There is an interesting post on Molecular Modeling Basics on the use of Wolfram Alpha to solve chemistry homework problems. I have to say I continue to be impressed by Wolfram Alpha, the breadth and depth of science that is covered is amazing.

For science apps for iOS have a look at the mobile science page.

 

I was just reading the end of year newsletter from [Molsoft] and I came across this interesting snippet.

MolSoft is excited to announce that Anaglyph 3D is now available to use in ICM and iMolview.

Sure enough the update on Dec 24th has this in the release notes.

Anaglyph stereo mode is added. (Set 'Stereo Type' to 'Anaglyph' in Tools menu) Any red-cyan 3D glasses will work in this mode.

There are a number of suitable glasses on Amazon 3D Red/Cyan Glasses

I think this is the first app to enable this sort of stereo viewing and it just underlines the strides that mobile platforms are making in scientific computing.

For science apps for iOS have a look at the mobile science page.

 

Ever had problems with an unusually formatted PDB file? PDBinout is a file conversion tool for PDB files that might interest you. It was created by Tomasz Woźniak at the Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences

PDB format is the most commonly used by various programs to define three-dimensional structure of biomolecules. Those programs however, often use different versions of this format. Therefore, it is often necessary to write own re-formatting scripts or change files manually, which makes PDB files less convenient to use. There are only few tools allowing to change one or two versions of PDB format into another and no comprehensive approach for unifying PDB format was developed. Here we present an open-source, Python-based tool PDBinout for processing and conversion of various versions of PDB file format for biostructural applications. Moreover, PDBinout allows to create one’s own PDB versions.

The download also includes a tutorial.

Reference Woźniak T. and Adamiak R.W. (2013) Personalization of structural PDB files, Acta Biochimica Polonica 60, Paper in Press

 

The iOS7 tech talk videos are now online.

Registered Apple Developers can watch full sessions from the iOS 7 Tech Talks to get in-depth guidance on developing for iOS 7. Discover how to create innovative, flexible, and intuitive apps that integrate the latest Apple technologies.

For science apps for iOS have a look at the mobile science page.

 

The hugely popular reference management application Papers has just been updated. Papers 3 has a new cleaner interface and a host of new features.

The mobile app Papers 3 for iOS has also been updated.

 

I noticed that CPMD a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. is now available on Crunchyard expanding the list of available Computational Chemistry packages. The following packages are also available. CP2K, LAMMPS, GAMESS, GROMACS , NWCHEM

 

I’ve added a minor update to the Export as mol file script.

One of the issues with the original script that the mol file contains in its first line the incorrect title of the file (it appears to be the name of the document template).

When you just launched your ChemDraw application, or created a new document, the title would be “Untitled **”, such as "Untitled ACS Document 1996-1". When you save it as Mol file, its header block will inherit the current document title "Untitled ACS Document 1996-2”.

Untitled ACS Document 1996-2
ChemDraw12201318592D

14 16  0  0  0  0  0  0  0  0999 V2000

It would be better to have the molfile title the same as the file name the user enters in the dialog box, one way to achieve this is to “edit” the file and then save again to the same file name. We can do this by adding a line to clean up the structure and then saving.

try
save first document in (molAttachment) as "MDL Molfile”
--This is to ensure the title of the mol file is set correctly
do menu item "Clean Up Structure" of menu "Structure"
save first document in (molAttachment) as "MDL Molfile"
close first document saving no

If you now look at the mol file in a text editor you can see the title is set more appropriately.

Mol file1.mol
ChemDraw12201319082D

14 16  0  0  0  0  0  0  0  0999 V2000

 

When I logged in the morning the first message I noticed announced the eagerly awaited MacPro was now available for order at the AppleStore with delivery on December 30th, within an hour or so that delivery time had changed to January, when I check now the delivery has moved to February. Well at least it is free delivery.

It will be interesting to see how long it takes Apple to sort out supply and demand.

It has been just over a month since I set up the Mobile Science database and I thought it would be good to have a look at how things were going. The aim of the database was to enable scientists to be able to search for scientific apps for iOS.

It took a lot of work to compile all the information so I’m delighted to see that it has been accessed nearly 1500 times with visitors from all over the world. A fair number of people have been voting for their favourite application and it perhaps not surprising that the chemical drawing applications, Elemental, ChemDoodle Mobile and ChemDraw are all in the top 5. The other apps picking up votes are popular scientific search and computation tool WolframAlpha and the award winning reference management app Papers3, together with ElementalDB an app that allows you to search a local copy of the 1.2 million record ChEMBL database, an app that really demonstrates the computing power now available in a hand-held device.

I will of course continue to update the database but since finding science apps on the iTunes Store can be a challenge I’d be delighted to hear about any that I have missed.

 

I thought I would highlight a recent publication I read in Journal of Cheminformatics “Molecule database framework: a framework for creating database applications with chemical structure search capability” Journal of Cheminformatics 2013, 5:48 DOI.

From the abstract

Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:Chemical structure searches combined with property searches. Support for multi-component compounds (mixtures) mport and export of SD-files. Optional security (authorization). For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files.

While not a drag and drop solution it provides a means to create your own personal chemically searchable database.

Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

 

OpenEye have just announced the release of pKa Prospector v1.0 a database of high quality experimental pKa determinations. The ionisation state of a drug molecule can have profound effects on affinity, dissolution, absorption, distribution, metabolism and off-target activity. The ability to predict pKa is often compromised by the lack of relevant experimental data, pKa Prospector is intended to address that issue.

