for Structure Determination) is designed to find all possible molecular structures of an organic compound that are compatible with the experimental spectroscopic data.

Structure building relies on connectivity data found in 2D NMR spectra, without any reference to a chemical shift database. Molecular structures containing up to 50 non-hydrogen atoms were investigated by means of the LSD program. The measurement protocol that is required by LSD includes the recording of 1D 1H and 13C as well as 2D COSY, HSQC and HMBC spectra. The status of each atom must be defined. It includes the atom symbol, the hybridization state (sp3, sp2 or sp), the number of attached hydrogen atoms, and the electric charge. This part of the data set is most often easily deduced by the user from elementary chemical shift knowledge. The status of the heteroatoms is deduced from the elemental molecular formula.

The CASA (Computer-Aided Spectral Assignment) program is intended to assign 13C NMR resonances to the carbon atoms in a user-supplied molecular structure.

It relies on an exploitation of chemical shift correlations in 2D NMR spectra and, optionally, on a comparison between experimental and estimated chemical shift values. The assignment of all resonances is possible if the hypothetic supplied structure is the good one, assuming that CASA input data is correct. CASA may therefore be seen as a 1D/2D NMR-based automatic structure verification tool. The result of the CASA program is a set of lists of possible assignments.

 

Now that I have my new MacPro I thought it might be interesting to try out a couple of the software packages that I’ve previously reviewed. ForgeV10 allows the scientist to use Cresset’s proprietary electrostatic and physicochemical fields to align, score and compare diverse molecules. It allows the user to build field based pharmacophores to understand structure activity and then use the template to undertake a virtual screen to identify novel scaffolds. I’ve previously reviewed ForgeV10 and as it was formally known FieldAlign so I’m going to focus on the support for multiple processors and a few of the new features.

Read the review here

There is a compilation of software reviews here

 

The very popular NMR application iNMR was updated recently to version 5.3.6. This is a minor update:

When the slider for the first-order phase correction reaches the end-of-the-run, a message appears at the center of the same dialog: "Move This!", meaning that, if you want to go further, it's enough to touch the "fine-coarse" selector.

I’ve updated the spectroscopy page to reflect this

 

Version 3.2 of ASObjC Explorer for Mavericks, the script editor built to take full advantage of AppleScriptObjC, is now available.

The two main new features are Apple event logging, similar to tradition AppleScript editor logging, in addition to Explorer's own logging; and the ability to specify which thread scripts are run on, to facilitate debugging of scripts that use callbacks and times.

There are also a raft of scripting changes, several extra sample scripts, and improvements in several other areas.

You can read more here:

http://www.macosxautomation.com/applescript/apps/explorer.html

 

Wizard Pro has just been updated. Wizard Pro is a data analysis application with easy exploration in mind. The new release notes include

FEATURES

• Database support: import from SQLite, MS Access, MySQL, and PostgreSQL
• Numbers '13 support
• Timestamp / time-of-day support
• Customizable data partitions. Separate numeric data into groups of equal size, intervals of equal width, or user-defined intervals
• Best-fit lines on scatterplots, and reference lines on Q-Q plots
• Visualize critical values and p-values with the new Bottom Line popover (see screenshots)
• New "Copy Predicted Values" menu item applies a predictive model to the full data set

CHANGES

• Histograms are much sharper now
• More tick marks and labels on all the graphics
• Full access to the Column tools from inside the Raw Data view
• New preference option: choose a "Friendly" or "Neutral" font for The Bottom Line
• Filtered and frequency-weighted models run much faster than before
• Excel output is much prettier -- with bold, italics, and indentation for clarity.

NICE TOUCHES

• Exporting data now has a progress bar and a Cancel button
• Support for up to 6 data filters
• Support for up to 5 pivot columns

There are more graphing or plotting applications on the data analysis page.

 

ChemPencil is an inexpensive chemical drawing application that has all the usual chemical drawing tools. However as fas as I can tell it does not currently support round-trip editing, structures are pasted into documents as images and can not be then copy and pasted into ChemPencil for further editing.

There is a listing of some chemical drawing apps here and a review of ChemDoodle here

There has been an update to ChemEquate automatically formats and balances chemical equations. Copy with one click for use in word processing applications. Molecular weights are also conveniently provided.

 

There is an interesting publication in the latest issue of Chemical Biology and Drug Design describing, Chem-Path-Tracker An automated tool to analyze chemical motifs in molecular structures DOI. This is a plugin for the molecular visualisation tool VMD that allows the user to highlight and reveal potential chemical motifs with a protein using only a few selections.

The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed Chem-Path-Tracker.

More details on the project page

 

I just saw that the highly regarded DataGraph has been updated, this update includes:

• Pivot Table command - great for data analysis.
• Hover information to inspect data in a plot.
• A new method to import text files.
• Runs faster when you have large data sets.
• Improvements to basically every drawing command.
• More formatting options.
• More operations to edit data, automatically fill in entries etc using menu and context menu entries.
• Can label graphs and export multiple graphs at the same time

There are more graphing or plotting applications on the data analysis page.

There is a review of DataGraph 3.0 in The Journal of Statistical Software

 

I gave a talk at the RSC 25th Symposium on Medicinal Chemistry in Eastern England meeting last week entitled “Bringing Open Source to Drug Discovery”.

The slides and pages of links are available here.

I also captured the laptop screen of the demo which I’ve now put on YouTube.

https://www.youtube.com/watch?v=sG9vDIfp0NE&feature=youtu.be

The aim was to show what was available and to show how they can be integrated into proprietary tools using scripting, many of the scripts are available on the hints and tutorials page.

 

I know what I’ll be playing with this weekend!

 

I’ve just added ChemiCal to the database of mobile science application.

ChemiCalc is a powerful unit converter for chemistry and physics calculations. Students and teachers can enter and simultaneously view converted values for energy, wavelength and frequency. Formulas and fundamental constants relevant for quantum mechanics are included.

There many more science applications for iOS here

 

The official PDB viewer has been updated

 

I use markdown extensively on my websites and I try to keep a track of Markdown editors that are available. I noticed that Easy Markdown has just been updated, according to the release notes the update provides Improved opening of files encoded in various formats and a Bug fix.

ScienceCloud is a secure, SaaS-based, mobile-enabled information management and collaboration environment that improves data and knowledge sharing for globally networked researchers. Bi-directional integration between ScienceCloud and existing on-premises systems lets life sciences organizations migrate to the cloud in a measured fashion, continuing to leverage critical legacy applications as long as needed.

Two mobile apps are now available ScienceCloud Projects and ScienceCloud Tasks.

There are many more mobile science apps here

 

Version 14 of the Amber software suite has been released (There was no "unlucky" Amber13.)

• Force fields: Amber has two new fixed-charge protein force fields, ff14SB and ff14ipq, a new modular lipid force field, Lipid14, and updates to nucleic acid and carbohydrate force fields.
• Improved options for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
• A completely reorganized Reference Manual
• QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available
• More features from sander have been added to pmemd for both CPU and GPU platforms, including performance improvements, and support for extra points, multi-dimension replica exchange, a Monte Carlo barostat, ScaledMD, Jarzynski sampling, explicit solvent constant pH, GBSA, and hydrogen mass repartitioning. Support is also included for the latest Kepler, Titan and GTX7xx GPUs.
• Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations, and a new absolute free energy method.
• New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

Amber Tools have also been updated.

