I had the SSD fail on my MacPro and so I needed to reinstall a variety of programs etc. and I took the opportunity to update a number of things. One thing I thought I'd mention is the custom chemistry dictionary, once installed it is available for all Mac OSX applications.
An early Christmas present from Chemical Computing Group
Chemical Computing Group have just released an up date to MOE, version 2015.10 includes:-
- Generate docked poses using FFT followed by all atom minimization
- Define receptor and ligand sites to focus docking
- Automatically detect antibody CDR sites
Integrated Alignment, Consensus and Superposition in the Sequence Editor
- Manipulate multimeric protein sequences using split side-by-side Sequence Editor panes
- Use dendrograms to visualize pairwise similarity, identity and RMSD relationships
- Select residues based on plotted values using resizable sequence editor plots
Distributed Pharmacophore Searching
- Run pharmacophore searches on a cluster directly from MOE GUI
- Perform fast corporate database searches
- Access multiple databases stored on a central server
Covalent Docking and Electron Density Docking
- Use reaction-based organic transformations to covalently docking
- Minimize ligand strain energy while maximizing ligand fit to electron density
- Run docking through an enhanced streamlined scenario-based interface
Extended Hückel Descriptors and pKa Model
- Compute molecular properties such as logP, logS and molar refractivity
- Determine populations of ligand protonation states at a given pH
- Calculate the pKa and pKb of small molecules
13C NMR Analysis
- Apply QM conformation refinement to calculate 13C NMR shielding
- Convert computed shieldings and predict 13C NMR chemical shifts
- Compare computed chemical shifts to experimental shifts for structure determination
I'll write a review in the New Year.
Chemical Identifier Resolver
I just got this message so I thought I'd pass it on, I'll update any scripts that use the chemical identifier resolver in the New Year.
To all users of programmatic services on the cactus.nci.nih.gov web server of the CADD Group at the NCI/NIH:
The CACTUS web server will move to a significantly reconfigured system on new hardware by the end of the year. This move is planned to take place during the last week of December 2015. This move will also entail a change of the host's IPv4 address. Concurrent with the cut-over, the HTTPS protocol will be enabled for all services. Both HTTP and HTTPS will be supported in parallel for a transition period. We plan to turn off HTTP permanently by end of March 2016. Disruptions to users caused by the move should be minimal. If you encounter any bugs or different behavior starting 1/1/2016, please let us know immediately.
Chemistry related LaTeX packages
LaTeX is used for the markup and publication of scientific documents, it is particularly popular in mathematics, physics, computer science. I know some chemists use it so I thought I'd mention this resource of Chemistry LaTeX packages. It includes packages for most of the major Chemistry journals.
Science Applications under El Capitan (Update 11)
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 an incremental upgrade I'm hoping most things will be unaffected. I’ll update the list regularly and feel free to send in information.
So far the only issues I've hit are those that involve Java, reading around it looks like this is widespread issue.
When I compiled a similar list for Yosemite it proved very popular with 13,000 page views, and I hope this page is similarly useful.
Aabel 3 seems to be working fine
Avogadro all OK
BBEdit all OK
ChemBioDraw I was in touch with their support and was told "No support for ChemBioDraw on El Capitan", however a couple of readers have said that it appears to work. No information yet on round trip editing. Looking the CambridgeSoft forum (http://forums.cambridgesoft.com/messageview.aspx?catid=12&threadid=3165&enterthread=y) it is clear that there are major problems with ChemDraw 15 and El Capitan, as ever it seems that a new release of Mac OSX comes as a complete surprise to ChemDraw developers, "Currently our products are not supported with El Capitan. We plan to support El Capitan for the future release/update".
ChemDoodle I had to reinstall latest version of Java
No issues reported for Cresset tools Torch, Spark, Forge
DataWarrior requires Java installation
Findings 1.2.4 is compatible with El Capitan
iPython Notebook all working fine
KNIME all working OK
MarvinSketch I had to reinstall Java for Mac OSX this is the last version of Java Apple created to support legacy applications, however trying to use the command line tool "evaluate" I got this error
line 128: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/java: No such file or directory
I updated ChemAxon Beans to version 18.104.22.168 and this seems to fix the problem.
MOE all working fine, XQuartz did not need reinstalling. There have not been any reports of issues with the license server which has been an issue in the past.
Mnova no reported issues
Papers 3 is compatible with El Capitan
Plane of best fit I got several errors after upgrading, brew update and recompile solved everything.
R all seems fine
Safari Extensions still seem to be working.
Schrödinger report all their software is supported under El Capitan, MacOSX 10.11 is supported for the 2015-4 release. You must upgrade your Schrödinger software installation to the 2015-4 release, as previous releases are not supported on MacOSX 10.11.
SeeSAR no issues so far
Stardrop not aware of any issues
Spartan 14 seems fine.
UCSF Chimera is also working on El Capitan.
Vortex no problems so far
Wizard Pro all seems fine
Updating Homebrew packages
Part of the OS X 10.11/El Capitan changes is something called System Integrity Protection or "SIP". SIP prevents you from writing to many system directories such as /usr, /System & /bin, regardless of whether or not you are root. However /usr/local is open for developers to use, so Homebrew can still be used as expected. To fix your Homebrew installation if you see permission issues type
sudo chown $(whoami):admin /usr/local && sudo chown -R $(whoami):admin /usr/local
There is a more detailed explanation here
You will also need to install the latest version of the command line tools
Then you can type
brew update brew upgrade
I did the usual simple tests on the following packages and all worked fine after brew upgrade.
OpenBabel RDkit CDK Opsin Osra Inch Chemspot
Whilst users upgrading a machine that already has XQuartz have not see any issues there seems to be some issues with installing XQuartz onto new machines. It seems the symlink from /usr/X11R6 to /opt/X11 is not present and a reference to /usr/X11R6/lib/libX11.6.dylib fails, a post-install script for XQuartz should have setup the symlink.
The suggested solution if for users to type
This installs both the /usr/X11 and the /usrX11R6 symlinks
More info on the X11-users mail list at Apple https://lists.apple.com/mailman/listinfo/x11-users
Update. This has been fixed in a third release candidate of XQuartz 2.7.8 so hopefully an update is imminent.
An updated version of XQuartz has now been released full details are available here and the installer is available here http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.8.dmg.
This also seems to fix X forwarding and window positioning issues some people experienced.
There can be an issue with installing Pymol under El Capitan, if you find it crashes on startup then there is a possible solution at the bottom of this page
Updated 12 December 2015
Pymol under El Capitan
When El Capitan first came out I upgraded a machine with an existing installation of a variety of cheminformatics tools installed using Homebrew and PIP as described here. Under this situation Pymol worked without problem. However I have had a few readers email me saying they are having problems so I took a new machine running El Capitan and tried to instal the same cheminformatics tools including Pymol using Homebrew and PIP. All worked fine except Pymol which opened but crashed with the following error.
Username:~ prompt$ pymol PyMOL(TM) Molecular Graphics System, Version 22.214.171.124. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at "http://www.pymol.org". Enter "help" for a list of commands. Enter "help <command-name>" for information on a specific command. Hit ESC anytime to toggle between text and graphics. Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: NVIDIA GeForce 8600M GT OpenGL Engine GL_VERSION: 2.1 NVIDIA-10.0.40 310.90.10.05b12 Detected 2 CPU cores. Enabled multithreaded rendering. libpng warning: Application built with libpng-1.6.19 but running with 1.5.23 /usr/local/bin/pymol: line 4: 3628 Segmentation fault: 11 "/usr/local/opt/python/bin/python2.7" "/usr/local/Cellar/pymol/126.96.36.199/libexec/lib/python2.7/site-packages/pymol/__init__.py" "$@“
The helpful on the Pymol user list pointed me to this message on the Homebrew-Science issues
First uninstall pymol and libpng
brew uninstall pymol brew uninstall libpng
then install pymol first.
brew install pymol brew install libpng
Now when you type pymol in a Terminal window you should see.
NASA Needs a FORTRAN Programmer
Any posts on Fortran always seem to attract attention so I thought I'd flag this opportunity.
Larry Zottarelli, the last original Voyager engineer still on the project, is retiring after a long and storied history at JPL. While there are still a few hands around who worked on the original project, now the job of keeping this now-interstellar spacecraft going will fall to someone else. And that someone needs to have some very specific skills …Know Cobol? Can you breeze through Fortran? Remember your Algol
More details here
Apple and Open Source
Whilst the decision to make Swift open source certainly captured the headlines, it is worth noting that Apple contributes to many more open source projects, there are more details about these open source projects on the developer and main Apple websites.
HELM integration with RDKit
The Pistoia Alliance HELM project have announced free MarvinBeans 5.0 licenses and integration of HELM with the RDKit cheminformatics suite.
The Pistoia Alliance HELM project has made two major announcements that help cement the reputation of HELM as the de-facto standard for describing and working with complex macromolecular structures. Firstly, HELM users can now take advantage of free MarvinBeans 5.0 licenses for the HELM toolkit. Secondly, RDKit is now HELM-enabled, making it a valuable addition to the extensive range of open source HELM-enabled tools.
Browser plugin-free CIF visualization
A nice comparison of the options for displaying crystal structures within a browser without the need for plugins/applets.
Full blog post is here
Here we compare four open-source browser engines for plugin-free rendering of the crystalline structures in CIF format.
Swift Open Source
As I previously highlighted after the WWDC Apple have announced that Swift is now open source.
More details are on the Swift blog
Swift is now open source. Today Apple launched the open source Swift community, as well as amazing new tools and resources including: Swift.org – a site dedicated to the open source Swift community Public source code repositories at github.com/apple A new Swift package manager project for easily sharing and building code A Swift-native core libraries project with higher-level functionality above the standard library Platform support for all Apple platforms as well as Linux
Swift.org is an entirely new site dedicated to open source Swift. This site hosts resources for the community of developers that want to help evolve Swift, contribute fixes, and most importantly, interact with each other. It also provides development snapshots for Apple and Linux platforms, requires OS X 10.11 (El Capitan) or Ubuntu 14.04 or 15.10 (64-bit).
Source code is available on Github
BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library
I just thought I'd flag a recent paper on sampling conformation space DOI.
The interaction of a small molecule with a protein target depends on its ability to adopt a three-dimensional structure that is complementary. Therefore, complete and rapid prediction of the conformational space a small molecule can sample is critical for both structure- and ligand-based drug discovery algorithms such as small molecule docking or three-dimensional quantitative structure–activity relationships.
The software is available from the MeilerLab home page
Orange NMR Updated
Orange NMR the iOS app to predict 13C and 1H NMR spectra has been updated, just draw a structure to see its spectrum.
What's New in Version 2.2
iOS 9 multitasking supported.
Optional calculation of MF, MW, Monoisotopic Mass and Elemental Composition added.
Ability to show terminal and all carbons on structure added.
Some minor bugs fixed.
Reactions in XMDS
I just heard about an update to the OSX Molecular DataSheet (XMDS)
After much procrastination, chemical reactions have started to make their way into the OSX Molecular DataSheet (XMDS) beta
This could be a very interesting development.