The built-in experimental pKa database was compiled by Tony Slater of pKaData Limited from a collection of IUPAC sources. Each measurement has been individually verified, curated, and assigned a metric of quality. There are more than 30,000 experiments across 12,000 molecules represented. The database is particularly relevant for medicinal chemistry due to the strong preponderance of room temperature aqueous measurements, the many molecules with multiple experimental records, and the presence of over three hundred different heterocycles.

It is also possible to add additional experimental results and have them integrated into the application thus expanding the chemical space covered. The search uses rooted maximum common substructure (MCS) with "electronically-aware" scoring, alternatively it can be searched by similarity or substructure. Ionizable groups are automatically identified and highlighted.

 

A number of publishers are seeking to add extra value to publications by including access to chemical structure information to aid searching and indexing. More details are included in this comment from Elsevier.

Elsevier would like to enrich online articles by visualising and providing details of chemical structures you define as the main chemical compounds described in your article. For this purpose, mol files of the key compounds can be uploaded in EES. Please use your preferred drawing tool to export chemical structures as mol files and ensure that they are well defined and do not contain aromtic bonds, R-Groups or other variables. Submitted mol files will be available for downloading from your online article on ScienceDirect. Furthermore, Elsevier will generate InChI keys from the mol files and include them in the online article, which increase the online searchability of your article e.g. in Google. InChI keys will also be used to link the article to additional data in Reaxys.

Since you need to export each structure as an individual file this will become somewhat tedious, fortunately Brian Myers has written an applescript that greatly helps the process for ChemBioDraw users

Now updated.

I’ve just added InkMark to the page of Markdown editors.

 

I thinking of upgrading my 5 year old MacBook Pro, in particular I was thinking of installing a solid state drive. I know I can replace the old hard drive but I was wondering if might be possible to replace the DVD drive which I actually never used. Has anyone any experience of this?

 

Originally Theodore Gray produced a beautiful coffee table book The Elements: A Visual Exploration of Every Known Atom in the Universe, this was later converted into an iPad app The Elements which gave access to more dynamic information than could be achieved with a hard copy book. Now the developers have gone one step further and created The Elements in Action a periodic table with video explorations of the properties of elements. Some of the videos look like they have been rescued from old research labs so this is probably your only opportunity to see them in action.

 

Whilst there are a number of desktop applications that allow for the creation or editing of 3-dimensional chemical structures there are not as far as I am aware any tools for editing the 3D structure within a web page. CH5M3D uses a combination of HTML5 and javascript to interactively draw and edit 3-dimensional structures of small molecules.

The details are described in a recent publication Journal of Cheminformatics 2013, 5:46 DOI, it can be downloaded from Sourceforge, and you can try it out on the CH5M3D website.

The latest update to the increasingly popular chemical drawing package ChemDoodle has just been released. ChemDoodle 6 is the latest update from iChemLabs and once again it supports Mac, Linux and Windows and works with most document creation packages. This is apparently a free upgrade for those who recently purchased ChemDoodle 5. I plan to write a review of ChemDoodle 6 when I have time but looking at the release notes this looks to be a substantial update.

New features in ChemDoodle 6:

• IUPAC naming with over 20 options!
• Carbon nanotube and prism builders. Both zigzag and armchair nanotubes can be built. These tools quickly produce 3D geometries.
• Auto updating labels can now be attached to molecules, so they will update with IUPAC names, molecular formulas and more.
• Mac OS X Quick Look plugin. Easily preview all your chemical files in Finder just by pressing the space key.
• More Windows support, including a more powerful tool for supporting Windows filetype associations with the option to unassign types, support for the MDLCT and MDLSK clipboard formats for copying and pasting between a wider array of chemical applications, and greatly improved OLE support to allow for double-clicking to edit structures.
• More glassware, including a new organized glassware window. You can now also remove liquid from the templates.
• Significantly improved graphics. Graphics in ChemDoodle were already very good, but we took a look at all the graphics at very high scales and resolutions. We have made sure to focus on all the little details. Bond join edge cases have been improved. Hashes are now auto centered, making recessed bonds and dashed bonds look much nicer. Other bond types have been scrutinized for the best aesthetics. Convex hull algorithms have been built for better placement of bonds around labels. Cis double bonds will now prefer the inside edge. Circles over charges now only surround the number. Aromatic ring circles now meld to the shape of aromatic circles. Arrows look nicer. You won't find better graphics in any other application.
• 3D coordinate generation.
• A new 180° chain angle clean option for easily creating Lewis structures and figures with 90° angles.
• Complex embedded ring systems (like corannulene) now clean very well in 2D.
• Added resolution controls to the Elemental Analysis widget.
• Meso stereochemistry support.
• An advanced formatted text system for the system clipboard. You can now copy and paste your molecular formulas, IUPAC names and others into word processing applications with formatting intact.
• Many other minor, but useful features: option for the delete key to decrement bonds, nominal mass counter, improvements to the TLC Plate widget, improvements to arc placement previews, alt and shift now modify attribute placement just like placing bonds, improved file chooser previews for data files, more templates for the Templates widget, and more.
• Squashing of dozens of bugs.

Remember also that there are also ChemDoodle Mobile.

ChemDoodle Mobile, the mobile companion to ChemDoodle, is provided for free to ChemDoodle desktop customers. ChemDoodle Mobile is available for both iOS (iPod Touch/iPhone/iPad) and Android devices. You can transfer structures between ChemDoodle desktop and ChemDoodle Mobile, to take with you into the lab

 

A couple of applications from Molecular Materials Informatics, Inc have been updated.

Open Drug Discovery Teams is a content management system providing crowd sourced information on a range of tropical and neglected diseases. The ODDT app is free. It can be used anonymously to browse topics. Submission of content requires the user's Twitter account to be enabled and made available to the app.