Among the new features in AmberTools14:

• The sander module, our workhorse simulation program, is now a part of AmberTools;
• Greatly expanded and improved cpptraj program for analyzing trajectories;
• new documentation and tools for inspecting and modifying Amber parameter files;
• Improved workflow for setting up and analyzing simulations;
• new capability for semi-empirical Born-Oppenheimer molecular dynamics;
• EMIL: a new absolute free energy method using TI;
• New Free Energy Workflow (FEW) tool automates free energy calculations (LIE, TI, and MM/PBSA-type calculations);
• Completely reorganized Reference Manual

 

After I posted the page on setting up a Mac for Cheminformatics I was asked if I could do something similar for writing chemistry (or Science in general) Python scripts on a Mac. So I’ve written a “How to” page on setting up your Mac to use the iPython notebook and write simple scripts that use Pybel to access OpenBabel.

The page is here Python, Chemistry and a Mac 1, and I’ll probably add more pages/scripts in the future.

 

A recently publication “High Performance in silico Virtual Drug Screening on Many-Core Processors” DOI describes porting BUDE (Bristol University Docking Engine) to OpenCL.

Our highly optimized OpenCL implementation of BUDE sustains 1.43 TFLOP/s on a single NVIDIA GTX 680 GPU, or 46% of peak performance. BUDE also exploits OpenCL to deliver effective performance portability across a broad spectrum of different computer architectures from different vendors, includ- ing GPUs from NVIDIA and AMD, Intel’s Xeon Phi and multi-core CPUs with SIMD instruction sets.

BUDE is now one the fastest HPC applications ever developed and nicely demonstrates the portability of OpenCL across different architectures.

There is a list of GPU accelerated applications here.

I’ve just finished a brief review of Asteris is a new iOS app that arose from a collaboration between Optibrium and Integrated Chemistry Design that allows medicinal chemists to design new molecules on their iPad and then calculate a range of physiochemical and ADME properties.

The complete review is here, and there is a full listing of reviews here.

 

CrunchYard is pleased to announce their academic offering for HPC in the cloud. The academic offering allows anyone with a valid academic e-mail to instantly access the online HPC facility.

Group accounts can be created for your research group, where simulation credits are shared. Credits are valid for 2 months after purchase.

Academic accounts include access to over 300 true CPU cores, and the following simulation software: FEKO CP2K NWCHEM GAMESS GROMACS LAMMPS

Other licensed codes are available on request (such as CPMD, STAR-CCM+ etc.)

 

I’ve just added a Radioactive Decay Calculator to the listing of mobile science applications.

 

I’ve just added the 250th entry on the Mobile Science database, and the honour goes to KiwiViewer

KiwiViewer is a free, open-source visualization app for exploring scientific and medical datasets. KiwiViewer opens a variety of file formats and provides flexible methods of accessing data, including Dropbox, Midas, iTunes file sharing, or download via url. Supported data types include meshes, images, and point clouds, with options for vertex coloring and texture mapping. File formats include: byu, g, jpg, kiwi, mha, obj, pcd, pdb, ply, png, stl, tiff, vti, vtk, vtm, vtp, vtu, and archive formats zip, gz, bz2.

The full MobileScience database can be found here.

Perkin Elmer are looking for input on ChemBioDraw

Calling all chemists! PerkinElmer wants to know what changes you would like made to the #ChemDraw ChemOffice suite? What features are important to you? Which ones are needed? Which ones do you never use? Please help us design the future direction of this product by completing this short (1 page) survey

Given the comments I’ve received from readers this seems like a chance to at least get your views registered and ask for better Mac support.

 

I’ve recently needed to set up a new Mac and I realised that the current installation process for all the applications, tools, chemistry toolboxes, and associated dependencies was unmanageable. I have a mixture of apps that I have compiled myself, others that I have simply used the precompiled binaries, others from Macports etc.

I decided to write a detailed account of the process of installing a number of toolkits and packages using Homebrew and PIP.

You can read the full account here in the hints and tutorials.

I’d be delighted to hear of any comments or suggestions for addition.

 

Shortly after announcing 100,000 downloads Dotmatics have posted an update to the chemical drawing app Elemental for iOS.

• Interface tweak for iOS 7

Previous improvements - iOS 7 update - Elemental drawing bug fixes - Property prediction bug fixes - iPhone 5 support - Updated predicted properties engine - YouTube video link for introduction to the app - App size reduces from 8MB to 1MB(!) - Dropbox and Twitter Integration - Calculated Properties Panel - Rate Elemental Button! Love Elemental? Please rate us! - Follow us on Twitter button - @ElementalApp - Full Retina Display Support - File association improved - Sketched molecules persist over restarts - Copy image to Camera Roll - Copy Image to Clipboard - File association (tap and hold to load in Elemental) - E-mail attachments have been improved - support for multi-centre bonds added - Multitouch gesture support Undo - double tap Zoom - pinch Scroll - two finger drag - E-mails now export a reaction/RXN file if the sketch contains an arrow - MOL file e-mails contain predicted molecular properties: MW, MolFormula, XLogP - Add text notes into your sketch - Now compatible with iOS 5.0 and up - E-mailing of images has been improved - Larger icons

There are many other Chemical Drawing Apps that support iOS

 

The official mobile app for viewing PDB structures RCSB PDB has been updated to include the April molecule of the month.

The molecule designer app Asteris has been updated to version 1.0.1 with a number of bug fixes and performance improvements.

 

I’ve just been told that the Absoft Pro Fortran 2014 v14 Compiler Suite For Mac OS X is available.

Pro Fortran 2014 v14 - A few of the new features for this release are: AWE-Chart, AWE-Plot, AWE-Form & Enhanced AVX Instruction set performance. Pro Fortran 2014 builds faster code with Absoft's Exclusive Dynamic AP Load Balancing Technology, OpenMP 3.0 support, SMP Analyzer, Tools Plug-in, New HPC Scientific & Engineering Math Library and more.

The Absoft IDE is the only commercial Fortran/C++ development environment designed by Fortran experts. It includes: programmer's editor, Absoft's SMP and Vector analyzer, Fx3 graphical debugger, SMP and MPI control features, optimized math libraries and 2D/3D graphics.

 

rNMR is an add-on for R.

rNMR is an open source software package for visualizing and interpreting one and two dimensional NMR data. In contrast to most existing 2D NMR software, rNMR is specifically designed for high-throughput assignment and quantification of small molecules. As a result, rNMR supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks.

I’ve added it to the spectroscopy page.

 

As Apple provide ever improved means to build fully fledged applications using Applescript the documentation from Apple has become ever more outdated. Fortunately Shane Stanley has continued to update his absolutely essential book AppleScriptObjC Explored. I started building applications using AppleScript Studio, but with Mac OSX 10.6 we gained a new framework AppleScriptObjC. AppleScriptObjC was a new framework in OS X v10.6 that allowed Cocoa applications to be written in AppleScript. Using AppleScriptObjC AppleScript code can work with any Cocoa framework, and can function as a first-class citizen in the Cocoa world. It also brought scripters into contact with Xcode. This daunting transition may have left many of us floundering if it was not for this book.

The Fifth Edition of the definitive guide to building AppleScript-Cocoa applications in Xcode is now available, covering Mavericks and Xcode 5. Mavericks introduces new syntax specifically for AppleScriptObjC projects, and the book and accompanying projects have been fully revised to cover this, as well as the important changes in Xcode 5.