NNSA, national labs team with Nvidia to develop open-source Fortran compiler technology
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 when I saw that the NNSA, national labs team with Nvidia to develop open-source Fortran compiler technology to integrate into LLVM I thought I'd mention it.
LLVM is a collection of reusable compiler and tool chain technologies with a modular design that facilitates support for a wide variety of programming languages and processor architectures.The Fortran front-end module created through this project will be derived from NVIDIA’s PGI Fortran compiler, which has been used in production across a variety of high performance computing systems for more than 25 years. PGI® software is a leading supplier of software compilers and tools for parallel computing.
I've compiled a list of Fortran resources for the Mac here.
SeeSAR has been updated, the description below gives full details.
This update of SeeSAR qualifies as major release 4, as several milestones have been achieved with it - namely the integration of the world-renowned ADME property calculator from Optibrium™, the display of the protein surface in the 3D view, and an update of the Hyde scoring function. Collectively, these changes have made an update of the SeeSAR storage mechanism necessary, so unfortunately old project files cannot be loaded with this version. We recommend you save your molecules from old projects to file and re-read them with this new SeeSAR version. As an additional bonus feature we implemented the multi-selection of favorites with a simple [Shift] and click. Just try it out, it works as you would expect.
As of version 4.0, SeeSAR is equipped with an interface that allows you to benefit from Optibrium's ADME property calculator from within SeeSAR. Any molecule loaded or edited is passed on to the property calculator, which itself applies multiple computational models to determine a variety of ADME properties. By default you'll see:
logD @ pH7.4
logS (thermodynamic, intrinsic aqueous solubility)
logS @ pH7.4 (in phosphate buffered solution)
Blood-brain barrier penetration (log([blood]:[brain])
hERG inhibition (pIC50)
CYP2C9 affinity (pKi)
Human intestinal absorption (HIA) classification
Blood-brain barrier penetration classification
CYP2D6 affinity (pKi) classification
Plasma-protein binding classification
P-gp transport classification
However, if you have additional models (within the Optibrium framework) you can add those too and have the respective values available at your fingertips. Note that the usage of this feature requires a separate license!
The binding site of a protein is oftentimes quite complex making it easy to lose the sense of depth, space and tightness of fit. The protein surface of the binding site is now available to aid with orientation and can be toggled on and off very simply using a switch underneath the molecules table. This way, it is easy to switch between the surface view to find the orientation when you need to and the atom-only view at other times.
Hyde is quite sensitive with regards to the numerical stability of the calculation, which we have significantly improved with this update. We also detected a small inaccuracy in the way the coverage of interactions is calculated which has now been corrected. Overall Hyde now has a higher hit rate with respect to the experimental data for high-quality structures and on average avoids overestimating the affinities, i.e. it now provides a more conservative estimate thereby reducing the rate of false positives.
RRegrs: an R package for computer-aided model selection with multiple regression models
I just thought I'd flag a paper in Journal of Cheminformatics, RRegrs: an R package for computer-aided model selection with multiple regression models DOI.
We propose an integrated framework for creating multiple regression models, called RRegrs. The tool offers the option of ten simple and complex regression methods combined with repeated 10-fold and leave-one-out cross-validation. Methods include Multiple Linear regression, Generalized Linear Model with Stepwise Feature Selection, Partial Least Squares regression, Lasso regression, and Support Vector Machines Recursive Feature Elimination. The new framework is an automated fully validated procedure which produces standardized reports to quickly oversee the impact of choices in modelling algorithms and assess the model and cross-validation results. The methodology was implemented as an open source R package, available at https://www.github.com/enanomapper/RRegrs, by reusing and extending on the caret package.
Wolfram Alpha has been updated
Wolfram Alpha has been updated.
Wolfram|Alpha. Building on 25 years of development led by Stephen Wolfram, Wolfram|Alpha has rapidly become the world's definitive source for instant expert knowledge and computation.
Wizard Pro updated
Wizard Pro has been updated.
What's New in Version 1.7.18
- Added support for Numbers 3.6 files
- Exporting data from the Summary view now has a progress bar and cancel button
- Exporting data now writes directly to disk instead of building the file in memory first
- Many other performance improvements throughout the program
- Added support for generating the R command for the Friedman test
- Added support for generating SAS/SPSS commands for repeated-measures tests
- Report the combined significance of constant coefficients for models with multiple sets of coefficients
- Fix a crash after exporting ROC curves
- Fix a bug when exporting DTA files with missing values
- Fix a bug where formatting options weren't showing in the Pivot view
- Fix a number of minor interface glitches
- Improved support for importing SAS and SPSS command files
- Improved support for SAS catalog files
There is a review of Wizard Pro here, and a listing of data analysis tools for Mac OSX here.
Flagging potential aggregators in Vortex
Promiscuous inhibition caused by small molecule aggregation is a major source of false positive results in high-throughput screening. A recent particularly valuable publication, Irwin, Duan, Torosyan, Doak, Ziebart, Sterling, Tumanian and Shoichet, J Med Chem, 2015, 58(1 7), 7076-7087 DOI, has collated over 12,000 organic molecules known to act as aggregators at concentrations used in screening campaigns, and provides a resource Aggregation Advisor that can be used to try and predict possible false positives. However in many instances it would be unwise to submit proprietary information to the public web service. Potential aggregators are flagged based on calculated LogP >3 and/or similarity >0.85 to a known aggregator (using path based fingerprint) this script calculates xLogP using the algorithm provided by Dotmatics and then uses OpenBabel fast search to calculate the closest similarity to a known aggregator.
Full details of the Vortex script are here.
Findings is an electronic notebook for scientists.
The main new features are:
- Much improved export, with options to export multiple experiments based on projects and dates, and many more options for PDF output (and print).
- A brand new archive format to export and import experiments and protocols, which makes it very easy to share documents and collaborate on their content. One subtle but powerful feature is that re-importing an experiment or protocol will not create a duplicate, but will instead merge the latest changes. This means collaborators can keep sending new versions of a document to each other, and it will magically update their library.
- Full-text search across all experiments (or protocols).
- Search within a document, with proper highlighting and keyboard-based navigation through the search matches.
- Much nicer experiment cards, in particular using a vignette thumbnail, showing a project color, and with the calendar strip functioning as a progress bar for multi-day experiments.
- In addition to the free Basic version, new unregistered users are now also offered a 30-day trial of the Pro version;for 30 days, the 20-day experiment limit is thus lifted.
There are also tons of improvements and bug fixes.
Collaboration also got better, you can also export experiments as archives, that anybody can read with the free Basic version of Findings.
There has also been some changes to the pricing structure, the basic individual version is free but there are discounts for group (5) purchases, and it sounds like if you have a bigger group it would be worth contacting them directly because larger discounts are available.
Data Creator Updated
Data Creator has been updated. This is an invaluable tool if you ever need to create a pseudo-random data-set.
What's New in Version 1.5 • New creator type: USA cities, Italian cities, French cities, German Cities. • Bug fix: Changing format to export, the file extension was not changing automatically • Other minor bug fix. • Optimized for OS X 10.11 El Capitan
Data Creator can create sample tables (rows and columns) as you like and fill them with pseudo-random proper content (rows of content) with a single click. You can select which kind of fields (columns) you like (name of animals, colors, fruits, english surname, german names and so on with over 50 different kind of data) and have all the contents filled for how many rows you like in a click.
OpenEye Toolkits v2015.October released
OpenEye have announced the release of OpenEye Toolkits v2015.October. These libraries include the usual support for C++, Python, C# and Java.
- FastROCS TK was added to the OpenEye toolkits collection
- Molecule reading performance improvement in OEChem TK
- The capabilities of the OEBio-Fragment Network have been expanded
- 213 new ring templates have been added to the OEChem TK built-in ring dictionary
The full release notes give more details
In particular note the 2015.Oct release is the last to support Mac OSX 10.8 so time to upgrade if you have not already done so.
MEL Chemistry is an iOS app that allows users visualize molecules in 3D. You can rotate, zoom in and zoom out to see molecule structure in details. There is also an accompanying bench chemistry kit that looks like a perfect christmas present for young (and not so young) home scientists. WolframAlpha has been updated
Remember the Star Trek computer? It's finally happening--with Wolfram|Alpha. Building on 25 years of development led by Stephen Wolfram, Wolfram|Alpha has rapidly become the world's definitive source for instant expert knowledge and computation. Parts of Wolfram|Alpha are used in the Apple Siri Assistant; this app gives you access to the full power of the Wolfram|Alpha computational knowledge engine.
iOS9 use increases steadily
It looks like iOS adoption is running smoothly, now over two thirds of iOS users.
Wizard Pro updated
The popular data analysis tool Wizard Pro for Mac has been updated. Wizard includes a full set of tools for doing professional research, yet its friendly interface makes statistics accessible to beginners. There is a review here.
New in 1.7.17:
• Show ellipses when data is truncated in the Raw Data view
• Fix a bug where Shapiro-Wilk and one-column Kolmogorov-Smirnov tests on highly repetitious data gave overly conservative results
• Improved support for exporting Stata .dta files
• Improved support for importing compressed SAS data files
• Improved support for importing SAS catalog files containing a large number of value labels
There is a comprehensive listing of data analysis tools for MacOSX here.
Mbook is an Electronic Lab Notebook designed by chemists for chemists, it is a cloud based solution focused on the needs of synthetic chemists. Runs on any web browser and therefore requires no application installation or updates. Zero footprint and always updated. Immediately scalable, you can grow your number of users without having to change infrastructure or installations.
- Reaction scheme and experimental conditions
- Stoichiometry table and experiment write-up area
- Analytical data (NMR, MS, etc.) for reactants, solvents and products
- MSDS datasheets for all experiment participants
- Literature references and other relevant documents
- Image files (product appearance, TLC, etc.)
It comes in various favours from a basic setup to an expert suite, the difference being the number of different spectroscopy plugins that are included.
There is an online guide and a test drive version.
This is probably the application that many programmers have been waiting for, CodeSwitch is the first Objective-C to Swift code converter for Mac OS X.
CodeSwitch will convert all of your Objective-C code into Swift code instantly. Simply copy-and-paste any Objective-C code into this program, and it will translate it to Swift in milliseconds.
So those legacy programs won't need a complete rewrite!
The latest post on the Swift blog highlights a new feature in Xcode 7.1, the ability to embed file, image, and color literals into your playground’s code.
For instance, there’s no need to type “myImage.jpg” in the editor – just drag your image from the Finder and the actual image will appear in-line with your code.
Useful if you tend to name images, image1, image 2 etc ;-)
Running mobihf on the iPhone
An interesting blog post describing how to run basic Hartree-Fock Quantum Chemistry code on an iPhone.
They used a python version of mobihf, there are a number of Python interpreters for iOS but they had success with pythoni and they note:
This is surprisingly well written app with custom keyboard shortcuts and well made editor for editing Python scripts. It is worth buying the pro features in this app if you do a lot of Python programming on the move.
They also used Sketch Python and found that it gave improved performance.
The work was undertaken on the A7 processor of iPhone 5s, and it would be interesting to see the performance on one of the latest iOS devices.