Living Molecules allows specially crafted molecular glyphs to be snapped by the device camera, which direct the app to chemical data: molecules, reactions and collections. This update fixes a bug that could cause the app to crash.

Mobile Molecular DataSheet update includes Sketcher improvements: crayon gestures for adding rings and lines; traversal gesture for growing rings from bonds; and a "band-aid" feature for fixing badly drawn chain bonds.

There is now a searchable database of mobile science apps

I’ve added CPMD to the alphabetical listing of applications.

CPMD is an ab initio electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory (DFT). It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimizations, Born-Oppenheimer MD, path integral MD, response functions, QM/MM, excited states and calculation of some electronic properties.

Full installation instructions are available on the website together with the user manual and examples.

The examples can run effectively on an Intel Core i5 (2.53 GHz, OS/X) with 4 GB of available memory (most of tests require ca. 1GB, few more). Nonetheless, references have been generated on an IBM Blade power7 (with 8 mpi tasks and 1 OMP task per CPMD run) with 64 GB of available memory. Estimates of the execution time and memory requirements will be given based on this more performant setup.

CPMD capabilities

• Works with norm conserving or ultrasoft pseudopotentials
• LDA, LSD and the most popular gradient correction schemes; free energy density functional implementation
• Isolated systems and system with periodic boundary conditions; k-points
• Molecular and crystal symmetry
• Wavefunction optimization: direct minimization and diagonalization
• Geometry optimization: local optimization and simulated annealing
• Molecular dynamics: constant energy, constant temperature and constant pressure
• Path integral MD
• Response functions
• Excited states
• Many electronic properties
• Time-dependent DFT (excitations, molecular dynamics in excited states)
• Coarse-grained non-Markovian metadynamics

CPMD is free for non-profit organisations.

 

I’ve just added Graph-R to the page of data analysis tools.

Graph-R is an application used to create 3-dimensional contours, contour lines, wire frames, and scatter diagrams from numeric data files(CSV files). Graph setting is easy. The perspective direction can be freely changed using your mouse. Graph that are created can be saved as PNG or JPEG files.

This software requires Mac OSX 10.8 or later.

 

SYBYL-X 2.1.1 is now available, the focus of this release is to extend the capabilities available via the standalone PYTHON interface to 3D-QSAR, which was introduced in SYBYL-X 2.1 earlier this year. The PYTHON API allows 3D-QSAR models (CoMFA, CoMSIA, and Topomer CoMFA) to be created and used for predictions outside of SYBYL-X.

1. Hologram QSAR (HQSAR) is a now available via Python.  HQSAR has been successfully applied to generate predictive global QSAR models for on- and off-target effects and models for important ADME related properties; the HQSAR method employs 2D-substructural counts as descriptors.

2. Similarity computations and similarity searches (UNITY 2D fingerprints) are now accessible via Python to support various workflows, such as lead expansion, lead hopping, and cluster analysis.

 

I use markdown extensively on my websites, “Markdown” is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. As the use of Markdown has increased in popularity there are now a wide choice of Markdown editors available for MacOSX and recently iOS so i’ve updated the listing of Markdown Editors.

 

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.

The update went smoothly albeit with an overnight download of the 5.5 GB file.

The update removes both X11 and java so both of these need to be reinstalled, if you forget you will be prompted to download the first time you try to use them.

No issues with cursory testing, users or vendors provided feedback

Avogadro
BBEdit
ChemDoodle
ChemSpotlight
Cresset software (forge, torch, spark) (no reported issues)
Elemental
FTranProjectBuilder
iBabel
ICM-Pro
ICM-Homology
ICM-VLS
ICM-Chemist
iNMR (No reported issues)
Matlab
Marvin
MOE
Openbabel
OpenEye (Command line tools OK, OMEGA 2.5.1 (OSX 10.8 version), FILTER 2.5.1 (10.8), ROCS 3.2.0 (10.8), SZMAP 1.2.0 (10.8), EON 2.2.0 (10.8), QUACPAC 1.6.3 (10.8), SZYBKI 1.8.0 (10.8), FLYNN 2.3.0 (10.8), The Python and Java toolkits work fine. The C++ toolkit can be made to work if some of the compiler flags are changed. Please email support@eyesopen.com for more details. For the OpenEye GUI applications, vROCS 3.2.0 (OSX 10.8 version) works fine, for other apps see below
R latest version R 3.0.2 ("Frisbee Sailing")
Reference Tracker
StarDrop
Vortex
XQuartz

Some issues :-(

MOE install
I downloaded the latest update as a zip file and unarchived it. When I double click on the installer I got a message that it was broken or corrupted. This seems be an issue with the Mac OSX Gatekeeper,

1. Open Apple menu, then go to System Preferences -> Security & Privacy -> General tab.

2. In the option list of "Allow Applications downloaded from", select "Anywhere".

Then installs OK. Once installed MOE seems to run fine.

CCDC Software
Mac OSX 10.9 causes most CCDC software to fail - there are now have patches available that address this issue. For enCIFer 1.4: http://www.ccdc.cam.ac.uk/SupportandResources/Downloads/pages/ProtectedDownloadAgreement.aspx?d=15 For the 2013 CSD System go to: http://www.ccdc.cam.ac.uk/SupportandResources/Downloads/pages/ProtectedDownloadAgreement.aspx?d=47  For standalone Mercury 3.1 or 3.1.1 go to:  http://www.ccdc.cam.ac.uk/SupportandResources/Downloads/pages/ProtectedDownloadAgreement.aspx?d=37
These updates should only be applied on Mac OSX 10.9. NB One reader reported issues with the update.