Whilst the book is excellent, what I’d like to highlight however are the sample projects, these are 20 fully-editable and annotated example projects that you can explore and modify.

This is the definitive guide and should be on every scripters bookcase.

There is more information on the Applescript Resources Page.

 

Dotmatics have just announced that the chemical drawing app Elemental for iOS has been downloaded 100,000 times. Whilst not in the same league as Angry Birds it surely marks an important milestone for scientific apps for mobile devices.

There are many other Chemical Drawing Apps that support iOS

 

I’ve just added KST to the list of data analysis applications for Mac OSX

Features of Kst include:

• Robust plotting of live "streaming" data.
• Powerful keyboard and mouse plot manipulation.
• Powerful plugins and extensions support.
• Large selection of built-in plotting and data manipulation functions, such as histograms, equations, and power spectra.
• A number of unique tools which dramatically improve efficiency, such as the "Data Wizard" for fast and easy data import, the "Edit Multiple" mode to bulk-edit most objects, or the "Change Data File" tool to compare results from different experiments
• Color mapping and contour mapping capabilities for three-dimensional data, as well as matrix and image support.
• Monitoring of events and notifications support.
• Built-in filtering and curve fitting capabilities.
• Convenient command-line interface.
• Powerful graphical user interface with non-modal dialogs for an optimized workflow.
• Support for several popular data formats.
• Multiple tabs.
• Extended annotation objects similar to vector graphics applications.
• High-quality export to bitmap or vector formats.

 

GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods.

Some capabilities include:

• Pure QC simulations - ab initio and SMO.
• Pure MM simulations - using AMBER, CHARMM or OPLS force fields.
• Hybrid QCMM simulations.
• Single point calculations.
• Energy minimization.
• Molecular dynamics.
• Reaction coordinate scanning.
• Umbrella sampling.
• Reaction path calculations - using NEB.

GTKDynamo is available for download for linux and Mac platforms . Please, make sure that you have installed:

• pDynamo
• Matplotlib
• Numpy / Pylab
• Pymol 1.x
• pyGTK
• ORCA, ab initio calculations.

J. F. R. Bachega, L. F. S. M. Timmers, L. Assirati, L. B. Bachega, M. J. Field, T. Wymore. J. Comput. Chem. 2013, 34, 2190-2196. DOI: http://dx.doi.org/10.1002/jcc.23346

 

I’ve updated the list of clipboard managers, there are a couple of new additions and a few updated products.

 

A couple of mobile science applications have been updated recently.

MyScript Calculator has been given an iOS 7 makeover.

Write the mathematical expression and MyScript technology will convert symbols and numbers to digital text and delivering the result in real time.

SUPPORTED OPERATORS

• Basic operations: +, -, ×, ÷, /
• Powers, Roots, Exponentials: 7², √, ∛, e³
• Misc. Operations: %, |5|, 3!
• Brackets: ( )
• Trigonometry: cos, sin, tan, cot, cosh, sinh, tanh
• Inverse trigonometry: acos, asin, atan
• Logarithms: ln, log
• Constants: π, e, phi.

SPRESImobile has also been updated, there a number of bug fixes and you can now search by reaction name.

SPRESImobile provides you with a powerful and convenient way to access ChemReact, containing around 410,000 chemical reactions and related references. InfoChem created ChemReact for chemists who need information about effective reaction transformations. We achieved this by selecting representative examples of each reaction type from the larger SPRESI data collection of 1974-2009.

 

The popular reference management application Bookends has been updated. This looks to be a significant update with many bug fixes.

• Fixed a bug that could cause mangled reference metadata to appear in the reference list.
• Fixed a bug where editing the Notes field on the main tab would not update the Notes field in the Notes tab.
• Fixed a bug that could cause an error to be thrown if you edited a tag while the tag cloud was showing and then clicked on the tag cloud.
• Fixed a scanning bug that prevented the year from being output when a citation used the year-only modifier (%) and had cited pages.
• Fixed a bug where the font size of scanned in-text citations would be different from that of the paragraph's style sheet.
• Fixed a bug in excluding words from capitalization where words consisting of a single accented character were ignored.
• Fixed several bugs in case conversion that affected Title Case and Sentence case.
• Fixed a bug that resulted in malformed citations if you scanned a Word document twice in the same session with an Author-Date format.
• Rating stars in the list view can no longer appear as white on a white background in refs that have been assigned a color label.
• Fixed a bug in Find in This Reference.
• Fixed a problem that prevented dropped text onto a note stream from being added to the new notecard.
• Cited Pages once again work in scanned text files. Bookends Server works once again.
• Fixed a problem where a Find/Replace with styles could change the style for an entire field.
• Fixed an issue with JSTOR where the search would have to be done a second time for it to succeed.
• Corrected the escaped BibTeX output for é.
• Importing metadata from Web of Science in Bookends Browser works again.
• The Key field, if shown in the reference list, will update automatically if you use Refs -> Generate BibTeX Key.
• Fixed a bug where an author's surname was always used if a secondary order field in the format had content, even if the popup told Bookends to use the same name format as the first time.

Bookends on Tap and Bookends on Tap lit the corresponding applications for iOS are unchanged.

There is a list of reference management applications for Mac OSX here.

 

The Vortex script that accesses Un1Chem has been updated. This is a minor bug fix.

Un1Chem is a new web resource provided by the EBI, it is a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between databases. Currently the uniChem contains data from 21 different data sources:-

 

QMForge is a program used to analyze the results of quantum chemistry (DFT) calculations. Gaussian 98/03/09, ADF, GAMESS (US), GAMESS (UK), PC-GAMESS, Jaguar, and ORCA files are supported. The following analyses are available:

• The support of several QM output formats including Gaussian, ADF, GAMESS (and its various derivatives), Jaguar, Molpro, and ORCA,
• Population analyses such as Mulliken, Lowdin, C-squared, and Overlap on user-defined sets ("fragments") of basis functions,
• Gross Population Analysis to compare Mulliken and Lowdin populations and spin densities for each atom and orbital,
• Fragment Analysis to interpret the contributions of fragment MOs to molecular MOs,
• Frenking’s Charge Decomposition Analysis,
• Calculation of Mayer's bond orders,
• Visualization of each step in a geometry optimization, with the ability to save any of those structures as XYZ or PDB files,
• Plots of Convergence and Energy in the Geometry Optimization tab,
• A simple, yet powerful, XYZ editor with tools that allow translations and rotations to align bonds to specific axes,
• Animation of the normal modes of a frequency calculation and the ability to save these as animated GIFs,
• Plots of IR and/or Raman spectra in the Frequency Tab, and
• A plot of electronic transitions and a easy-to-read list of the corresponding orbital excitations from TDDFT/CIS calculations.

QMForge has been created using the following dependencies:

• The Python scripting language (2.7.5),
• The Qt4 toolkit and its Python extensions PyQt4,
• NumPy (1.7.1),
• PyQwt (5.2.0), and
• The cclib computational library (v1.2b).
• OpenBabel and its Python bindings
• The Python Imaging Library (PIL)
• simplejson

QMForge has only been extensively tested on Mac OS X Snow Leopard and Mavericks

Tenderholt, Adam L. QMForge, Version 2.3.2, http://qmforge.sourceforge.net.
Tenderholt, Adam L. "QMForge: A Program to Analyze Quantum Chemistry Calculations", Version 2.3.2, http://qmforge.sourceforge.net.