But I can say that these mobile processors have reached the performance levels of the most desktop processors for all practical purposes.
Laptop Upgrade by Mac:Upgrades
I've had my MacBook Pro since early 2008 and it has proved to be a great uncomplying hero as I've traveled all over the world with it, but recently it has taken a longer to boot up and there have been the occasional freezes. This was confirmed by a quick check with Disk Utility. Whilst I keep regular backs ups of key data I decided to do a full backup of the entire disc and I got in touch with Mac:Upgrades.
Those guys were extremely helpful in going through the various options, in the end I replaced the hard drive with SSD, replaced the optical dive (which I can't remember ever using) with a new larger hard drive and upgraded the RAM. I dropped the machine off late afternoon and picked up the next day and it was like getting a new machine! Without doubt this has been the best value upgrade ever.
ImageVis3D and Orange NMR updates
I've just got details of a couple of updates to mobile science apps.
ImageVis3D Mobile is a mobile visualization application one to visualize and share volume and surface data while you are on the go. With ImageVis3D (available for free at www.imagevis3d.com) and ImageVis3D mobile you can transfer your own data directly from the desktop to your mobile device.
What's New in Version 5.1 - new iOS 9 compatible UI (support for Slide Over and Split View) - numerous improvements in the rendering engine - slice viewer visualizes geometry in addition to volume data
Orange NMR is an App to predict 13C and 1H NMR spectra: draw a structure to see its spectrum. The accuracy of the algorithm is about 1.9 ppm for 13C and 0.21 ppm for 1H (RMSD=3.4 and 0.31 ppm correspondingly). The number of heavy atoms in structure to predict for free is restricted to 12 atoms. This restriction can be removed by purchasing additional licenses.
What's New in Version 2.1. Table of peaks added. Structure drawing enhanced: Touch and drag from bond to draw ring. Double click inside ring to make it aromatic. P and I elements added. Help added.
There are now an increasing number of mobile spectroscopy apps available.
Everyday AppleScriptObjC Third Edition
El Capitan has brought a few changes to ApplescriptObjC and so I thought it would be a good time to mention Shane Stanley's absolutely invaluable book Everyday AppleScriptObjC now in it's Third Edition.
AppleScriptObjC was a new framework in OS X v10.6 that allows Cocoa applications to be written in AppleScript, AppleScriptObjC was the replacement for AppleScript Studio. Using AppleScriptObjC, your AppleScript code can work with any Cocoa framework, and can function as a first-class citizen in the Cocoa world. The only problem was that documentation for AppleScriptObjC was pretty scarce and none of it was written from the viewpoint of a scripter looking to take advantage of the new options. Everyday AppleScriptObjC filled that void superbly giving a helping hand with the initial learning curve and offering detailed worked examples to demonstrate key features.
Computational chemistry guides & tools
The Medicines for Malaria Venture have an interesting page in which they are accumulating a list of computational tools and guides describing the use of the tools to address key issues within the drug discovery process.
Tools were chosen to address common needs expressed by medicinal and computational chemists working in the not-for-profit area. Recognising that this is a global effort, we have selected software packages on the basis of being free for all users.
The guides are either text descriptions or webcasts showing the tool in action. To date they include DataWarrior, KNIME, YASARA, ChEMBL and PK Tool.
Manuscripts next Beta now out
The new beta version of Manuscripts is now out, sign up if you would like to evaluate and try it out, and particularly if you want to provide feedback.
Manuscripts is intended as an scientific/technical writing tool.
MyScript Calculator - Handwriting calculator
MyScript Calculator - A calculator that supports handwritten input has been updated.
New in version 1.3.2: - iOS 9 support - Jot down a quick calculation or check the history while you're using another app. Only available on iPads compatible with iOS 9 multitasking features.
Protein-Ligand Interaction Profiler has been updated
The PLIP Protein-Ligand Interaction Profiler has been updated.
According to the Changelog
- Support for DNA and RNA as ligands__
- Detection of metal complexes with proteins/ligands, including prediction of geometry__
- Extended result files with detailed information on binding site residues and unpaired atoms__
- Support for zipped and gzipped files__
- Rich verbose mode in command line with information on detected functional groups and interactions
- Automatic fixing of common errors in custom PDB files
- Refined binding site selection
- Better overall performance
- Initial test suite for metal coordination
- Classification of ligands
- Improves detection of aromatic rings and interactions involving aromatic rings
- Single nucleotides and ions not excluded anymore as ligands
- Generation of canonical smiles for complete (composite) ligands
- Generation of txt files is now optional
- Basic support for PDBQT files
- Correct handling of negative chain positions of ligands
- Improved check for valid PDB IDs
- Fixes several bug
The web service includes all the updates and integrates BioLip for flagging biologically relevant interactions. Since ligand molecules (e.g., Glycerol, Ethylene glycol) are often used as additives (i.e., false positives) for solving the protein structures, not all ligands present in the PDB database are biologically relevant.
CLC Drug Discovery Workbench updated
CLC Drug Discovery Workbench 2.5 has been released.
- Protein optimizer: New interactive tool invoked from the side panel in molecule projects. It allows for manual mutation and repair of amino acids, flipping of side chains, manual selection of side chain rotamers, and local adaption of protein structure to point mutations.
- Ligand optimizer: The ligand optimizer allows now for custom modification and creation of ring structures. 3D molecule viewer:
- Molecule surfaces can now be transparent, A clipping plane can cut into surfaces and secondary structures, Options for creating atom groups and visualizing hydrogen bonds have been improved
CLC Drug Discovery Workbench is your virtual lab bench. It gives you access to atomic level insights in protein-ligand interaction, and allows new ideas for improved binders to be quickly tested and visualized.
El Capitan Review in Guardian
The latest version of Apple’s laptop and desktop operating system OS X 10.11 El Capitan will genuinely speed up your computer, particularly if you’ve got an older Mac
A nice blog post describing the use of Torch to analyse molecules
The choice of which molecule(s) to progress into synthetic chemistry depends on a number of properties – potential for activity, logP, MW, flexibility etc.. The problem faced by most project teams is one of balance in that although there is usually an ideal range of values for each property, not every property is equally important. For example, the ideal may be to have MW<500 and logP<3 but there may be more tolerance for a high MW if logP is well within range.
Mobile Science Updates
I've just added a few more apps tο the Mobile Science site, these include Organic Named Reactions, Atomsmith Molecule Lab and Molecule World DNA Binding Lab.
Chemistry Keyboard updated
Chemistry Keyboard has been updated. This update includes the addition of a triple bar character and compatibility with iOS9.
Chemistry Keyboard is a specialised Keyboard Extension for anyone who needs to enter chemical formulae.
Grand Challenge 2015: Prediction of ligand poses, and affinity ranking
Grand Challenge 2015: Prediction of ligand poses, and affinity rankings, for the protein targets HSP90 and MAP4K4. Stage 1 predictions are due November 16, 2015; Stage 2 predictions are due February 1, 2016. For details, and to sign up and participate, please see https://drugdesigndata.org/about/grand-challenge-2015
SAMPL5: Prediction of aqueous host-guest binding free energies and, optionally, enthalpies for three host-guest series. A series of aqueous-organic partition coefficients may also be added in the next several weeks. Predictions are due February 1, 2016. For details, and to participate, please see https://drugdesigndata.org/about/sampl5.
These challenges are organized by the Drug Design Data Resource, which is based at UC San Diego and supported by a grant (U01GM111528) from the NIH's National Institute of General Medical Sciences. They are made possible by generous donations of data, pre-publication, from AbbVie, Genentech, the CSAR initiative at U. Michigan, and Professors Lyle Isaacs (U. Maryland) and Bruce Gibb (Tulane U.)
PolyPharma and Wizard Pro Updated
The iOS app using Bayesian models to predict biological activity PolyPharma has been updated, Molecule overlays now have a contrast slider to increase/decrease emphasis on atom contributions to the overall prediction.
The user friendly data analysis and visualisation application Wizard Pro has been updated.
New in 1.7.13:
• Improved support for importing multiple tables from RData files
• Fix a glitch when exporting logistic models to Excel
• Fix a crash when dividing one column by another in a Stacked Table
• Fix interface glitches when defining a Recode Variable
There is a review of Wizard Pro Here.
A new version of SeeSAR is now available. SeeSAR is intended as an interactive tool for designing/improving ligands for drug discovery. In the SeeSAR review I write about an earlier version one of the issues I flagged was a problem when dealing with covalently bound ligands, this has now been addressed.
This version also allows such visual assessment of covalently bound ligands. They are now listed in the Molecules table together with reversibly bound ligands and co-factors. As with all the other small molecules, a focussed view showing the individual atom contributions to binding is shown in 3D when the covalently bound ligand is selected in the table. We don't, however, provide an overall binding affinity for covalently bound ligands since it is meaningless in this context.
This new version also has the the ability to choose which water molecules to consider, this way overwriting the Hyde-default in cases where you know better.
Papers 3 for iPhone and iPad, now available for free!
As of today, Papers for iPhone and iPad is available for free! Full functionality, no in-app purchases or small print.
iOS versions in use
Developers often ask me about the versions of operating systems that are used to access the site so I keep an occasional eye on the analytics.
Looking at iOS I notice that version 9 is now appearing at just over 6% of the visitors. Version 8 accounts for around 92% with an occasional visitor still using versions 5-7. Just in case the site visitors are not representative I thought I'd check on the Mixpanel site, they also show >90% using iOS 8 as shown below.
The lack of fragmentation in iOS adoption makes it easy for developers to decide on which version of the operating system they need to support.
ROCS 3.2.1 released
OpenEye have just announced the release of a new version of ROCS.
ROCS is a fast shape comparison application, based on the idea that molecules have similar shape if their volumes overlay well and any volume mismatch is a measure of dissimilarity. It uses a smooth Gaussian function to represent the molecular volume, so it is possible to routinely minimize to the best global match. Novel and interesting molecular scaffolds can be identified using ROCS against targets often considered very difficult for computational techniques to address.
Scientific application for iOS are getting more and more sophisticated, PolyPharma is a new application for looking at Structure-activity generated by a wide selection of predictive Bayesian models.
The results are then displayed using a variety of visualisation methods, a "radar plot", molecules coloured , using the "doppler" signature (blue = low, white = intermediate, red = high) indicating which parts of the molecule contribute most to the predicted activity/property. The activity in all models can be displayed
and the structure activity in a selected model explored using the "honeycomb" display. For each of the targets within the profile, the app stores a selection of representative molecules from the training set that was used to build the Bayesian model. These are shown as a series of thumbnail summaries using the honeycomb-style clustering layout, with the current molecule at the centre, the is support for gestures allowing the user to "pinch" or "sweep" to zoom in or browse.
OS X Molecular DataSheet (XMDS) app updated
The OS X Molecular DataSheet XMDS app has been updated recently. This is a chemically aware spreadsheet editor: it operates on a grid of editable cells, made up of typed columns, that can be molecules, numbers or plain text.
The latest update brings drag and drop, as you might imagine moving cells containing molecules is rather more complicated than numbers or text. You can read full details here
Dalton 2015 entry updated
The Dalton2015 suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilities.