ChemBioDraw
Chemdraw 13 files pasted into Keynote 6 cannot be copied and pasted back into ChemDraw. In addition, if you open old Keynote files in Keynote 6 all the ChemDraw cannot be copied and pasted. It pastes into Chemdraw as a picture with an all black background. In Mac OS 10.9 with Keynote 5 - round trip editing still continues to work. According to the PerkinElmer Support Forum there are issues with copy/paste in CD 13 to Office 2011 for Mac. Any CD structures that are pasted into PPT or Word cannot be opened or edited with CD.

EndNote X7
We have tested EndNote X7 with Mac OS X 10.9 Mavericks to determine compatibility. We have found some minor issues and are working on a free update patch to be released in the next few weeks.

EndNote X6
EndNote X6 is not officially compatible with Mac OS X 10.9 Mavericks. We are testing EndNote X6 with Mac OS X 10.9 Mavericks to determine informal compatibility and will report any exceptions found on this page.
EndNote X5 and earlier
Due to major compatibility issues, it is not recommend to attempt to use EndNote X5 or earlier on OS X 10.9. When attempting to launch EndNote X5 or earlier, a warning message comes up that will include "unable to load ....ENCore.Bundle". EndNote X5 and earlier will fail to launch after receiving this message. There are no known workarounds for this issue besides moving to a more recent version of EndNote or restoring your computer  (using a Time Machine Backup for example) to a previous version of Mac OS X.

OpenEye Command line tools that require setting the OE_ARCH environment variable (FRED 3.0.1 (OSX 10.7 version), HYBRID 3.0.1 (10.7), POSIT 1.0.3 (10.7), LEXICHEM 2.1.0 (10.6), BROOD 2.0.0 (10.5)

export OE_ARCH=osx-10.9-x64:osx-10.8-x64:osx-10.7-x64:osx-10.6-x64:osx-10.5-x86

For the OpenEye GUI applications, vROCS 3.2.0 (OSX 10.8 version) works without any issues. VIDA requires the OE_ARCH modification shown above but also needs the following additional fixes:

sudo mkdir -p /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore.framework/Versions/4
sudo ln -s /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore.framework/Versions/4/QtCore

Unfortunately, the current vBROOD, AFITT, and MAKE_RECEPTOR GUIs do not work on Mavericks. We are actively investigating these issues. More details

Using Aabel v3 on Mavericks is not recommended due to cosmetic glitches such as misalignment of graphic viewer icons on the Mavericks buttons. Mavericks will be supported in the next major version of Aabel

Papers2 update about to be released

If I hear of anything, I’ll update this page.

 

Both ChemDraw and Chem3D have been updated, the release notes don’t give much information on the updates other than Redesigned for iOS7 and bug fixes.

The use of mobile devices in teaching has offered new opportunities and a recent presentation by Layne Morsch illustrates this quite nicely. Using ChemDraw for iPad and Flick-to-Share to Increase Engagement in Organic Chemistry. The page has a couple of embedded videos that give more details.

The other feature that is now becoming mainstream is the 3D-printing and since Chem3D can export in .stl format it is not surprising people have started to experiment with creating 3D models of molecules, there is a brief video here, unfortunately it is a loop of the printing process so don’t expect to see the final product. CambridgeSoft have also produced their own videos of these apps in action

 

A couple of apps have been updated recently

WolframAlpha the world's definitive source for instant expert knowledge and computation.

Living Molecules allows specially crafted molecular glyphs to be snapped by the device camera, which direct the app to chemical data: molecules, reactions and collections

There is now a database of mobile science apps

 

I just saw this message from Shane Stanley

As some of you have probably found already, Xcode does not recognize AppleScript's new interleaved syntax when used for action handlers -- you cannot make connections to them from controls. The workaround is to keep using the underscore syntax for action handlers until the problem is resolved. That's not ideal if you use an external editor, though. FYI, I've just released a new version (3.0.7) of ASObjC Explorer for Mavericks to deal with this issue. There is a new preference setting in Preferences -> Other. When checked, every time you save a .applescript file, any single-argument handlers will be changed to use old-style underscore syntax. (The new syntax will appear in Xcode and in the saved file, while the new syntax will still appear in Explorer.)

 

XQuartz has been updated this contains X11 2.7.5 the first release supported on Mavericks. Full details are available here

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.

 

There was a blog entry on In the Pipeline about a bug in ChemDraw. Actually this has been known for a while (and present in previous versions) but it seems it still has not been fixed in the latest version of ChemBioDraw 13 on the Mac. As you can see in the image below including explicit hydrogens in your structure significantly impacts the calculated LogP. Whilst people don’t often add explicit atoms to phenyl rings, (expect perhaps in SAR studies) they often add them to heteroatoms.

At the moment there is no bug fix and no date set for a fix to any version of ChemBioDraw, the only approach is to avoid adding explicit hydrogens to structures if you want to calculate LogP. I’ve looked at a number of other applications and there seem to be no issues with ChemDoodle, Elemental, Marvin or OpenBabel.

 

I just got a message about an update to Graph Builder a very popular and powerful application from VVimaging, Inc rich in graphic editing, creation and programming to facilitate the visualization of information. It has a excellent 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. Also supports dynamic graphs.

 

As the MobileScience site expands I’ve started to add other resources in addition to the applications. There are now a couple of useful additions for iOS programmers if you are looking for a training course, a plotting library or a chemistry toolkit.

I’d be delighted to add any more useful resources.

 

ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.