 

SMILES (Simplified Molecular Input Line Entry System) is a simple yet comprehensive chemical language in which molecules and reactions can be specified using ASCII characters representing atom and bond symbols. This system is compact and human readable which has made it an attractive way to store chemical information within a database.

Some examples

Ethanol CCO Cyclohexane C1CCCCC1 Nicotine CN1CCC[C@H]1c2cccnc2

In order to search for specific sub-structures it is necessary to create a query that describes the pattern of atoms and bonds (subgraph) required within the molecule (graph). SMARTS is a language that allows you to specify substructures using rules that are straightforward extensions of SMILES. That said complex queries can get challenging to interpret which is why the SMARTS viewer and SMARTS editor from BioSolveIT, two tools developed by Karen Schomburg and Lars Wetzer at the Center for Bioinformatics at the University of Hamburg, are so valuable.

The tools are provided free until June 30th 2014

K. Schomburg, H.-C. Ehrlich, K. Stierand, M.Rarey From Structure Diagrams to Visual Chemical Patterns J. Chem. Inf. Model., 2010, 50 (9), pp 1529-1535 http://pubs.acs.org/doi/abs/10.1021/ci100209a

K. Schomburg, L. Wetzer, M. Rarey Interactive Design of generic chemical patterns Drug Discov Today (2013) http://dx.doi.org/10.1016/j.drudis.2013.02.001

We are starting to see companies exploit the client server model in bringing ever more sophisticated scientific applications to the iPad.

Asteris is a joint development from Optibrium the creators of StarDrop and Integrated Chemistry Design who created Chirys Draw. Asteris uses Chirys Draw’s touch interface to design novel molecules and then uses StarDrop’s predictive modeling power, guided by the Glowing Molecule™ visualization, instant feedback dramatically reduces the time it takes you to identify high quality compound designs. Using Asteris you can calculate a range of simple “core properties”, and ADME properties, including solubility, hERG inhibition and CNS penetration, using rigorously validated models from the StarDrop platform.

• CORE PROPERTIES
• Molecular Weight
• Number of rotatable bonds
• Flexibility
• Number of hydrogen bond donors
• Number of hydrogen bond acceptors
• Topological polar surface area.
• logP
• STARDROP ADME PROPERTIES
• logS
• logS7.4
• logD
• 2C9 pKi
• hERGpIC50
• BBB log([brain]:[blood])
• BBB category
• HIA category
• P-gp category
• 2D6 affinity category
• PPB90 category

All of the predictions are calculated using StarDrop ’s ADME QSAR module. You will need to be connected to the internet to perform these calculations using the secure Asteris cloud server.Alternatively, you can run the calculations on your own server with the “Enterprise” edition.

All communications with the server uses industry-standard SSL encryption. No compound structures or data are stored on the server. Calculate "core properties" for an unlimited number of molecules for free. Calculate ADME properties for 20 new compounds each month, free of charge. Additional ADME property calculations can be purchased via an in-app purchase.

There are demo videos on the support site.

 

Whilst Papers3 remains an extremely popular desktop reference management application Papers3 for iOS has come in for some criticism, in particular poor synchronisation with the desktop and the use of unintelligible file names. The latest version seems to address some of those concerns.

What's New in Version 3.1.5 New:

• Supplemental file support.
• Sharing PDFs via email now use human readable file names.

Stability fixes:

• Fixes a crash related to syncing.
• Improved performance on syncing.

Other:

• General bug fixes.
• Improved general appearance on iPhone.

The Mobile Science website contains more science apps for iOS.

 

Since it has been just over three months since I built the Mobile Science website I though it might be interesting to see how it is performing. After a slow start there have been around 6000 page views and looking at the weblog it is clear many people are starting to use the search facilities to explore. Currently there are around 250 scientific apps listed and I’ve started to add iOS programming resources.

The top 25 viewed apps are:-

Wolfram|Alpha
Papers for iOS
ChemDoodle Mobile
The Elements in Action
ChemDraw for iPad
Elemental
iMolView
The Elements in action
Play to cure: Genes in Space
Living Molecules
iOS Chart Library
Chemistry by Design
TouchPlot
Learn NMR FID
SciVerse Science Direct
Mobile HyperChem
Mobile Molecular DataSheet Toolkit
Reaction 101
Mathematics with PocketCAS pro
RCSB PDB Mobile
Tydlig - Calculator Reimagined
PyMOL
ElementalDB
Plasmid.io
Named Reactions Pro

Whilst the number of chemistry apps is perhaps unsurprising it is great to see other areas of science starting to make an appearance.

 

The ACS Mobile Meeting Application is your full featured guide to manage your experience at the 247th ACS National Meeting & Exposition in Dallas, TX. App features include: - Native app: No wifi connection required to access the conference program, schedule, or maps. - Home: Quick access to technical, social, and governance meeting program browse and search features, exposition information, and app user guide. - Program: Browse the entire event program to build your personal schedule, bookmark sessions or speakers, or access session handouts as available. - Take notes and share them via email. - Connect your meeting experience with social media. - Exhibitors, Maps, related conference info and much more

There many more mobile application on the MobileScience website.

 

Diversity Genie is a small but powerful utility to analyze datasets of small organic molecules. Its features include:

• Calculation and comparison of diversity of chemical sets
• Ability to handle sets of millions of molecules
• Sorting, slicing, and merging large SD files
• Conversion between SMILES, InChI, and SDF formats
• Filtering based on property values and structural uniqueness
• Computation of 2D and 3D atomic coordinates
• Addition/Removal of implicit hydrogens
• Computation of molecular properties such as molecular weight, number of rotatable bonds, number of HBD, HBA, as well as other descriptors
• Export and import of data to/from CSV files
• Data visualization

 

I know that Fortran is still very important in scientific computing so this may be of interest.

CLFORTRAN is an open source (LGPL) Fortran module, designed to provide direct access to GPU, CPU and accelerator based computing resources available by the OpenCL standard.

Added to the GPU Science page.

 

At the WWDC on June 10 2013 Apple announced the latest version of the Mac OSX operating system and on the following October 22 they announced it was available as a free instal from the Mac App Store. Since then there have been two updates leading to the current 10.9.2.

As soon as the update was announced at the WWDC many software companies started checking and updating their software so that when Mac OSX 10.9 was released they had compatible updates available immediately or shortly after. I kept a list of scientific applications under Mavericks and have updated the list periodically. Most software is now compatible, or there are workarounds. However recently I was made aware of the situation with ChemBioDraw from Perkin-Elmer (formally Cambridgesoft). ChemBioDraw has been a major chemical drawing package on the Mac for as long as I care to remember however the current version is not compatible with Mavericks. Indeed when you look at the support forum there are reported issues with retina display dating back to 2012! A support topic that has been viewed nearly 6000 times but not yet fixed apparently. There are many comments of the support forum but perhaps this gives you a flavour.

I confirm, the copy/paste issue in Mac version of ChemDraw 13 makes it totally unusable!!!! I suggest this is not only a problem with the compatibility with Mavericks. It never worked in Mountain Lion too! This issue is at least one year old and the developers just continue to ignore this issue. ChemDraw 13.0 crashes >90% of the time when you copy/paste a structure.

As of writing there is no indication when there will be a fix or whether earlier versions of ChemBioDraw will also be updated. This software is very expensive $1140 for a one year license! So my question is what is a reasonable length of time to expect to wait for an update?