Together, the two programs provide an extensive functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are only available in the Dalton2015 suite.
Dalton can be run on a variety of systems running the UNIX operating system. The current release of the program supports Linux, Cray, SGI, and MacOS using GNU or Intel compilers (we plan to publish patches for PGI and XL compilers).. The program is written in FORTRAN 77, FORTRAN 90 and C, with machine dependencies isolated using C preprocessor directives. All floating-point computations are performed in 64-bit precision, but if 32-bit integers are available the code will take advantage of this to reduce storage requirements in some sections.
The popular GUI for GAMESS MacMolPlt has now been renamed and moved to GitHub, wxMacMolPlt is a cross-platform (Mac OS X, Linux and Windows) GUI for preparing, submitting and visualizing input and output for the GAMESS quantum chemistry package. Features include a graphical molecule builder, GAMESS input generation, animation of output and visualization of molecules, normal modes, orbitals and other properties
wxMacMolPlt can be downloaded from here
Bode, B. M. and Gordon, M. S. J. Mol. Graphics Mod., 16, 1998, 133-138. DOI
Periodic Table apps
I notice that the Royal Society of Chemistry have just added another mobile app, the Periodic Table is based on the Periodic table on the RSC website and contains lots of interesting facts about the elements.
There are actually a few other Periodic Table apps, including Molar, EleMints, Periodic Table of the Elements, Merck PTE HD, The Chemical Touch, The Elements and my favourite The Elements in Action.
The Elements in Action has videos describing the elements, so if you have ever wanted to know what happens when rubidium is dropped into water this is the app for you, bear in mind however it is a 557MB app.
@MatToddChem recently tweeted
Chemdraw file containing lots of molecules --> separate png/jpg images of each molecule. Anyone got a script that automates that? #headache
Whilst it is possible to convert a ChemDraw file to an image the problem is you get a single png file containing all the structures. In order to get individual image files it is first necessary to separate the individual structures. The easiest way to this is to convert from cdx to SMILES format. We can then take each of the individual SMILES strings and generate an image using OpenBabel all controlled by an Applescript.
I've mentioned the Swift blog before and I note there is a new entry describing the additions to Xcode 7.
I've also come across a couple of blogs that also be of interest Inessential by Brent Simmons, Kickingbear, and Weheartswift which helps you learn Swift from scratch.
Mac OSX installer for Coot
A reader sent me a link to a posting on the brilliant Crystallography on OS X website highlighting the availability of a stand alone version of Coot for Mac OSX
With considerable help from Nat Echols, we can now build coot automatically every night a new revision is available. I have two versions, built on two different computers. The 10.6 version should run on 10.6.8 or greater. The 10.9 version is for 10.9 or later.. The package installer will install everything in /Library/Coot. Unfortunately, it breaks if you move it. A wrapper shell script called "coot" will reside in /usr/local/bin/coot when you are done.
Coot (Crystallographic Object-Oriented Toolkit) is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.
Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.
I've also added a link on the Spectroscopy page.
SPRESImobile has been updated.
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 1974-2001
New in Version 2.3 Updated for iOS8. 64-bit version
New in Version 2.2
NAME REACTION SEARCH: After registration users see a new button for name reaction searches in the reaction search form. Furthermore, all users (including those not registered) will see a new hyperlink with the Name Reaction in the reaction hit list, when named reactions are hits for a reaction search. This hyperlink allows users to retrieve all reactions assigned to the specific mechanism.
New in Version 2.0
REACTION SEARCH: Users are now able to perform a range of reaction searches, such as exact, substructure, similar and all-in-one within the new reaction search page
REACTION EDITOR: The MMDS structure editor by Molecular Materials Informatics has been modified to enable intuitive and easy reaction query submission.
INFO FOR SPRESIweb CREDENTIALS OWNERS: SPRESImobile users who own credentials for the SPRESIweb application containing now over 11.8 million molecules (5.4 million abstracted from the literature and 6.4 million from catalogs) and 4.2 million reactions, are now informed about the database they are searching via a short notice visible at the bottom of the SPRESImobile homepage.
There are now nearly 400 science apps on the Mobile Science website.
GPU-Accelerated Scientific Applications
There has been a discussion about GPU-Accelerated Scientific Applications on CCL so I thought it was a good time to update the GPU Science page.
Many thanks to all those who contributed.
Brood v3.0 released
OpenEye have announced the release of Brood v3.0 a bioisostere replacement program.
- Custom Fragment Conformations: Fragment geometries can now be derived from any 3D source, including the CSD.
- Fragment Joining and Cyclization: Finding a fragment to bridge two disconnected molecules or cyclize a molecule is now directly supported.
- Improved Filter Properties: Property filters can now have both minimum and maximum values.
- Mapping Fragments to Source Molecules: Molecules BROOD constructs now include the source molecule from which the replacement fragment is derived.
- Results Navigation: BROOD’s results navigation tool has been redesigned to be more intuitive, giving users an easy way to quickly explore the clustered and aligned analog molecules.
Full details are available in the release notes.
csvkit is a suite of utilities written in Python for converting to and working with files in csv format. csvkit is designed to be used a replacement for most of Python’s csv module simply
It can also be called from the command line
in2csv data.json > data.csv
To install on a Mac you can use use PIP a tool for installing and managing Python packages.
pip install csvkit
It is supported on OSX and Linux. It also works–but is tested less frequently–on Windows.
LSH-based similarity search in MongoDB is faster than postgres cartridge
There is a great blog article on ChEMBL-og, describing their work evaluating chemical structure based searching in MongoDB. MongoDB is a NoSQL database designed for scalability and performance that is attracting a lot of interest at the moment.
The article does a great job in explaining the logic behind improving the search performance.
They also provide an iPython notebook so you can try it yourself.
KNIME 2.12 released
The latest update to KNIME has been released.
The KNIME Analytics Platform incorporates hundreds of processing nodes for data I/O, preprocessing and cleansing, modeling, analysis and data mining as well as various interactive views, such as scatter plots, parallel coordinates and others. It integrates all of the analysis modules of the well known Weka data mining environment and additional plugins allow R-scripts to be run, offering access to a vast library of statistical routines.
What's New in KNIME 2.12
Analytics - Decision Tree to Rule Set (New node) - Rule Handling (New node) - Statistics measure as aggregation methods in GroupBy node - Extended PMML Support (New node) - Data Generation (New node) - More Statistics Nodes (New set of nodes)
Finding Duplicate structures
It is always interesting to note which scripts attract the most attention, often it is scripts that aid with relatively simple tasks. Among the Applescripts it is the script to simply print the clipboard.
Recently I wrote a script to remove duplicate structures from within Vortex
When working with multiple data sets of molecules, particularly if combining them from multiple sources, one of the most common tasks is removal of duplicates. This can be a time-consuming and error prone process if carried out manually and this script should hopefully make this a much easier task.
This seems to have attracted interest but I got a comment that it "works fine but is slow for larger data sets". So I've been looking at improving performance.
In order to test the performance I took around 150,000 random structures from ChEMBL and then duplicated 0.01% to give a test set of 160,146 molecules. The original version of the script took 95 mins, using the same test set, version 2 of the script took less than 3 mins! This increase in performance means that it is now practical to use the script on much larger datasets.
You can read full details and download it here.
There are many more Hints, scripts and tutorials here.
Fortran has a long history with scientific programming and so it is perhaps not surprising that overtime I mention Fortran there is an uptick in readers. FTranProjectBuilder is the only IDE specifically designed for Fortran programming on the Mac and has recently been updated to version 2.0.
This update brings improvements to the interface, context sensitive autocompletes, and in addition derived type, Intrinsic procedure, module and procedure popovers
In addition the Nocturnal Aviation Software has been updated with screenshots of the updated FTranProjectBuilder, Mac Fortran Blog and a section of free Fortran code snippets.
A while back I compiled a list of resources for Fortran on a Mac.
Polyphony is an open source software suite written in python. Its purpose is the superimposition free analysis and comparison of multiple 3D structures of the same or closely related protein molecules.
python 2.6 or later, scipy, numpy, Biopython, especially the Bio.PDB module
All following documentation assumes that you have these installed.
ipython , for interactive python scripting, matplotlib, for graph plotting, PyMOL, for interactive 3D visualisation. Open source version available on SourceForge
William R Pitt, Rinaldo W Montalvão and Tom L Blundell, BMC Bioinformatics, 2014, 15:324 doi
I recently became aware of a new company specialising in software for scientists Shazino have developed a number of interesting applications for both Mac OS X and iOS.
The best known app is PaperShip an iPad, iPhone, and Mac application designed to help you keep your articles organized with your Mendeley or Zotero library. However they also provide a couple of smaller apps that make life easier in the lab.
Laboratory Timer, Fast Counter and SciKey a scientific keyboard.
The latest addition is an electronic labNotebook called Hivebench, this is available for both MacOSX and iOS. Looking at the website it seems to be aimed at molecular biologists/biochemists, and there is a free version that allows unto 10 scientists to collaborate.
Wi-Fi syncing in Papers 3
The Papers Team have just announced that Wi-Fi syncing is now available in Papers 3, available in Papers 3.3.0 for Mac and iOS or later.
Whilst many of our users find Dropbox syncing convenient for keeping their Papers library in sync across multiple devices, users have also been asking for more flexibility. Wi-Fi library syncing is easy-to-use and keeps your devices in sync without being bound by the Cloud storage limits of services like Dropbox.
Strings in Swift 2
The latest entry on the Swift Blog discusses a change in the way Strings are handled in Swift.
SeeSAR version 3.2 released
SeeSAR 3.2 can now be used in cases where there is no protein. For example if for the analysis of a ligand-based virtual screen
Release Notes version 3.2 2015-07-24
Utilizing SeeSAR without a protein
- SeeSAR has grown from a single purpose affinity assessment tool to a multi purpose 3D structural viewer for compound design and prioritization. With this update it is now also possible to use all these nice features for 3D ligand-based projects. You may, for example, visually inspect small molecules alignments. You may filter a hit list by means of calculated and external properties...
- Big data booster, With version 3.0 we first equipped SeeSAR with database functionality. Version 3.2 comes with a load of performance enhancements that speed up the calculation by up to a factor of 5, now utilizing all available CPUs in your computer even more efficiently.
- 3D graphics enhancement, In this version we updated the graphics support and SeeSAR is now compatible with more graphics cards than ever before. Especially the compatibility with integrated graphics cards (the type most frequently found in laptop computers) - which used to be the major trouble makers - has been greatly improved.
ChEMBL python update.
Excellent blog post on the ChEMBL python update.
Accessing Open Source Malaria Data using an iPython Notebook
The Open Source Malaria project is trying a different approach to curing malaria. Guided by open source principles, everything is open and anyone can contribute. To date a lot of people around the world have made contributions and the project is at a very exciting stage. Whilst everyone can see the compounds that have been made and the biological data, it is often spread over multiple web pages and can be tricky to link molecule with identifier with data. Over the last couple of months a significant effort has been put into populating a spreadsheet with all the information.
I've recently published a Vortex script to access the information, I've now published an iPython notebook that also shows how to import the data. Why not give it a try and then contribute your findings and suggestions to the Open Source Malaria project.