More details here

 

An interesting article on plans to build a supercomputer based on cellphone chips. It seems the low power consumption of ARM processors make construction of a supercomputer based on those chips an attractive proposition.

Wired Article

His project is part of a larger movement towards this new breed of low-power chips. As Ramirez builds an ARM supercomputer in Spain, web giants such as Facebook and Amazon are exploring the use of these low-power chips in the servers that run their massive online services.

Finding scientific applications for your iPhone to iPad has always been a little hit and miss since there is no “science” category on the iTunes store. To help out I created a page listing applications that I knew about, unfortunately as the number of applications increased the page became unmanageable. In addition an alphabetical listing is not the most useful way to search through them.

I’ve now transferred all the information to a database that can be searched via a web interface.

The site is available at http://www.macinchem.org/mobilescience/, I’ve started to categorise applications to aid navigation but I’d be interested to hear of any suggestions. Currently there are over 200 entries covering an extensive area of science, if I’ve missed any please let me know and I’ll add them.

In the news section I’ve added links to publications and presentations that might be interesting.

I’d encourage to have a look around and I’d be interested to hear any comments or suggestions.

 

 

OpenEye have just released an update to SZYBKI with a host of new features. SZYBKI is used to optimise the three dimensional structure of molecules prior to their use in other programs. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.

• New utility program called FreeForm is available for Szybki users. It provides two distinct functionalities: evaluation of the solvation free energy of the input molecules and free energies of solution conformations. Please Note: FreeForm is not available under 32-bit Windows because of the high memory requirements of this application.
• A new forcefield for protein-ligand interations is available upon selecting a new option -ff followed by AmberMMFF94 or AmberMMFF94S. It is a combination of MMFF94 (or MMFF94S) with Amber. In this combined force field, MMFF94 (or MMFF94S) is used to describe the intramolecular interactions of the ligand and the Amber force field is used for the VdW and Coulomb interactions between ligand and protein. Currently, this force field can be used only for ligands inside rigid proteins.
• Entropy estimation based on analytical MMFF Hessian is extended for ligands bound in a rigid protein using the option -entropy.
• Constraining torsion potential in the form: , where is the user specified force constant and is the reference torsion dihedral angle is available with the use of the input flag -tor_constr.
• New option -optMethod is introduced for optimization method selection. The possible choices of optimizers type are BFGS, conjugate gradient, steepest descent and mixtures of steepest descent preoptimization followed by BFGS of conjugent gradient. Option -conj is no longer supported.
• Optimization of molecular systems with large number of degrees of freedom (>= 500) is by default done with the conjugate gradient method unless specifically requested with the option -optMethod.
• New option -optGeometry is introduced for selection of coordinate system to be used during optimization. It replaces no longer supported options -optcart, -opttorsions, -solid and -noopt. It can be also used to optimize hydrogen atoms positions only, instead of using for that purpose -fixsmarts.
• Molecules from the input file which failed during processing are by default written to the separate molecular file. See the description of new option -keepFailures.
• Starting from this release flags -fixsmarts and -harmsmarts are followed by the name of the text file containing a single line with a SMARTS pattern used to fix or constrain atoms. Input of SMARTS strings on the command line for those flags are not used anymore because some SMARTS strings may contain special characters which may be interpreted incorrectly on some platforms.

 

The popular reference management package Reference Tracker) has been recently updated and fully supports Mavericks.

Improved ISBN lookup. Improved article search.

Fixed a bug where incomplete reference styles could be shared to the cloud. Fixed a bug where ISBN lookup results could be imported with missing data. Fixed a bug where open link buttons in documents could reposition incorrectly when the document window was resized. Fixed a bug that could cause Reference Tracker to crash on startup on OS X 10.7. Fixed tabbing between fields in the Publication Search sheet.

I also note that there is a special offer at the moment

Reference Tracker is available at a special 30 % discounted price until 30 November 2013!

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

 

ChemAxon have released a new update to Marvin.

Bugfixes MarvinSketch GUI MSketchPane setPiece(Molecule) method did not work, it set the molecule on the canvas instead of putting it on the cursor. Import/Export CXSMILES/CXSMARTS CXSMARTS containing valence property information was recognized and read as SMARTS. SKC Some reaction was read as R-definition from SKC format.

 

I just learned of an interesting site that is currently under construction. Speakable-Workflows has a number of tutorials on how to use the new speech recognition features in automator actions.

Well worth spending a few minutes watching the video tutorials.

One of the big changes with Mavericks is the enhanced security and this has an impact on all developers even those who write a “simple” applescript to avoid a tedious or repetitive series of actions.

Developers have often relied upon AppleScript’s ability to control the user-interface, to provide an automation solution when no direct scripting support of an application or process was available. While this valued ability continues to be fully supported in Mavericks, the enhanced security focus of the new OS requires a few changes in how scripters access and apply the Accessibility frameworks.

There is a really comprehensive discussion of Accessibility Preferences and GUI Scripting over on Mac OS X Automation. Well worth a read.

 

I’ve just updated the listing of Scientific Applications under Mavericks and I thought I’d highlight one application. The page I have on Tools for Fortran Programmers is consistently one of the top accessed Blog entries. I’m sure one of the reasons for this popularity is FTranProjectBuilder the only Mac-native Fortran development environment (IDE) it works with the gfortran, g95, ifort, Absoft Pro Fortran, NAG nagfor and PGI pgfortran compilers. Since I mentioned it last FTranProjectbuilder has been updated six more times, in April, May, July, August and October with new features like the ability to build static libraries, trackpad interaction and compiler errors now being marked in the source code. Full details are in the project notes on the Nocturnal Aviation Software website , and yes, all of the tools, including FTranProjectbuilder are compatible with 10.6.8+, and run fine on 10.9 Mavericks. 