 

RCSB PDB Mobile has been updated to include molecule of the month.

There is a comparison of Molecule Viewers for iOS here.

 

A little while back I posted a comment on the Apple SciTech list asking about options for stereoscopic viewing of molecular modelling on a Mac.

Many thanks to those who contacted me directly, it seems there are a number who have suffered the trials and tribulations of trying to set up stereo viewing. I suspect the combination of different graphics cards, driver, emitters, special connectors, special glasses, program software, X11, operating system changes means that this is a real pain to coordinate support., something always seems to get "updated" breaking everything else.

Which is why this email from Stephan Keith caught my eye.

Let me tell you my solution.  It is not necessarily cheaper, but for me, a whole lot easier. I am a 3D software engineer, but I am seriously interested in stereoscopic 3D.  I program in C, OpenGL and GLUT. I became weary of all the glasses, buffers, nVidia cards that didn't really work, emitters ... the whole mess. What I do, now, is I write my OpenGL software to create a sidexside or top over bottom stereo display that takes up the entire screen. I then connect an HDMI connector to my LG Stereo 3D Television.  I turn on the Stereo3D, put on my RealD glasses.  The S3D is passive, not active, so I don't get the annoying flicker, and I don't have to worry about nVidia 3D glasses running out of power (most annoying, at what was $185 a pop). No special glasses, no emitters, no special code, no special connectors.  All .... Gone.

I thought I’d try this out, so armed with a copy of MOE a MacBook Pro and a mini display port to HDMI cable I headed down to PCWorld in Cambridge to try it out (many thanks to the people at PCWorld who were really helpful).

Passive 3D

I first tried out an LG ELECTRONICS 27MT93V LG MT93V . The first thing I’d say is that the set up was trivial, from connection to viewing a protein in 3D was only a couple of clicks. This gave a good impression of a 3D protein structure, both in stick display to see side-chains and in cartoon display to see the overall structure of the protein, colours were excellent. However I found that it was necessary to sit facing absolutely in the centre of the screen to get a good display, also if you move close to the screen then the 3D effect is lost and you get jagged line artefacts. This might not be an issue for a TV but if you paln to use it as a computer monitor I suspect it might be a deal-breaker. I suspect it would be difficult to sit alongside colleagues and have them all have a good 3D impression.

Active 3D

I then tried an active 3D display on a Samsung UE46F6800 46-inch Widescreen TV, this was much larger than I needed but I understand there are smaller models available. Once again setup was a breeze, this gave a good impression of a 3D protein structure, both in stick display to see side-chains and in cartoon display to see the overall structure of the protein, colours were excellent, and the brightness did not seem to be impacted at all by the active glasses. The 3D viewing was acceptable at a wide range of screen angles and distances and it should be possible to sit beside colleagues to discuss a project and all have a good 3D view.

I wear prescription glasses and I found the active glasses fitted comfortably over my glasses. They were also a lot more lightweight than I remember in the past. In the past active shutter glasses have been very expensive but prices have dropped significantly.

Personally I found the Active 3D much superior, especially if you planning to use this mainly as a computer monitor rather than a TV that you view from the comfort of your sofa.

 

Marvin has been updated to version 6.2.1

 

I’ve put together a page briefly describing the molecule viewers I’ve found for iOS.

I’ve included both small molecule and large biomolecule viewers, together with some that use a client server model.

 

Graph Builder has been updated to version 10.9.16.

• Made the heat map (aka: image map, point fill) and 3D scatter, surface and volume color mapping editor significantly better.
• Added a palette that shows how to script a multi-level animated pie chart.
• Removed depreciated system calls.
• Adjusted many items under the hood in preparation for v11.
• Special Note: The v11 build is being worked on and your feedback to support@vvi.com is very welcome.

Graph Builder is a powerful application rich in graphic editing, creation and programming to facilitate the visualization of information. It has a good complement of 2D and 3D graph features, a full-fledged user interface and is programmable. Paste data into table editors, write scripts to generate data, load a Xcode plugin you write for data generation and to retrieve data from external sources.

There is a comprehensive list of data analysis tools for Mac OSX here.

 

On the 10th anniversary the OEChem toolkit from OpenEye has been updated,

• Added support for OSX 10.9 Mavericks.
• The next toolkit release, 2014.Jun, will be the last release to support OSX 10.7.
• This release will be the last release to support OSX 10.6.
• The next toolkit release, 2014.Jun, will be the last release to support 64-bit Ubuntu 10.04.
• GCC 4.8.2 support added for RHEL6. GCC 4.8.1 had a bug that made it impossible to compile OpenEye header files. Please use 4.8.2+.
• Experimental support for Python 3.3 added.

 

Everyones favourite physicist Brian Cox has just brought out a new app. The wonder of Life app allows you to explore nature in 3D with Professor Brian Cox as your personal tour guide. This is a follow up the highly successful Wonders of the universe.

Brian Cox is an excellent presenter and these apps are based on the highly successful BBC TV series, Wonders of Life and Wonders of the Universe.

 

TB Mobile from Collaborative Drug Discovery been updated.

TB Mobile makes available a set of molecules with activity against Mycobacterium Tuberculosis, and known targets available in CDD. It links to pathways (biocyc.org), genes (tbdb.org), literature (PubMed).

The latest update adds support for iOS7, and adds further compounds and molecular targets. So now there are 96 unique targets and 805 compounds. There is also major new functionality including interactive clustering, personal favourites, target prediction and exporting capabilities.

 

I’ve just been sent details of a number of iOS apps that would be useful to those involved in spectroscopy, (NMR, IR, MS) so I’ve added them all to the mobile science site.

 

Learn NMR FID is a great teaching tool to learn the basics of NMR data collection and processing. Use simulated free induction decays (FIDs) and spectra to see apodization, noise and relaxation effects. Move peaks and see how the FID changes. Real and imaginary FIDs prior to and after processing are displayed as is the resultant spectrum after the Fourier transform.

There are more science apps for iOS on the mobilescience site.

I also thought I’d mention this framework that was brought to my attention recently. There is a trend to move massively parallel tasks to the GPU, GPU Image is a framework (BSD license) that simplifies the creation of GPU filters. This framework is built around OpenGL ES 2.0, so it will only work on devices that support this API. This means that this framework will not work on the original iPhone, iPhone 3G, and 1st and 2nd generation iPod touches. All other iOS devices are supported.

 

Whilst the update to PYMOL was announced as part of the Schrodinger update I thought it deserved a separate blog entry.

Graphics

• Greater user control over color settings ◦ Color settings can be set as hexadecimal, colors, or floats ( [1., 1., 1.])
• New ‘focalblur’ command

• New ‘callouts’ for scene annotations

  Usability

• Improved and extended Filter Wizard

• New commands ◦ Retrieve bond properties with get_bond ◦ Load structures from PubChem by SID and CID codes with fetch
• Improved PDB Loader graphical interface
• Expanded documentation of settings
• Access settings and properties from the iterate/alter commands via “s.” and “p.”
• Improved labels to include customizable connectors to atoms, multiline labels, and more
• Ability to select atoms by coordinates or by user-defined property
• New selection keywords: metals, sidechain, backbone

• CTRL-F to find objects or selections in the Object Menu Panel

  Bug Fixes

• Dynamic measures now stored in session files

• Sequence viewer colors fixed
• Fixed inversion problem with ‘cealign’

• Improved stability for shader-based rendering

  AxPyMOL

• New option to embed content within a PowerPoint file

• Support PowerPoint PPTX file format
• Improved installer
• AxPyMOL control displayed as an “Add In” on the PowerPoint Ribbon
• 32-bit and 64-bit Office Support
• Embeddable presentation content
• Initial support for MAE files
• Shader-based rendering support for volumes and improved graphics
• Many bug fixes

The compiled PYMOL binaries are available for paid download with different options for academic, industrial and non-profit.