Kinetiscope, interactive method for the accurate simulation of chemical reactions.
Kinetiscope is a scientific software tool that provides the bench scientist with an easy-to-use, rapid, interactive method for the accurate simulation of chemical reactions.
The program package is completely self-contained, and requires no programming or extensive user training. This lets you become immediately productive,
Kinetiscope comes with a User's Manual, a set of tutorials and an extensive library of example simulations that show you the kinds of systems that can be studied with it and that illustrate techniques for handling various types of physical situations. The library includes simulations of gas phase, solution phase and solid state reactions such as co- and terpolymerization ... radical chain-initiated polymerization (including a sample spreadsheet for extracting molecular weight distributions) ... kinetic resolution of enantiomeric mixtures ... chemistry in supercritical media ... pH-dependent model enzyme kinetics ... thermogravimetric analysis ... temperature programmed desorption ... smog chemistry ... silane chemistry in a chemical vapor deposition reactor ... model batch and flow catalytic reactors ... curing of polymers with significant volume shrinkage ... synthetic protocols for preparation of a photosensitizer ... chemical oscillators ... electrochemical reactions studied by cyclic voltammetry ... photochemical reactions from a pulse light source ... pharmacokinetics of drug dosing ... and imaging chemistry in photoresist materials.
Kinetiscope is a 64-bit application and requires Mac OS X 10.6 or above.
- D. L. Bunker, B. Garrett, T. Kliendienst and G.S. Long III, Combustion and Flame 23, 373 (1974).
- D. T. Gillespie, Journal of Computational Physics 22, 403 (1976).
Workshop on Resources for Computational Drug Discovery
I just thought I'd mention this upcoming workshop, as ever there is a top class line up.
EMBL-EBI/Wellcome Trust Workshop on Resources for Computational Drug Discovery 2-6 November 2015 Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
BioTuple Open Beta
iChemLabs the developers of ChemDoodle the very popular chemical drawing application have just announced the open beta of a new product BioTuple.
If you are looking for a bioinformatics system that encompasses all the aspects your workflow in one program, BioTuple™ is the solution for you. BioTuple works on all operating systems (both 32 and 64 bit), allows for easy importing and exporting to common biological file types, and keeps all the functions you would want organized into views. This allow you to easily switch between running an alignment, visualizing restriction sites and more in one cohesive interface
- Clean and clear graphics representations of sequences that are dynamic and responsive to keyboard and mouse input.
- Quickly and easily import sequences from external databases such as NCBI and RCSB.
- Visualization of features either manually or computer assisted for small and large sequences.
- Highly customizable parameters for pairwise and multiple sequence alignments.
- Alignment reports including phylogenetic trees, statistics, and consensus comparisons.
- Clear visualization of all reading frames for RNA and DNA sequences.
- Viewing of content analyses and properties of a given sequence.
- Visualize the 3D structure of a sequence using PDB files imported from the RCSB.
As I mentioned this is an open beta and thus offers a unique opportunity to have an input into the design of the software, so please let your friends, colleagues and students know that this tool is available to them.
You can sign up for beta testing here: http://www.biotuple.com/beta-signup.
pro Fit 7 released
pro Fit has been updated to version 7, it is a Mac OS X application for data/function analysis, plotting, and curve fitting. This is a complete rebuilding of pro Fit from the ground up to complete the transition to cocoa and the latest Mac OS X technologies.
The release notes give full details but a couple of notable features are
- 64 bit architecture: pro Fit comes as a universal binary and runs in 64 bit mode by default. If you need to run pro Fit under 32 bit (e.g. because you want to link to a 32 bit plug-in or Python module), you can set it to run under 32 bit mode by choosing Get Info in the Finder.
- Global search: It is now possible to search for a text string simultaneously in all text, data, and drawing windows.
- Sandboxing: pro Fit 7 is a sandboxed application, supporting all standard security features offered by the OS. As a side effect, the location of the plug-in folder has changed. To locate it, choose "Open user's plug-in folder" from the "Customize" menu.
- Scripting: pro Fit 7 changed the interfaces to some commands, which sometimes required that some of the programming interfaces be modified, too. In addition, we harmonized some naming conventions in our programming interfaces. Please see the "programming" read me file for more details.
- The fitting engine now can (optionally) use long-double precision for enhanced accuracy.
- pro Fit now supports high-resolution images on retina displays.
Sandboxing does of course mean a few changes.
pro Fit cannot access files outside its application container without explicit user permission. The application container is found under "~/Library/Containers/com.quansoft.profit". Therefore:
If you are running a script that accesses files outside pro Fit's containers, e.g. in your Documents folder, you must grant pro Fit explicit permission to do so: Choose Preferences form the pro Fit menu, and navigate to the tab Security. Then, add the desired directory to the list of accessible directories. The permission will be permanently stored, i.e. it will persist even if you restart pro Fit.
The "pro Fit plug-ins" folder, which contains scripts and plug-ins to be automatically loaded during start-up, is now placed in pro Fit's container (under ~/Library/Containers/com.quansoft.profit/Data/Library/Application Support/com.quansoft.profit/pro Fit plug-ins). To navigate to that folder, choose "Open User's Plug-in folder" from the cutomize menu.
There is a list of data analysis tools for Mac OS X here.
myChEMBL and Docker under MacOSX
Following on from the release of ChEMBL 20 earlier in the year we now see the release of the MyChEMBL virtual machines supporting a CentOS-based image, along with the existing Ubuntu version. What might be of interest to Mac OS X users is are myChEMBL Docker images.
Docker is an open platform for building, shipping and running distributed application. Docker scontainers wrap up a piece of software in a complete filesystem that contains everything it needs to run: code, runtime, system tools, system libraries – anything you can install on a server. This guarantees that it will always run the same, regardless of the environment it is running in. Installation under Linux is straightforward and instructions for Mac OS X are provided.
Installation on OS X is more complicated. This is because the standard OS X installation downloads and configures VirtualBox and runs a very lightweight 64-bit Linux with docker installed. Now the problem is, that it won't work in case of myChEMBL. This is because this Virtual Machine has only 20GB of available disk space and our myChEMBL container is 23GB after decompressing. So in order to use it, you first have to resize the volume, which is explained here: https://docs.docker.com/articles/b2dvolumeresize/.
Once done the steps are very simple:
Download the MyChEMBL image from the FTP. Uncompress Load image into docker Run it
Detailed instructions are provided here
After successful completion of the steps above, you can open you browser and go to http://127.0.0.1/ if you are running docker locally or http://someotherhost/ if you are running docker on some other host. You should then be able to see myChEMBL launchpad page.
MacVector 14 released
A new version of MacVector has been released, the updated is now a 64-bit application meaning that it can take full advantage of all of the memory installed on your computer, allowing it to handle larger sequences and alignments. MacVector14 is no longer dependent on the deprecated “CarbonLib” compatibility library. This helps ensure that MacVector will continue to work with future releases of OS X where this library is likely to be removed.
Bowtie has been updated to support version 2 which can handle gaps in the aligned reads. This allows the use of much longer input reads (which typically have more indels) and provides far more accurate coverage information because, with the older version, reads with indel mismatches would be discarded even if they were "real" matches. The Primer Design (Primer3) “Test” mode now has a text output similar to the old Test PCR Primer Pair functionality, allowing you to view details of all of the possible products generated by the pair of primers. There are some cool new "Rounded Rectangle" feature graphics types. You can now directly select residues in the Map view in the default "zoom" mode. This lefts you use the Map tab for all editing operations except for actually typing residues (but you can select then click on the Editor tab to do that). MacVector now supports the new Regulatory GenBank feature type. You can import features into a sequence with files formatted using the Sequin Table format. More options in the way the sequence Editor and Map views are initialized are now saved to preferences so that MacVector “remembers” how you like to view your sequences. The cut sites and recognition sequences of restriction enzymes and now listed in the text outputs. Colored residues or background in the single sequence Editor tab are now only displayed if the underlying feature is located on the sequence line. This provides much finer control over which regions of the sequence you would like to see highlighted in color.
ChemDoodle Web Components
There is a very nice review of ChemDoodle Web Components in the latest issue of Journal of Cheminformatics 2015, 7:35 DOI
Script to remove duplicates in Vortex
When working with multiple data sets of molecules, particularly if combining them from multiple sources, one of the most common tasks is removal of duplicates. This can be a time-consuming and error prone process if carried out manually and this script should hopefully make this a much easier task.
There are many more Hints, scripts and tutorials here.
SeeSAR has been updated to version 3.1, the release notes highlight two significant new features.
SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution.
- Working with "big data" With this update we lifted the limit of handling only a maximum of 5000 poses in SeeSAR. We know that a lot of people like to do their compound analysis and prioritization after virtual screening campaigns also with much bigger sets. It is not likely that you will look at more than a couple of hundred poses, however, since the filtering (see also below) is extremely efficient, it provides quite an attractive opportunity to load all your data (not just the top x) and do your prioritization with all properties at hand right here in SeeSAR.
- Enhanced filtering Behind the scenes SeeSAR knows so much more about your compounds than what is displayed in the table. The basic stuff like no. of acceptors and donors, rotatable bonds, etc. to do the usual Lipinski-type filtering is of course available, but also more elaborate stuff like the number of hydrogen bonds formed or the number of torsions that lie outside the statistical "norm". All of these are now available for filtering to help you optimally trim down your data to find the really interesting part.
NOTE! SeeSAR project files from older versions are incompatible and cannot be loaded. By default SeeSAR puts a new version in a separate location. The recommendation is to export your data from the old project file with the old version and import it into the latest SeeSAR. This is a one-time effort, which allows you to benefit from the features of the most up-to-date version.
Findings and SZMAP updated
Findings 1.2.3 the electronic notebook has just been released. Already using Findings? Menu Findings → Check for updates...
OpenEye have just announced the release of SZMAP v1.2.1. This is a critical upgrade that fixes several bugs.
- The Water Orientation VIDA Extension now saves orientation probability data and ensemble energy, vdw and order data on probe molecules as SDData. When probes generated by this extension are written to an .sdf file, these values will be written as well.
- The Water Orientation VIDA Extension (version 1.1.3) now displays the correct water orientations for results from szmap version 1.2.0. It is also more compatible with 2D depictions in the 3D display.
- gameplan no longer crashes when all stabilization test sites clash.
- pch option -nonsymmetrized_charges now works to control AM1BCC partial charges. The default has been changed to true so as not to alter the default behavior.
- pch no longer treats CYS residues bonded through the sidechain to a non-CYS as anionic.
- pch no longer duplicates non-standard groups containing a metal (such as cofactors) and groups they are bonded to.
- The hydrogen charge on the standard water probe is now correctly listed as +0.327 not +0.237 in SZMAP Theory.
Wizard Pro Updated
The popular data analysis and plotting application has been updated New in 1.7.9:
• Fix a crash when opening a document with a Quantile column
• Fix a crash when attempting to use a column as its own join key
• Fix an occasional crash after entering or leaving Full Screen mode
• Fix a few minor interface glitches
• Bug fix: the XLS and JSON exporters did not properly respect Data Filters
• Bug fix: Time-of-day columns derived from other columns were not properly displayed in the Raw Data view
• Bug fix: weighted log-linear models sometimes produced an error
• Bug fix: a model's constant term was not included when exporting the coefficient table as XLS
• Feature: Include prediction intervals when exporting prediction tables
There is a review of Wizard Pro here.