Fortran still has a significant user base in the scientific community where the speed, portability, array handling and access to shared memory make it a very powerful option.

There is a nice comparison of programming languages from the viewpoint of scientists here

 

I’ve just been sent a link to GenomeBrowse, this allows the user to explore DNA-seq and RNA-seq pile-up and coverage data in an intuitive manner. Whether viewing one file or many, an integrated approach is taken to exploring your data in the context of rich annotation tracks. Features include: * Zooming and navigation controls that are natural as they mimic panning and scrolling actions you are familiar with. * Coverage and pile-up views with different modes to highlight mismatches and look for strand bias. * Deep, stable stacking algorithms to look at all reads in a pile-up zoom, not just the first 10 or 20. * Context-sensitive information by clicking on any feature. See allele frequencies in control databases, functional predictions of a non-synonymous variants, exon positions of genes, or even details of a single sequenced read. * A dynamic labeling system which gives optimal detail on annotation features without cluttering the view. * The ability to automatically index and compute coverage data on BAM or VCF files in the background.

GenomeBrowse integrates with the powerful Golden Helix SNP & Variation Suite (SVS) analysis platform. SVS can be used to build custom annotations and perform variant analysis, while GenomeBrowse can visualize findings and validate the evidence for putative variants.

 

The free univariate data modeling package Regress+ has been updated to version 2.7.1.

Regress+ offers:-

• Plain textfile input
  • Equations, with or without uncertainties (weights)
  • Distributions, continuous or discrete data
  • Discrete data grouped or ungrouped
• Datasets up to 4,294,967,295 points (minimum 7)
• Up to 10 parameters
• User-selected optimization criterion (where appropriate)
  • Least squares
  • Minimum average abs(residual)
  • Maximum likelihood
  • Minimum K-S statistic
  • Minimum chi-square statistic
• Full, dated Report (textfile)
• Robust goodness-of-fit testing for distributions
  • Tunable precision
• [Optional] State-of-the-art (BCa) central confidence intervals (90, 95 and 99 percent)
  • Tunable precision
• High-quality (PDF, PNG) plots with one keystroke!
  • X/Y plot, with or without error bars
  • PDF plot
  • CDF plot
  • Probability plot for goodness-of-fit (see above)
  • [Optional] Logarithmic axes (when appropriate)
  • Editable axis labels
  • Automatic tick marks/labels (see above)
• [Optional] Predictions for unobserved values or percentiles
  • With confidence intervals if desired
• [Optional] Constant parameter(s)
• 21 Built-in Equations
  • Plus user-defined model
  • [Optional] Test residuals for systematic error
  • [Optional] List data with fitted estimates and residuals
  • [Optional] Simulated-annealing mode for initial parameter estimates
• 59 Built-in Distributions
  • 9 continuous, symmetric
  • 27 continuous, skewed
  • 11 continuous mixtures
  • 6 discrete
  • 6 discrete mixtures
  • [Optional] Creation of synthetic samples
• No hidden assumptions anywhere
  • No approximations, apart from those common to sampling and bootstrapping generally
  • No data transformations of any kind
• Extensive documentation

There is comprehensive listing of Mac OSX data analysis packages here.

 

I’ve been looking at the rate of Mavericks adoption here currently it stands at 13-15% which is quite impressive. Interestingly most of the early adopters seems to be those running Mountain Lion, the numbers using Lion and Snow Leopard seem to be pretty much unchanged.

I’ve also updated the post regarding Scientific Applications under Mavericks, if anyone has any more comments I’ll continue to update the page.

 

Myriad Communications has released its successor to AppleScriptObjC Explorer, available immediately. The new editor takes advantage of the improvements to AppleScript in the latest release of OS X, which make access to Objective-C frameworks from AppleScript easier than ever.

"The changes to AppleScript in Mavericks have largely flown under everyone's radar, but script libraries open lots of doors for scripters," says the application's developer, Shane Stanley. "Bridging between AppleScript and Objective-C code has become much easier. This sets a new direction for expanding AppleScript's abilities."

ASObjC Explorer for Mavericks is designed to make developing AppleScriptObjC-based script libraries simple, with everything you need in one window. It features customised syntax formatting to take advantage of the new interleaved syntax; intelligent code-completion and shortcuts to take the tedium out of entering code; logging, stepping and breakpoints to aid in debugging; and a built-in simplified scripting-definition editor for adding English-like terminology.

It also makes an ideal external editor for AppleScriptObjC-based Xcode projects in Mavericks

ASObjC Explorer for Mavericks can be downloaded from <http://www.macosxautomation.com/applescript/apps/explorer.html>, and can be used free for 30 days. The purchase price is $US49.95.

For further inquiries, contact Shane Stanley at <sstanley@myriad-com.com.au>.

 

New features and improvements

• MarvinSketch Dialog
• 'Zoom to scaffold' checkbox option has been added to the "Preferences>Save/Load" tab. Documentation
• Structure Checker
• External structure checker configuration file URL can be set via Java System Property.