In addition the source code is available for free download. Not all new features make it to the source code right away, but eventually all features will, usually within a few months

 

The Schrodinger Small Molecule Drug Discovery Suite was updated over the weekend, this is a major update that brings in a host of new features and improvements.

Maestro Graphical Interface

Improved flexible ligand superposition Additional graphics settings
Real-time antialiasing Real-time ambient occlusion, outlines, and cartoon shading effects Multivariate ranking in the Project Table
Simultaneously maximize or minimize up to four property values, and rank entries based on the optimization Date Created and Date Modified fields automatically generated in the Project Table Workspace responsiveness of atom labels is up to 2.5x faster Click and drag to rearrange atom, measurement, and adjustment labels in the Workspace Support for bond labels Installed scripts and Tools menu items now searchable in the Task Tree Significant improvements to the Property Calculation interface in the project facility
Simultaneously calculate multiple properties Additional 2D properties now available: AlogP, #Hbond acceptors, #HBond donors, #rotatable bonds, polar surface area, molar refractivity, and polarizability

Ligand Docking

Ligand efficiencies are now calculated from the DockingScore instead of the GlideScore Generate per-residue interaction energies in Virtual Screening Workflow (VSW) for visualization New server mode in Glide Ligand Designer enables near real-time interactive docking (Glide Ligand Designer Script)

Pharmacophore Modeling

Performance improvements to Phase database operations, including faster deletion and insertion of ligands Automatic restart of Phase database subjobs

Field-Based QSAR

Use QM-calculated fields in 3D QSAR (command line only; phasefqsar script)
phasefqsar script generates Jaguar input files for computing QM electrostatic fields for use in 3D QSAR

Molecular Dynamics

Monitor secondary structure elements over the course of the trajectory (Simulation Interactions Diagram; SID)

Quantum Mechanics

New interface to compute thermodynamic properties for reactions New faster TDDFT algorithm and graphical interface Compute Raman intensities Several improvements to the results script Jaguar pKa displays the computed pKa as an atom label by default Heat of formation graphical interface now supports bromine and iodine Improved numerical stability of the 1st and 2nd derivatives of the D3 correction Increased utility of canonical.py script
Script acts on a group of isomers and skips structures with unique stoichiometries

Protein X-Ray Refinement

Optionally set hydrogen B-values

Workflows & Pipelining

Includes the latest version of KNIME (v2.9)
Many new features including a Send Email node and ability to save workflows under different names; see http://tech.knime.org/whats-new-in-knime-29 for a complete list of new features Use any Glide simulation option in the Glide Ligand Docking node Employ a specific template in the Prime Build Homology Modeling node Import ungrouped structures to PyMOL from Run PyMOL node

Job Control

Improved fault tolerance Improved handling of suspended jobs in queueing systems

There are also updates to the Biologics Suite and the Materials Science Suite.

 

Marvin 6.2 from chemAxon has been released.

This is a major update and the release notes can be found here, of particular note are

• TIFF AND EPS FORMAT SUPPORT: Chemical structures can be exported to TIFF or EPS image formats in MarvinSketch and MarvinView
• R-GROUP DISPLAY AND EDITING: In MarvinSketch editing and displaying R-groups were modified and improved in several cases.
• COPY – PASTE BETWEEN MARVINSKETCH AND MARVIN FOR JAVASCRIPT: Structures can be copied from and to the canvas of our Java based MarvinSketch and Marvin for JavaScript .
• R-groups added to Marvin for JavaScript: R-group definitions can be created and edited; and attachment points can be added to a structure
• Chinese Name to Structure: Frequent OCR errors in Chinese characters are now corrected automatically

 

A while back in a very neat demonstration of the portable coding approach Dotmatics released ElementalDB for the iPad an iPad application that does a substructure search of a 1,200,000 Chembl structure database in less than a second. Well now they have gone even further and ported their data visualisation tool Vortex to the raspberry Pi.

Raspberry Pi is a $35 credit-card sized computer that plugs into your TV and keyboard. It is used in electronics projects and for many of the functions usually assigned to a desktop PC such as spreadsheets, word-processing and games.  It features a 700MHz ARM processor and can run a Debian Linux derived operating system. Compiling Vortex on this platform took just a few minutes as it involved building upon Oracle’s JDK 7 which was recently released for the Pi.

 

I just noticed that ChemSpider has just passed 30,000,000 records, the molecule registered to mark this impressive milestone is shown below.

ChemSpider is a free chemical structure database that brings together structures, properties, sources and publications. ChemSpider enables researchers to discover the most comprehensive view of freely available chemical data from a single online search. It is owned by the Royal Society of Chemistry.

There is a Safari extension that uses ChemSpider for depiction of chemical structures.

 

The new release comes with a long list of new features and improvements such as multi-sample RNA-Seq visualization, a completely new look and feel, and a new beta plugin with a memory-efficient read mapper. A few highlights from the release are:

• A substantial update of the RNA-Seq Analysis tool
• New statistical tools for analysis of differential expression
• A number of new tools now being workflow enabled
• Several new options for Workflows
• Great improvements on speed and memory usage for copying data in the Navigation Area and between CLC Genomics Server and a Workbench
• Complete redesign of the graphical user interface including new options for Side Panels and Views and a redesign of Zoom tools

 

I keep an eye out for Markdown editors and I recently came across a new addition that has some interesting features.

Archimedes is a text editor for OS X that combines support for Markdown and LaTeX. Archimedes is a fully-featured plain text and Markdown editor. It includes a fast syntax highlighter and provides convenient keyboard shortcuts for common actions, such as inserting images and links. The bonus is that in Math Mode, Archimedes lets you write mathematics in a subset of LaTeX. Just enter $$ to get started. Over 700 intuitive commands, such as \sqrt{a^2 + b^2}, help you produce stunning mathematical output. Archimedes even autocompletes commands and intelligently matches closing braces, brackets, and parenthesis as you type.

For anyone writing scientific text Archimedes is certainly well worth a look.

 

Nebiocalculator from New England BioLabs is actually web app using HTML5, javascript and CSS3, but it has been formatted for touch use so it works nicely on iPhones and iPads. Requires active internet connection.

• molarity/dilution calculation
• OD260 conversion
• ligation calculation
• mass/moles conversion for both dsDNA and ssRNA

 

MolSoft have announced that a new version of ICM is now available for download from the support site . A description of the key new features can be found on the news page and release notes. To help you get to know the new features we will be holding a free webinar next week (2/11) - we hope you can join us, please register here.

Some of the key new features include:

• Anaglyph Stereo
• MolSkin - high quality surface graphics
• Movies from Slides
• SCARE - induced fit docking
• Fragment screening
• MolScreen - >360 high quality fingerprint and 3D pharmacophore models
• Blast search direct from the GUI
• ToxScore - new score for drug reactivity and toxicity

 

This is an update to a blog post from early 2013 incorporating some valuable readers comments.