Tabula 1.0 released
If you have ever been in the situation where supporting information for a publication is provided in PDF format then you will appreciate Tabula. Tabula allows you to extract that data into a CSV or Microsoft Excel spreadsheet using a simple, easy-to-use interface.
I've added it to the page of data analysis tools.
Mobile Science Applications
I was tidying up a couple of things on the Mobile Science site and I thought I'd just give a mention to the top 5 most upvoted applications.
1, ChemDoodle Mobile
4. Medicinal Chemistry Toolkit
5. Papers 3 for iOS
All worth having a look at.
A review of cApp
One of the most common tasks for those involved in cheminformatics is handling files containing molecular information, these files can be in a variety of file types and usually the task involved is relatively minor. cApp is Java application that provides a simple interface to a variety of everyday activities.
cApp requires JRE7 and uses the Chemistry Development Kit (CDK), an open-source Java library for chem- and bioinformatics, and associated software, JChemPaint as chemical editor, and routines developed within the Program Collection for Structural Biology and Biophysical Chemistry by the Hofmann group. Full details of cApp are described in a J Cheminformatics paper DOI.
Cresset update Torch and Forge
The update of Forge, a computational chemistry workbench for ligand-based design, includes over 170 new or improved features. Of particular note is Activity Atlas a new component enables you to summarize the SAR for a series into a visual 3D model that can be used to aid new molecule design. Forge V10.4 can now connect to an external web service, through a REST interface, to import external properties and data computed or retrieved by such web services as additional columns in the Molecules Table.
The latest version of Torch now includes Multi-parameter Optimization (MPO) options including condensing many activity and physicochemical properties into a single score representing the fit to the project profile, this has been coupled to an improved radial plot visualisation and tile display.
InChI, the IUPAC International Chemical Identifier
InChI is the International Chemical Identifier developed under the auspices of IUPAC and are intended to be unique identifiers, they are freely usable and non-proprietary; they can be computed from structural information and do not have to be assigned by some organization;most of the information in an InChI is human readable (in theory!).
A recent paper in J Cheminformatics DOI describes the design, layout and algorithms of InChI, if you want to understand or implement the code this is a great starting point.
The paper is organized as follows. First, we discuss the general concepts associated with chemical identifiers. Then we outline the design goals of InChI and our general approach, focussing on the InChI model of chemical structure and the hierarchical layered structure of the Identifier; the concept of Standard InChI is introduced. This is followed by a detailed description of each of the possible major InChI layers, accounting for molecular connectivity, charge, stereochemistry, isotopic enrichment, position of hydrogen atoms and bonding in metal compounds, and the sublayers associated with these layers. We then describe the workflow of InChI generation (normalization, canonicalization, and serialization stages), as well as generation of the compact hashed code derived from InChI (InChIKey); the related algorithms and implementation details are briefly discussed. Finally, we provide information about InChI Software, licensing, known problems/limitations, and future prospects for InChI.
The source code and documentation can also be downloaded from here http://www.inchi-trust.org/downloads/
Importing Open Source Malaria Project data
The Open Source Malaria project is trying a different approach to curing malaria. Guided by open source principles, everything is open and anyone can contribute. To date a lot of people around the world have made contributions and the project is at a very exciting stage. Whilst everyone can see the compounds that have been made and the biological data, it is often spread over multiple web pages and can be tricky to link molecule with identifier with data. Over the last couple of months a significant effort has been put into populating a spreadsheet with all the information.
Whilst this is useful for viewing results it is not ideal for trying to build predictive models. Vortex is a chemically intelligent data analysis and visualisation platform. This script provides a one-click access to the OSM data and creates a workspace containing all the data, and since it is linked to the live spreadsheet you will always have access to the latest data.
Installing Open Drug Discovery Toolkit (ODDT)
A recent paper in J Cheminformatics described Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field DOI a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. Open Drug Discovery Toolkit is released on a permissive 3-clause BSD license for both academic and industrial use. ODDT’s source code, additional examples and documentation are available on GitHub.
To install ODDT on a Mac you first need to install the appropriate toolkits, the easiest way is to use Homebrew, I've written a page detailing how to do this here.
Once installed you can install ODDT using PIP as described here.
The page I wrote on 3D printing has proved to be pretty popular so I thought I'd mention that the NIH 3D print exchange has been updated with new features to improve printability.
AstroPrint is a neat way to slice, store, and manage your print files in the cloud. The service works by taking your uploaded 3D model, adding supports, slicing it, and saving the gcode in your account online. You can then access, download, and print your models. It's like a combination of 3D printing software, such as Cura or Repetier Host, with cloud storage.
A cloud-based 3D mesh repair application from Netfabb. Sometimes the mesh of a model can contain errors that are hard to find, and even more difficult to fix. Holes, inverted normals, intersecting faces, and isolated pieces can all cause problems during 3D printing. These mistakes can occur frequently when models are generated from "messy" datasets, such as image stacks or CT data.
OpenEye toolkits updated
OpenEye has announced the release of OpenEye Toolkits v2015.June. These libraries include the usual support for C++, Python, C# and Java and are now available for download.
New Features Highlights:
- PDB Splitting in OEBio TK
- PAINS (Pan Assay Interference Compounds) filter in OEMolProp TK
- Matched molecular pair improvements in OEMedChem TK
- Custom ring template dictionaries in OEChem TK
- Anaconda support for easier Python toolkit installation
The recently updated AMBER tools now includes software to analyse the structure and thermodynamics of water at protein and other surfaces. In addition to 3D-RISM, AMBER Tools now includes a new method, called Grid Inhomogeneous Solvation Theory, uses the same underlying theory as WaterMap but generates 3D grids of water properties, rather than focusing on discrete hydration sites.
The method is described in this paper, Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbituril DOI.
Solvation and desolvation plays a critical role in ligand binding but can be difficult to determine computationally.
AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers.
LaTex chemistry templates updated
I've been involved in collaborations to write a couple of papers recently and when I mentioned the trials and tribulations of editing and version control when you have multiple authors someone suggested I look at Overleaf. If you are a LaTex user this looks like a very useful option, there are certainly templates for a number of chemistry journals and based on the description on the website it looks like a pretty impressive way for collaborative writing. It looks like they also support iOS.
There is a free option which would certainly be sufficient to try it out.
More news on Swift 2.0 on the Swift Blog
Today at WWDC, we announced Swift 2.0. This new version has even better performance, a new error handling API, and first-class support for availability checking. And platform APIs feel even more natural in Swift with enhancements to the Apple SDKs.
Open Source In addition to new features, the big news is that Apple will be making Swift open source later this year. We are all incredibly excited about this, and look forward to giving you a lot more information as the open source release gets nearer. Here is what we can tell you so far:
Swift source code will be released under an OSI-approved permissive license. Contributions from the community will be accepted — and encouraged. At launch we intend to contribute ports for OS X, iOS, and Linux. Source code will include the Swift compiler and standard library. We think it would be amazing for Swift to be on all your favorite platforms. We are excited about the opportunities an open source Swift creates for our industry. Baked-in safety features combined with excellent speed mean it has the chance to dramatically improve software versus using C-based languages. Swift is packed with modern features, it’s fun to write, and we believe it will get used in a lot of places. Together, we have an exciting road ahead.
Swift Open Source
Clipboard Managers for Mac OSX
I've added a couple of new additions that readers have suggested to the page of clipboard managers .
Findings Electronic Lab Notebook
I just noticed that Findings have altered their pricing structure, you can now download a free version that contains all the functionality of the full version but is limited to 20 experiments.
Findings Basic is the entry point for users that have limited needs, or newcomers that just want to try things out. With Findings Basic, you can create up to 20 experiments. The entire app is otherwise fully functional, including export and sync, and you can create and edit an unlimited number of protocols.
There is a review of Findings here
OLCF’s second OpenACC hackathon
The GPU Science page is always pretty popular so I thought I'd thought I'd mention an upcoming event.
OLCF’s second OpenACC hackathon will take place the week of October 19th, 2015
The goal of each hackathon is for current or prospective user groups of large hybrid CPU-GPU systems to send teams of 3-6 developers along with either (1) a (potentially) scalable application that needs to be ported to GPU accelerators, or (2) an application running on accelerators which needs optimization. There will be intensive mentoring during this 5-day hands-on workshop, with the goal that the teams leave with applications running on GPUs, or at least with a clear roadmap of how to get there. Our mentors come from national laboratories, universities and vendors, and besides having extensive experience in programming with OpenACC, many of them develop the OpenACC-capable compilers and help define the OpenACC standard.
The application period is now open and closes on 3 July, 2015. Space will be limited to a maximum of eight teams, with two mentors for each team. Groups will be notified about acceptance or rejection of their application by Friday, July 31, 2015. See below how to apply. Prior GPU experience is not required! Those groups whose application successfully passes the selection process will receive further information regarding registration.
MoSS Molecular Substructure Miner
MoSS is mainly a program to find frequent molecular substructures and discriminative fragments in a database of molecule descriptions. It can be used in the context of drug discovery and synthesis prediction for the purpose of analyzing the outcome of screening tests. Given a database of graphs, MoSS finds all (closed) frequent substructures, that is, all substructures that appear with a user-specified minimum frequency in the database (and do not have super-structures that occur with the same frequency).
MoSS has been included in CheS-Mapper
Poll on data analysis tools
The results of the 16th annual KDnuggets Software Poll on data analysis tools is in.
The top 10 tools by share of users were
R, 46.9% share ( 38.5% in 2014, 37% in 2013)
RapidMiner, 31.5% ( 44.2% in 2014, 39% in 2013)
SQL, 30.9% ( 25.3% in 2014, NA in 2013)
Python, 30.3% ( 19.5% in 2014, 13% in 2013)
Excel, 22.9% ( 25.8% in 2014, 28% in 2013)
KNIME, 20.0% ( 15.0% in 2014, 6% in 2013)
Hadoop, 18.4% ( 12.7% in 2014, 9% in 2013)
Tableau, 12.4% ( 9.1% in 2014, NA 2013)
SAS, 11.3 (10.9% in 2014, 10.7% in 2013)
Spark, 11.3% ( 2.6% in 2014, NA in 2013)
The results very much reflect my own interactions, whilst R has a significant installed user base and of course a vast repository of open source packages, Python seems to be gaining traction. Certainly in part because Python seems to have become the lingua franca for scientific computing.
I've always thought of KNIME and Tableau as excellent tools for implementing workflows but looking at recent iterations it is clear there is now greater emphasis on interactive analysis.
There is a listing of data analysis tools for Mac OS X here.
CheS-Mapper has been updated. CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets with small compounds. Whilst executable jar files can be downloaded from the website the source code is available on GitHub.
There is a review of an older version of Ches-Mapper here.