Bugfixes

• Editing
• Electron-flow arrow could not be drawn from the A-B bond to the incipient A-C bond of an A-B-C structure. Forum
• Import/Export
• MolInputStream and MolImporter could have different format options.
• MolImporter did not close its inputstream when an exception was thrown in the constructor.
• MOL, SDF, RXN, RDF
• Molecule type property was allowed in SDF, CSSDF export.
• The coordinates of the sequence residue imported from SCSR MOL files were wrong if the residue had three attachment point.
• CDX/CDXML
• Color and text format of atom label is exported to CDX and imported from CDX and CDXML. Forum
• Graphical brackets were not imported from CDX files.
• Gaussian Z-matrix input format
• Command line, title line, and extra input properties were not exported to Gaussian Z-matrix input format. Forum
• Clean 2D
• Cleaning of position variation bonds could create overlapping bonds.
• Cleaning of bridged systems could result in overlapping atoms. Forum
• Calculations
• Topology Analysis
• Missing method has been added: TopologyAnalyserPlugin.getFsp3(). API Documentation
• logD
• New logD training documentation has been added. Documentation
• Structure Checker
• Fixer options in MarvinSketch are updated with newly defined settings.
• External checkers can be loaded from JAR file in case the JAR file contains a space.

 

Chemical Computing Group have just announced the release of the latest update of MOE (Molecular Operating Environment).

General Updates

Extended Hückel Theory for Pharmacophore Discovery

• Apply EHT strengths to identify and discover weak and strong interactions
• Annotate non-standard interactions: halogen and CH bond donors
• Score pharmacophore hits using sum of interaction energies

de novo Loop and Linker Modeler

• Search and browse for de novo and knowledge-based loop candidates
• Generate multiple loop conformations and score loop-loop interactions • Investigate linkers for fusion proteins and dual variable domains

Protein Alignments and Superpositions

• Superpose protein structures independent of sequence
• Apply new threading methodology for sequence to structure alignments
• Align sequences and superpose structures using STOVCA criteria

Core System Enhancements (with 64-bit support) The default versions of MOE for Linux, Windows, and Mac OSX are now all 64-bit. The current release also includes 32-bit versions for each architecture.

• Create additional data grouping level in System Manager
• Handle large number of protein:ligand complexes in real-time
• Colour database viewer text and cells by data values for enhanced analysis, Empty cells can be specially colored

Interface to Mogul from CCDC

• Access a knowledge-based library of small molecule crystallographic data
• Visualize histograms and statistics fo rbond angles, dihedrals and torsions • Ensure ligand conformation is consistent with the CSD

Solvent Analysis using 3D-RISM Enhancements

• Calculate water densities on full protein or protein:protein interface
• Accurate placement and stability prediction of water sites
• Use3 D-RISM densities to validate water position in crystal structures

chEMBL Library. MOE's SD Pipeline Command Tools were used to generate fragments from Release 14 of the ChEMBL database of bioactive drug-like small molecules. The resulting database of conformations, chemblr14_frag.mdb, for approximately 830,000 fragments, suitable for Scaffold Replacement or combinatorial chemistry methodologies

Mac OS X Enhancements.

1. OS X Dock Icon Enhancements. A new Dock menu, accessed by right-clicking (or control-clicking) the MOE Dock icon, allows for standard Mac OS X operations – Hide, Show, and Quit – across all open iterations of MOE. The Dock Menu also contains menu items in order for users to view the About panel bundled in MOE, as well as access the Preferences panel. Additionally, the Dock indicator light under the MOE Dock icon remains persistent after having launched a new instance of MOE, until all opened MOE instances have been closed. Users continue to be able to drag and drop compatible MOE documents (i.e. .pdb, .svl, etc.) onto the Desktop and/or Dock icons for direct opening in MOE.

2. New Preferences Menu. A new Preferences panel allows for certain parameters to be set and/or changed graphically. These parameters include the defaults key and path to MOE, the current configuration of MOE (32- or 64-bit, or Auto-select), as well as a selection of common command line tags, with a custom section for inputting other command line options.

3. Output Continuity. stdout and stderr received from MOE have been standardized to be displayed in a native panel in a scrollable text box.

 

Experimental Assistant from Nano3D Biosciences. This application helps organize and analyze data from experiments. It take manual photos and automatic shooting for multiple images and time lapse movies, and stores them in albums for easy access later

 

There are updates to both ChemDrawand Chem3D) for iPad. There is little information available about the update to version 2.0 other than “bug fixes” and the apps have been redesigned for iOS7 and now have a minimum requirement for IOS7.0 or later.

The mobile science page contains a listing of science apes for iOS.

 

A reader just pointed out that the support site for a couple of the items on the widgets page is no longer available.

The Amino Acid Table widget
The Genetic Code widget
The Nucleic Acid Nomenclature widget
The ProtParam widget

Whilst the widgets are still available from a number of download sites the support site "http://www.aborygen.com/" domain is labelled as for sale.

 

I just noticed that there is an update to R on the CRAN website

This binary distribution of R and the GUI supports 64-bit Intel based Macs on Mac OS X 10.6 (Leopard) or higher. Since R 3.0.0 the binary is a single-arch build and contains only the x86_64 (64-bit Intel) architecture. PowerPC Macs and 32-bit Macs are only supported by building from sources or by older binary R versions. The default package type is "mac.binary" and the binary repository layout has changed accordingly.

There is a listing of data analysis packages for Mac OS X here.

 

OCHEM is a free open access site of annotated models and chemical data. OCHEM contains 1831772 experimental records for about 477 properties collected from 12457 sources you are free to upload your own data and also build predictive models using existing or your own data.

There are also a number of already built models that the public can access, these include

• Ames test
• CYP1A2 inhibition
• LogP and Solubility

You can run predictions on OCHEM using simple REST-like web services, these vortex scripts submit tasks to the various models and then retrieve the resulting prediction.

 

If you want to automate a process but don’t want to learn Applescript then Repeater may be of interest.