For many years I’ve used the excellent Clipboardsharing to exchange the clipboard contents between my laptop and desktop machines, it also supports multiple clipboards. However it is not supported under Mac OS X 10.7.x (Lion) and the developer website seems to have disappeared. I spent a while looking at various alternatives and I thought I’d summarise my findings.

 

Beating cancer through a space game never seemed possible. Until now….

Every day, scientists across the globe are painstakingly analysing the genetic faults in thousands of cancer samples. They are looking for clues that will help develop new cancer treatments. This game let’s you help.

Play to Cure™: Genes in Space is a pioneering way of helping these scientists in their mission to beat cancer sooner and all via this world first mobile game supported by Cancer Research UK.

A mysterious substance is discovered in the voids of deep space. Dubbed Element Alpha, the substance is refined for use in medicine, engineering and construction and soon the Element Alpha industry explodes galaxy wide.

As an employee of Bifrost Industries, one of the biggest traders of the substance, your job is to collect as much Element Alpha as you can and trade it for upgrades to your spacecraft to help you manoeuvre the asteroid filled space course.

Game features:

• Arcade/action space gameplay
• Rise through the ranks at Bifrost Industries from Recruit to Galactic Legend
• Upgrade and customise your ship with unique items, weapons and colours
• Plan your route to maximise your Element Alpha haul
• Maximise your profits by trading your Element Alpha when the market is high or sell immediately for a guaranteed return

HOW THIS HELPS TO BEAT CANCER SOONER

Element Alpha represents genetic cancer data that scientists across the world analyse on a daily basis. Genes in Space has successfully translated this data into an interactive, asteroid-strewn intergalactic assault course.

By collecting Element Alpha and navigating your spaceship through the cosmos you’re finding the significant genetic changes which help scientists to discover cancer causing genes and develop new life saving treatments.

So gamers take note. The Genes in Space story may not be real, but the impact of what you’re doing is far from science-fiction.

Why not download Play to Cure™: Genes in Space and do your bit.

This application is designed for iPhone 4S and higher, along with iPad 2 and higher. You can play on older devices but your gaming experience may not be the same

 

The Wolfram|Alpha iOS app has been updated. This is an essential app whether or not you are a scientist.

This update fixes a few bugs and supports iOS7 design.

There are more apps on the MobileScience website.

 

Un1Chem is a new web resource provided by the EBI, it is a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between databases. Currently the uniChem contains data from 21 different data sources.

This script originally created by Sune Askjær first calculates the InChiKey for molecules in a workspace and then uses Un1Chem to search for information in multiple databases, then it provides a summary and a link to a locally generated summary table.

Full details are here Scripting Vortex 18.

 

I’ve just added SVGgh from GenerallyHelpfulSoftware to the MobileScience website.

SVGgh is a collection of classes for using SVG as artwork in iOS Apps. Includes a UIView and a button class.

No excuse for using bit mapped images!

 

The ChemSpider Safari extension has been updated. It sports a cleaner interface and provides fixes a bug introduced by an update to ChemSpider.

 

I see that Papers3 for iOS has just been updated to version 3.1.1.

This version now includes article level metrics (Altmetrics) on the article you're reading now available in the landmarks view (PDF reader).

• General bug and stability fixes.

• Improved performance on syncing.

There are more science apps for iOS here http://www.macinchem.org/mobilescience/.

 

In the tutorial Scripting Vortex 15 I showed how it is possible to create a contextual script for Vortex that downloaded a specific PDB file, then a FlexAlign Vortex script first identifies the structure column and then get the SMILES string of the selected molecule generates a 3D structure and uses Flex Align to do a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.

While this is useful if you have similar structures (perhaps analogues in a series) there will certainly be situations where it may be preferable to dock the new ligand into the binding site. The Scripting Vortex 17 tutorial describes how to achieve this.

 

Apple has released updates to their iWork productivity suite, perhaps most interestingly Numbers now regains applescript support. If you open the Applescript dictionary most of the classes and commands are now available again, still absent are “split into columns” and “split into rows”.

The mobile version of Numbers for iOS has also been updated.

 

Interestingly since I set up the mobile science site several people have sent me links to security concerns on mobile devices. The latest from Cisco suggests that 99% of all mobile malware targets Android devices, and 91% of web exploits target Java. iOS so far does not appear to be a major target but I’m sure there are people trying to breach the “walled garden” that Apple have created.

 

QMForge 2.3.1, a cross-platform, open-source program for interpreting and analyzing the results of QM calculations has just been released

QMForge 2.3.1 builds upon the previous versions with the addition of the following features:

• Plots of Convergence and Energy in the Geometry Optimization tab,
• Plots of IR and/or Raman spectra in the Frequency Tab,
• Ability to save the normal modes of a Frequency calculation as animated GIFs,
• Gross Population Analysis to compare Mulliken and Lowdin populations and spin densities for each atom and orbital

Other notable features include

• The support of several QM output formats including Gaussian, ADF, GAMESS (and its various derivatives), Jaguar, and ORCA,
• Population analyses such as Mulliken, Lowdin, C-squared, and Overlap on user-defined sets ("fragments") of basis functions,
• Fragment Analysis to interpret the contributions of fragment MOs to molecular MOs,
• Charge Decomposition Analysis,
• Mayer's bond orders,
• Visualization of every step in a geometry optimization, with the ability to save any of those structures as XYZ or PDB files,
• A simple, yet powerful, XYZ editor with tools that allow translations and rotations to align bonds to specific axes,
• Animation of the normal modes of a frequency calculation, and
• A plot of electronic transitions and a easy-to-read list of the corresponding orbital excitations from TDDFT/CIS calculations.

 

Several sites are now using javascript rather than java plugins to render 3D chemical structures, ChemTube 3D contains interactive 3D animations and structures, with supporting information for some of the most important topics covered during an undergraduate chemistry degree.

ChemTube3D news - 2014 version uses Javascript and so works on iPads. It is slower but less problematic than Java. Please use latest versions browsers for best results.

Henry Rzepa has used his blog to offer insights into reaction mechanisms. However the issues of security have made the use of java plugins an onerous task to maintain. His solution:-

Replace the use of Java applets with one not dependent on Java. In the last 18 months an amazing effort to do this has resulted in JSmol, which uses only JavaScript (which has nothing to do with Java despite the name).

I see more and more sites using the javascript and HTML5, recently we have see and update the ChemDoodle Web Components, I suspect all chemical drawing packages will need a javascript version in the future for both 2D and 3D rendering.

 

I’ve just added GAUSS Mathematical and Statistical System to the page of data analysis tools for Mac OS X.

The GAUSS Mathematical and Statistical System is a fast matrix programming language widely used by scientists, engineers, statisticians, biometricians, econometricians, and financial analysts. Designed for computationally intensive tasks, the GAUSS system is ideally suited for the researcher who does not have the time required to develop programs in C/C++ or FORTRAN but finds that most statistical or mathematical “packages” are not flexible or powerful enough to perform complicated analysis or to work on large problems.

iChemLabs have just announced the release of ChemDoodle Web Components 6, this is a major update to their javascript based chemical structure drawing and rendering package.

One of the most important changes from a developers point of view is the external libs (jQuery, jQuey UI, jQuery plugins, glMatrix) are now included into the ChemDoodle scope. This offers several advantages, including eliminating all library conflicts, reducing the number of files required to be installed, and controls the versions used by ChemDoodle. You can now include these libraries yourself at any version and not worry about conflicts. To use the libraries inside of ChemDoodle, call them from the ChemDoodle.lib closure. When I created the interactive graph using FLOT this was one of the issues.