Gamess-US on a Raspbery Pi
GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. In an interesting development it is now possible to compile Gamess-US on the $40 Raspberry Pi, full instructions are available here. This provides a low cost system for demonstrating quantum chemistry.
To aid construction of the chemistry input WebMO-14.0, a web-based interface for computational chemistry programs, now has an App for iPhone/iPad. This allows you to compose e.g. a Gamess computation on your iPad or iPhone and send it to your Raspberry Pi (in the local network or on the web with a forwarded IP) to run the job and get the results back for visualizing and printing.
ChemSpider website update
The ChemSpider Website has been updated.
ChemSpider is a free chemical structure database providing fast text and structure search access to over 34 million structures from hundreds of data sources.
The authors kindly supply a demo web page demonstrating different chart types and functions of the SpeckTackle library. Example data is embedded in the web page (800 kb file size). Click on the buttons at the top of the page to see the data displayed. For the Chromatogram, Difference Chart and Spectral Match click the button then the Add Data button.
Highlighting a section of the spectra expands the view and mouseover on the 2D NMR spectra provides a tooltip giving chemical shifts
I've added this to the spectroscopy resources page
DataWarrior 4.1.1 is available for download, in addition to precompiled binaries all Java source files and the script to build DataWarrior on Linux/MacOSX can be downloaded for free use under the GNU public license. DataWarrior is a free data visualization and analysis program with embedded chemical intelligence.
There is a review of DataWarrior here.
A Review of Medicinal Chemistry Toolkit
The Medicinal Chemistry Toolkit is one of the best examples yet to show how mobile devices are making an impact in science. It is becoming the "swiss army knife" for medicinal chemists with an increasing calculators that are critical for drug design. To be honest I think a lot of biologists will find it useful as well.
Wizard Pro 1.7.4
The popular data analysis tool Wizard Pro has been updated to version 1.7.4.
New in 1.7.4:
- Fix a display issue in the Summary view when unchecking filters
- Fix a crash in the Predict view when a model has either no outcome variables or no explanatory variables
- Fix "Can't connect" error when attempting to connect to a database using a password containing special characters
- Support for connecting to databases over IPv6
- Support for schemas in PostgreSQL
- Support for character types in PostgreSQL
- Improved support for importing CSV files with improperly quoted values
- Improved support for importing variable labels and frequency weights from SPSS files
- Increased maximum length of exported SPSS variable labels from 120 characters to 256 characters
There is a review of Wizard Pro here, and there is a listing of data analysis tools for Mac OS X here.
I just got this message regarding MacMolPlt a graphics program for plotting 3-D molecular structures and normal modes (vibrations).
I have just finished posting the final binaries for MacMolPlt 7.6. In addition to the code changes I have had to move the home site and binaries download sites due to the impending shutdown of Google code.
This version includes the following changes:
- Energy plot window now accepts the same keystrokes as the main display window to change frames (left, right, home, end)
- Fix a parsing issue with ROHF GAMESS log files
- Account for an $EFRAG group change to allow all fragment atoms rather than only the first three.
- Fixed a crash in the frequency window (when no normal modes are present)
- Fixed the positioning of lone pairs in the builder when the coordination number plus the number of lone pairs is 5.
- Fixed a couple of parsing issues with MolDen and Molekel (mkl) files.
- Added GIF and TIFF export image formats (requires wxWidgets 2.9 or newer).
I have also reworked the 3D orbital generation code to significantly improve performance. Please report anything that doesn't look quite right.
Binaries and source files are available at: http://brettbode.github.io/wxmacmolplt/
At long last ChemDraw for Mac has been updated. The latest version now supports Mac OS X 10.10 (Yosemite) and supports the retina display.
Whereas in the past we had Std, Pro and Ultra we now have Prime and Professional and cross grades are available.
A reader just sent me the official ChemDraw 15 feature chart
The ability to search SciFinder is now available in ChemDraw Professional Mac version, and the only differences are lack of OLE editing, and the absence of the pKa LogP LogS calculations.
Findings LabNotebook Updated
The electronic lab notebook Findings has been updated to version 1.2.
Probably the big new feature is the ability to add tables to experiments, I'm sure this was a much requested feature. Also interesting to see the added areas of science, sounds like the user base is diversifying ;-)<
- New: tables in experiments and protocols. Insertion of new tables can be done using the corresponding menu item in the Format menu or the table icon in the top toolbar of a document. After creation, the cells can be navigated using the tab and shift-tab keys. For insertion/deletion of columns and rows, use the corresponding menu items in the Format menu.
- New: countdown timers. Timers can be created for any paragraph in an experiment or a protocol by clicking on the timer button in the gutter of the text view. Findings sets the duration based on the content of the paragraph, but it can also be adjusted manually using the 'gears' button. Timers can be started, paused or stopped from the text view of the experiment, from the experiment card, or from the timer panel (via the Window menu). Local notifications will be displayed when the timer is done.
- New: timestamps. A timestamp can be created for any paragraph in an experiment and will by default indicate the time at which it was created (it can be edited as needed to change the time).
- New: stopwatches. Clicking a timestamp will change it into a stopwatch, showing the time elapsed since the timestamp. It can be stopped to record the end time as well.
- New: field for 'Computer Science', subfield 'Microfabrication' in Engineering, subfield 'Proteomics'. Let us know if you have more requests for missing fields or subfields.
There are also a number of improvements and bug fixes
These features have also been added to Findings for iOS.
There is a review of Findings here.
Lucas, Molecule viewer and editor
Lucas is a novel program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus is able to visualise dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to reveal a geometrical feature or a physical quantity. The program is developed as a graphical interface for the MOLCAS program package, however its adaptive nature makes possible to use luscus with other computational program packages and chemical formats. All data files are opened via simple plug-ins which makes easy to implement a new file format in luscus. The easiness of editing molecular geometries makes luscus suitable for teaching students chemical concepts and molecular modelling.
Journal of Cheminformatics 2015, 7:16 [DOI](http://dx.doi.org/10.1186/s13321-015-0060-z}
The source code is available on Sourceforge
Point-of-care quantification of blood-borne filarial parasites with a mobile phone microscope
There is a very interesting publication in the latest issue of Science, Point-of-care quantification of blood-borne filarial parasites with a mobile phone microscope DOI describing the use of a smart phone to captures and analyzes videos of microfilarial motion in whole blood.
Parasitic worms are a major health hazard in many parts of the developing world and the drugs used to treat the disease can have serious side-effects so it is important to restrict the medicines to the appropriate patients. Researchers had previously tried developing ways to test blood for antibodies or to stain the parasites for easier identification under a microscope, but the techniques were never fast, cheap, or effective enough.
Instead they use a mobile phone microscope that uses motion—the “wriggling” motion of individual microfilariae—instead of molecular markers or stained morphology to count microfilariae in whole blood. This means that the results are available in minutes as opposed to many hours or days.
The technology uses an unmodified iPhone and readily available components, at the moment the devices are built by hand. Analysis is carried by a custom iPhone app that controls operation of the mobile phone microscope and enable one-touch counting of L. loa microfilariae in whole blood. All source code is available on GitHub.
Collaborations with the CellScope developers at UC Berkeley mean this technology is now being applied to many other applications
How CellScope Loa Works
Rack mounted MacPros
've posted a couple of entires where I've been looking at the computing power of the new MacPros however this site caught my eye because it shows how the MacPro can be rack mounted.
imgix is an image processing and delivery service that provides a supremely flexible, high performance, ultra–reliable solution to the problem of serving images on the modern internet. We operate our own hardware, run our own datacenters, and manage our own network infrastructure. At imgix‘s scale, maximizing efficiency and performance in image processing is critical for success. For this reason, we decided to incorporate Mac Pros in planning the build of our next generation image renderers. Because no existing Mac Pro server rack suited our needs, we designed and built our own.
The rack mounted Mac minis also look pretty impressive.
Photo Credit to: Miguel A. Cardona Jr. / imgix
Replacing Photoshop With NSString
A really clever way to create icons using ascii art. It is open-source and released under the MIT license on GitHub.
I think one of the real advantages of this is you can actually see the image you want to create in the code.
is rendered as..
You can read more here
Parallel CompuCell 3D
I've been asked if I could give a mention of Parallel CompuCell 3D, a multi-scale, multi- cell simulation environment.
There is a listing of publications describing the use of Parallel CompuCell 3D here.
Apple watch app to monitor chemotherapy
A limited number of cancer patients at the King’s College Hospital NHS Foundation Trust will have access to an Apple Watch app developed by tech company Medopad to support their chemotherapy.
The rheumatology department at King's College Hospital NHS Foundation Trust has adopted a smartphone app to support outpatients living with chronic arthritis.
The electronic lab notebook Findings for Mac has been updated, this free update includes a new table layout feature, and timers and timestamps. It also includes a couple of bug fixes. The iOS version has also been updated and there is now also a Findings app for the Apple watch. So if you were looking for an excuse to buy a new Apple watch this seems like the ideal reason!
There is a review of an earlier version of Findings here.
Mobile Science Updates
Orange NMR has been updated 1H NMR prediction (12 atoms restriction) added.
Allow to draw structures with S, F, Cl and Br.
13C NMR prediction accuracy improved.
ElementalDB has been updated to version 2.1 to fix a bug to improve display under iOS8. ElementalDB is a really impressive demonstration of the computational abilities of an iPad, allowing chemical structure based searching of the 1.4 million structures within ChEMBL. There is a review of ElementalDB here.
iSpartan a interesting tool for molecular modelling under iOS has been updated.
Now 64-bit enabled.
Improved performance of graphics surface code
iOS 7 improvements for Save, Search by Name, and Sketch palette
Improved notification for job errors when using the Spartan Server feature
HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales
To be honest I can't remember when I last used Perl but this publication brought back a few memories DOI.
HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods.
Source code and example scripts are available online at http:// github.com/demianriccardi/HackaMol. There is also a description of an IPerl Notebook in the supporting information.
There is also a very interesting extension HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program
Protein-Ligand Interaction Profiler
Whilst this is not a Mac application I thought I'd mention it since it seems a very nice implementation.
The Protein-Ligand Interaction Profiler (PLIP) is a web service and command line tool for fully automated characterization of non-covalent interactions between proteins and ligands in 3D structures.
You can either upload a PDB format file or use the search facility to use a PDB by protein, ligand or enzyme-commission number. You can combine multiple search terms to be more specific (AND search).
I used the PDB code 3EQB, the software correctly identified two ligands, ATP and the more interesting ligand CHEMBL485945.
You can view the results using the embedded 3D molecule viewer JSmol shown in the image below.
PLIP is based on a python command-line application. In case you plan local mass/batch processing, you may want to use this one directly. The source code can be found on PLIP on Git Hub.
I first tried this out on my desktop machine and it worked beautifully, I then tried it out on my iPad and iPhone and the website functioned exactly as expected.
I use markdown extensively on my websites, and whilst I mainly use BBEdit I do keep an eye out for new Markdown editors to add to this listing. I was recently alerted to Texts is a cross platform editor that uses plain text Markdown as file storage format. Documents can be published to PDF, HTML, DOCX, EPUB, and other formats from single source.