Repeater provides a much needed and very convenient platform for recording repetitive actions without having to learn and understand Automator or AppleScript, which are well beyond most user's abilities. Moreover, not all apps can be scripted at all, but Repeater can help you anyway. Furthermore, you can integrate Repeater with popular scripting languages to dramatically improve their possibilities. Repeater is a tool specially designed for recording and playback user actions such as mouse movements and clicks, standard and hardware keystrokes, vertical and horizontal scrolling & zooming. It is also capable of storing information about currently running applications to launch them on playback.

There are also some scripting capabilities for more advanced use. Looks like it could be useful for giving demonstrations.

 

I’ve recently been sent details of SeqAn, an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It is released under BSD/3-clause license and is supported under Mac OS X: GNU/g++, LLVM/Clang (3.0+).

Andreas Döring, David Weese, Tobias Rausch and Knut Reinert. SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9:11, 2008. DOI

 

I’m hearing more and more concerns about security concerns with regard to mobile devices. I guess this was to be expected as more people have smart phones and tablets start to replace laptops. It seems Google's executive chairman Eric Schmidt drew laughter when discussing security on the Android platform, Executive chairman dances around straight answer while talking up Android security.

Schmidt said in the distant future there would be an assumption that nothing is secure and that security will be devised on a per app basis for each user.

I’m not sure whether many people would find that situation very helpful. His view is perhaps a consequence of a recent study issued by the Department of Homeland Security (DHS) and the Federal Bureau of Investigation (FBI) suggesting Android devices represent a significant security threat. Of the malicious attacks documented in the study, 79 percent took place on an Android device and 19% on Symbian whilst Apple's iOS received just 0.7 percent of the recorded malware threats. One of the key sources of threats appear to be the installation of apps from insecure sites, so whilst the approval process for the Apple iTunes store occasionally causes complaints it also acts as a significant security barrier. Whilst the Google Android should have the same role it is perhaps worrying to find that recently 50 malicious apps had to be removed. There have however now been reports of threats distributed via email spam.

The Android trojan known as Stels began distributing via fake U.S. Internal Revenue Service-themed emails, using an Android crimeware kit to steal sensitive information from the device, and monetizing by making calls to premium numbers.

Apple does seem to be taking the security concerns seriously, the AppStore provides an initial check on apps, the new fingerprint authentication provides an extra level of device protections. In iOS7 we have Activation Lock so that someone who’s got hold of your device can’t disable Find My iPhone without knowing both your Apple ID and that Apple ID’s account password. The person with your lost device can’t erase data on the device, also if you designate your device as being lost it can’t be restored to reactivate it—the phone displays only a phone number and a custom message about contacting you.

Keeping the operating system up to date helps, and the adoption rate for iOS7 is very impressive.

 

Anyone involved in a drug discovery programme will be aware of the challenge presented by trying to visualise and explore structure-activity relationships (SAR), in particular visualising questions like :-

“What is the largest change that can be made whilst maintaining activity?”

Activity Miner from Cresset is a new tool designed to rapidly interrogate and decipher SAR in both Torch and Forge. Activity Miner is intended to help identify key elements of the SAR by starting from a set of aligned molecules and then automatically comparing them to each other.

More details are here

 

I use markdown extensively on my websites, “Markdown” is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I mainly use BBEdit and regard it as the “gold standard” but I keep an eye out for other markdown editors and wrote a summary of my findings, I’ve just been sent details of two more apps.

Eratois a simple Markdown editor for the Mac. It is fast, extremely easy to use and gets out of your way. It offers full support for both regular Markdown syntax, GitHub flavoured markdown and YAML front matter.

Marked2 is a previewer for Markdown files. Use it with your favourite text editor and it updates every time you save.

I’ve added them to the summary page.

 

Graph Builder has been updated

• Added data input for 2D vector field presentation.
• Added programmed and animated 2D vector field palette.
• Updated script documentation for 2D vector field animation and programming.
• Added a preference option to turn on the built-in network graphing server.
• Added ability to display dynamic and programmed Graph Builder document results over the web.
• Updated the manual to explain new features

There is a listing of data analysis applications for Mac OSX here.

 

OpenEye have just announced that the virtual screening tool ROCS v3.2 has been released.

Several noteworthy features have been added to this version including a -subrocs option that can drastically improve substructure alignments. Also included is an application rocs-report that uses our 2D depiction technology to make pdf reports of hitlists displayed with 2D similarity, shape and color overlaps, as well as property histograms. Substantial upgrades have been made to vROCS. An improved sketcher now highlights unspecified stereochemistry in atoms and bonds in query structures, and requires the user to correct any unspecified stereochemistry.

ROCS is available for download here.

 

I’ve just updated the Applescript Resources page, in particular I’ve included updates to the great tools provided by Satimage-Software. These include Smile a programming and working environment that you can use in a variety of situations. You may want to perform a scientific work, to handle cgi requests, to automate an intensive file processing task, to produce computed graphics, to edit XML files, to work with Unicode texts, to make GUI of your scripts, and SmileLab the SmileLab license adds the data visualization features to Smile, the automation environment by Satimage-Software.

In SmileLab you can

• extract data from files (default data formats supported: text, binary, FITS, XNF, ...),
• perform data processing using commands provided with Smile or controlling external code
• visualize your data in the most usual forms (curves, scatter plots, bar graphs, contour lines, color maps and vector fields in 2D, and 3D surfaces),
• customize the interaction of the user with the plots (handling mouse clicks, contextual menus, keyboard events...) and create custom interfaces,
• export your plot as a PDF file, as a bitmap picture (PNG, JPEG, TIFF, BMP, PSD) or as a QuickTime movie.