There is also a new EditorCanvas3D canvas which is the 3D component allowing you to interact with and alter chemical data as the 2D Sketcher does in 2D. The 3D editor supports many new WebGL features including picking, highlighting and measurements (distances, angles and torsions).

Lewis Dot Structure style bonds can now be rendered.

As well as editing and drawing structures ChemDoodle web components provides an means to simulate NMR and mass spectra in a web browser

There are also a number of bug fixes and other improvements.

Please Note

This update includes some major refactors, such as the renaming of the sketcher files and packages and inclusion of the external libraries internal to the ChemDoodle scope, so pay careful attention when upgrading.

 

I’ve just updated the Data Analysis tools for Mac OSX page. I’ve fixed the broken links and added another eight packages to bring to total upto ninety. Browsing through it looks like just about every area of science is covered, from open-source packages to enterprise focussed applications.

 

Whilst much computational work is undertaken to support, library design, virtual screening, hit selection and affinity optimisation the reality is that the most challenging issues to resolve in drug discovery often revolve around absorption, distribution, metabolism and excretion (ADME). Whilst we can measure the levels of parent drug in various medium tracking metabolic fate can often be a considerably more difficult proposition requiring significant resources. For this reason prediction of sites of metabolism has become the subject of current interest.

FAME DOI is a collection of random forest models trained on a comprehensive and highly diverse data set of 20,000 small molecules annotated with their experimentally determined sites of metabolism taken from multiple species (rat, dog and human). In addition dedicated models are available to predict sites of metabolism of phase I and II processes.

FAME offers a high performance prediction of sites of metabolism mediated by a wide variety of mechanisms.

The full review is available here

There is a list of software reviews here.

Marvin has been updated

Bugfixes, Java Webstart did not run on Macintosh computers.

It can be downloaded from here

Note, many of you have bumped into the problem when the Gatekeeper Security of OS X blocks launching applications downloaded not from the Apple store. The solution is to modify the default settings of the Gatekeeper:

• 'Apple > System Preferences > Security & Privacy '
• In the 'General' section the setting of ' Allow applications downloaded from :' should be set to ' Anywhere'

After this you would not get the "damaged dmg" popup and you can install the downloaded dmg. After install it is probably a good idea to reset the Security settings.

If you are using Java applets it is probably worth reading this article

Apple just have introduced some new security settings in Safari for Java. In an average browser to make  a Java Applet to be able to touch your file system that Applet must be signed. In the new security update of Safari this Applet must be trusted as well. This means that you have to allow for the Applet to read and write you file system. Marvin starts with accessing some files on your computer, which means that it might not start without this permission or might not behave correctly

 

I’ve just added FierceBiotech and FiercePharma to the MobileScience website. Those are two very popular industry news monitors.

 

A while back I was asked to help with an Applescript to help automate the transfer of notes from an iPad to Evernote on the desktop. Since then I’ve kept an eye on the increasing interaction between mobile device and desktop. It is clear that more and more applications now have versions that run on the iPad allowing you to access information on the move. I noticed a recent review of Notebook from Circus Ponies that again emphasises the importance of the iPad version that automatically syncs with the Mac version.

I’ve never been on a business trip without my MacBook Pro but I wonder if we are getting close?

 

Chemical Computing Group have just announced an update for MOE.

A patch update is now available for MOE 2013.08. This patch contains a series of important updates for better performance, s

In the MOE 2013.0801 patch update:

• System Manager browsing speed-up for large systems
• System Manager tag/group expansion only on Ctrl-click during browsing
• Mac OS X NVIDIA graphics driver bug workaround
• Mac OS X real-time ray tracing now supported by default on the new Intel Iris and Intel Iris Pro graphics cards
• Bug fixes

 

I recently came across this brilliant collection of software from Michel Petitjean

• ARMS: Spatial Alignment with the RMS (Root Mean Square) method. (fixed pairwise correspondence)
• ASV: Analytical calculation of van der Waals surfaces and volumes. (or any union of spheres)
• CCCPP: Computes Cavites, Channels, Pores and Pockets in proteins.
• CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules. (pairwise correspondence computed)
• CYL: Minimal radius enclosing cylinder. Minimal radius circumscribed cylinder.
• DIVCF: Selects by clustering major conformations of a molecule in a set of its conformers.
• DOG: Docking Geometrically two molecules. (fixed pairwise correspondence)
• GRD: Computation of the Radius and Diameter of a molecular graph. (computes also the topological shape index)
• MCG: Optimal Partition (classification): numerical variables and non-euclidean spaces. The number of classes is computed.
• POP: Optimal Partition (classification): categorical variables. The number of classes is computed.
• POSE: Computes the RMSD between two ligand poses. No rotation translation is performed.
• QCM: Quantitative Chirality Measure of a conformer (graph automorphisms enumeration included)
• RADI: Computation of the Radius and Diameter of a spatial set. (computes also various other geometrical parameters)
• VIRAPOPS: A forward simulator dedicated to rapidly evolved viral populations.

Binaries are available for MacOSX and Linux.

 

Whilst I’m not a full time programmer I do keep an eye out for tools that are suited for scientific computing on a Mac. Julia is a high-level, high-performance dynamic programming language for technical computing with an extensive mathematical function library.

The library, largely written in Julia itself, also integrates mature, best-of-breed C and Fortran libraries for linear algebra, random number generation, signal processing, and string processing. In addition, the Julia developer community is contributing a number of external packages through Julia’s built-in package manager

Julia’s LLVM-based just-in-time (JIT) compiler combined with the language’s design allow it to approach and often match the performance of C. The table below taken from the Julia website gives an idea of the relative performance for a number of simple benchmarks.

Julia was designed to support multiple cores and cloud computing. IJulia is a Julia-language backend combined with the IPython interactive environment. This combination allows you to interact with the Julia language using IPython's powerful graphical notebook, which combines code, formatted text, math, and multimedia in a single document

For the Mac a Julia-version.dmg file is provided, which contains Julia.app. Installation is the same as any other Mac software – copy the Julia.app to your hard-drive (anywhere) or run from the disk image. The core of the Julia implementation is licensed under the MIT license.

 

Over 55,000 unique visitors, 40% of which are returning visitors

175,000 page views with visitors reading 2 pages per visit on average.

63% of the visitors use MacOS, 22% Windows and about 8% iOS, interestingly if we look at just the week after Christmas iOS usage increases to 15-20%.

The five most popular pages are

MacInChem Home
Mobile Science
MacInChem Blog
iBabel
Applications A-C

Other sections that deserve an honourable mention are

Data Analysis Tools
Reviews
Hints and Tutorial

The two most popular blog entries were

Installing Molden
Science Applications under Mavericks

The two most popular blog categories were chemical drawing and Markdown editors

Chemical Drawing
Markdown Editors

The two most popular applescripts were

Applescript and curl
Applescript and Geektool

The two most popular reviews were

Knime
Markdown Editors

The two most popular hints and tutorials were

Safari Extensions
Remote Printing using Dropbox

The top search queries were
chemdoodle,
markdown pro,
knime tutorial,
jsmol,
ispartan

This is the review that everyone has been waiting for, the AnandTech review of the latest MacPro. A comprehensive analysis of all aspects of the latest Mac Pro, from GPU and CPU options to real life performance comparisons.

There is also an interesting thoughts into the directions for desktop computing