Scientific Applications under Yosemite
I just thought I'd like to thank all those who contributed to the Scientific Applications under Yosemite web page, many users and developers contacted me either via email or in the comments section and they certainly added information about applications that I don't have access to.
To date the page has been viewed well over 10,000 times with readers from 188 different countries. Viewers spent an average of just under two minutes on the page and it still attracts 800 pages views a month.
Given that 75% of the visitors to the site are now using Yosemite I suspect most scientists have now made the transition and I won't be updating the page any more. Once again thanks for the contributions.
BioSolveIT has just announced the release of SeeSAR 3.0.
This update of SeeSAR qualifies as major release 3, since it covers two milestones in its development. So far every SeeSAR session has started from scratch. The only way to retain molecules was to save them to file and re-load them again in a subsequent session. Needless to say that loading meant recalculating all Hyde-scores again...
Project files Starting with Version 3.0, SeeSAR allows you to store all session data in a project file. This includes the protein, ligands loaded from file and new (edited) ligands. Resuming your work on a project is now as easy as double-clicking on the project-file. As a result, everything just got a hell of a lot faster! Whilst calculating Hyde-scores for say 1000 compounds took around half an hour (depending on your hardware), loading the same information from a project file now takes only a few seconds. Note that you can also generate a project file on the command line, allowing you to outsource the calculation of Hyde-scores to a different machine. This enhancement is also a great way to exchange data and ideas with a colleague! Simply store your SeeSAR session as a project file in a commonly accessible location (e.g. a network drive). Your colleague can take a look with just a double-click.
Hyde update Hyde is quite sensitive with regards to the precise geometry of a binding pose. Even the tiniest difference in a pose can distort an anyway stretched hydrogen bond just so much that it is not recognized anymore - thereby leaving you with a huge desolvation penalty for such atoms, without the gain from the h-bond. This "sharpness" of Hyde is its greatest strength (for example by highlighting real activity cliffs), but also its greatest weakness (especially if the structure has flaws or is of low resolution). In order to minimize such troubles, we optimize each pose before the Hyde affinity assessment. We improved this optimization significantly. It is now fully flexible and with sharper clash criteria, making it suitable for docked poses as well as edited compounds. All of this as efficient as before, just perfect for interactive use.
There is a review of an earlier version of SeeSAR here
More on ResearchKit
There continue to be announcements about Apple's medical research software platform, an interview with Steve Friend gives some insights into how ResearchKit and HealthKit were born.
IBM (NYSE: IBM) today announced its Health Cloud and Watson cognitive computing capabilities will support health data entered by customers in iOS apps using Apple's ResearchKit and HealthKit frameworks. The move, which complements IBM's new Watson Health business unit, will arm medical researchers with a secure, open data storage solution, as well as access to IBM's most sophisticated data analytics capabilities.
ResearchKit is an Open Source framework developed by Apple intended to be used for building apps for medical research.
There is more information here
and the GitHub repository is here
To get the latest stable release
git clone -b stable https://github.com/ResearchKit/ResearchKit.git
Ars Technica will be reviewing in detail over the next few days.
I've added ResearchKit to the MobileScience site.
The 3rd International Workshop on OpenCL
The 3rd IWOCL (International Workshop on OpenCL) takes place at Stanford University, California from Monday 11 to Wednesday 13 May 2015, and includes the addition of an Advanced Hands-On OpenCL course to the schedule on Monday.
Acceleware will be offering two 4-day training courses in Canada. The first course will be in Calgary Alberta from May 26-29, 2015. The second course will be offered in Montreal, June 9-12, 2015. These professional four day courses are designed for programmers who are looking to develop comprehensive skills in writing and optimizing applications that fully leverage data parallel processing capabilities of GPUs.
The Khronos Group has released revision 30 of the SPIR-V specification. This revision of SPIR-V includes multiple corrections and synchronizes all token spellings to the official headers. These official C/C++ headers are available along with the specification in the registry.
The latest update to Xcode 6.3 includes Swift 1.2, latest reports suggests a significant improvement in speed.
Rather than feeling like using a computer that’s 10 years obsolete, algorithms that were borderline rate limiting running in the main UI thread just happen like they ought to. As a reality check, I re-ran the horrendously underperforming algorithm that I complained about awhile back, and rather than taking 320 seconds to calculate 7 log P values, it now gets the job done in 30 seconds.
The latest entry on the Swift blog also describes means to improve performance.
Mobile Science updated in particular I've added a collection of apps for programming as well as adding notes on a number of applications that have been updated. There are now 370 entries in the database and if you know of any that have been missed please add a comment below.
I've updated the page of clipboard managers since there have been a couple of new applications appear and some seem to be no longer available.
MOE2014.0901 Update is now available. MOE is a fully integrated molecular modelling and drug discovery software package.
MOE 2014.0901 updates:
- Option for AMBER residue name
- Append/prepend multiple residue sequence specified by single-letter names Builder:
- Added H’s inherit color if there is a consistent coloring in the residue
sddesc: New -smi:p option causes field headers to be written to the output ASCII file
- MOESVLRUNPATH now properly honored
- Combinatorial Builder now honors different attachment point locations on the same R-group
- Database Save As one entry per file mode now properly generates unique filenames
- Dock Template Forcing batch file now correctly generated
- Saved views in .moe files now properly restored
- Auto-save when Database Viewer display attributes are changed can now be disabled to prevent changes to the database file modification date when only the display is changed and not the database content
- SVL function Deprotonate now works properly
- Various MOE Project and Project Database Update bugs
- Various minor bug fixes
There are reviews of MOE available here
Moe:- Molecular modeling
Moe Update (Jan 2009):- Molecular modeling
Review of MOE (2009.10 release):- Molecular modeling
Moe Update (December 2010.10 release):- Molecular modeling
Moe Update (December 2011 release):- Molecular modeling
Moe Update (December 2012 release):- Molecular modeling
Decoy Finder 2.0
DecoyFinder has been updated to version 2.0. Decoy Finder is a graphical tool which helps finding sets of decoy molecules for a given group of active ligands. It does so by finding molecules which have a similar number of rotational bonds, hydrogen bond acceptors, hydrogen bond donors, logP value and molecular weight, but are chemically different, which is defined by a maximum Tanimoto value threshold between active ligand and decoy molecule MACCS fingerprints. Optionally, a maximum Tanimoto value threshold can be set between decoys in order to assure chemical diversity in the decoy set.
There have been some changes in the dependencies, it now needs RDKit (with OpenBabel being optional) and PyQt4 instead of PySide.
Installation of RDKit was already described in the page on setting up a Mac for Cheminformatics, and I've now added the instructions for pyqt
brew install pyqt
cinfony is a common API to several cheminformatics toolkits. It uses the Python programming language, and builds on top of Open Babel, RDKit, the CDK, Indigo, JChem, OPSIN and cheminformatics webservices. Currently it is hosted on Googlecode which is closing down. Fortunately the source code is also hosted on github, but you will need to look at the Google code site to read full details of the project. So the installation is:-
git clone https://github.com/cinfony/cinfony.git cd cinfony python setup.py install
Then download the DecoyFinder2 source, and run
A few applications have been updated over the week or so.
Wizard Pro for Mac has been updated to version 1.7.0 highlights from the update include:-
1-click Data Refresh: Suppose you've imported and cleaned your data, perhaps built a few models -- and then your data changes. Now, thanks to the new "Refresh" button in the toolbar, you can instantly update all of your analyses using fresh data from the original source. Customize how columns are matched up with a convenient popover, and feel free to move or rename the source data file on your computer -- Wizard will automatically keep an eye on it. Command-R to refresh the data, Command-E to configure the link.
Revamped menu system: Wizard has a new modular architecture that means you'll only see menus relevant to what you're doing -- that is, Raw Data, Pivot, Summary, Model, and Predict each have their own menu now. Most of the menus are more concise, so you can find what you're looking for faster.
There is a review of Wizard Pro here.
Plot2 a scientific 2D plotting program 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. The latest update fives and export bug.
MyScript Calculator for iOS, fixes problems with tutorial being played repeatedly and a drag and drop bug.
Scripting Vortex 25
Whilst most of the Vortex scripts mentioned on this site to date involve chemical structures we should not forget that Vortex is an excellent general data analytics tool and the data set does not have to include any molecular structures. Recently I was asked about the number of publications associated with a particular potential therapeutic target and it struck me that Vortex might actually be an excellent tool to investigate this.
Cymbol added to MobileScience
Cymbol is an iPad app providing fast, easy access to symbols, special characters, and scripts used in scientific writing. The application includes full sets of subscript and superscript numbers used in math, chemistry, and physics documentation. Cymbol also provides extra functionality for the iPad. A snippet editing and management tool, the app has been designed by writers for writers, providing fast, easy access to special characters not currently available on the iPad’s onscreen keyboard. You can also, put and save a variety of enhanced character sequences to the scratch pad and then paste into scientific publications.
PYMOL under Yosemite
Reading through the discussion on Scientific Applications under Yosemite it seems some people are having problems with PYMOL, I thought I'd mention that installation of PYMOL using Homebrew is included on the page describing how to set up a Mac for Cheminformatics. The page also describes how to install a wide range of other useful tools.
New playgrounds in Swift
The latest entry on the Swift blog highlights additions to the playgrounds within Xcode 6.3 beta 3.
Playgrounds are now represented within Xcode as a bundle with a disclosure triangle that reveals Resources and Sources folders when clicked. These folders contain additional content that is easily accessible from your playground’s main Swift code. To see these folders, choose View > Navigators > Show Project Navigator (or just hit Command-1)
There is an example playground that calculates Mandelbrot set which looks like fun to play with.
iOS8 hits 80%
More than 80% of students use mobile devices to study
According to this report by McGraw Hill 81% of students are now using mobile devices to study.
The rise of studying via mobile isn't simply due to the ubiquity of smartphones and tablets on campus, it's a case of mobile suiting the way students study now.
ChemStack is a collection of components that allow users to build chemically intelligent systems, such as collaboration tools, information portals, electronic laboratory notebooks, eLearning systems etc.
Some examples of useful chemical interfaces include:
- A sketcher to draw molecules
- Viewers to display molecules
- Components to display and interact with spectra
- 3D graphics engines to investigate 3D structures
- Text based input for IUPAC names and queries
There is a demo here that searches the ChEMBL database of 1.5M structures.
SeeSAR it is an interactive tool for designing/improving ligands for drug discovery from BioSolve-it, that has been recently updated. Looking through the updates it is clear they have been very receptive to user feedback.
- Solution filter, Finding interesting solutions in larger sets of compounds has become much easier in SeeSAR. Compounds can now be filtered based on any available property – allowing you to easily trim down the compound set to the most interesting subset. As before, you can browse through and sort the remaining table entries to further refine your selection. Properties can be those generated by SeeSAR (such as the Hyde affinity assessment, the torsional strain, TPSA, logP, ...) or alternatively properties loaded from an SD file.
- Joined poses, You can now join the ligands found in the protein structure, compounds loaded from file and compounds newly generated within the SeeSAR editor into one “super” table and now provide quick-links to the previous view of only those from a certain origin. This allows you to see in one table the bound ligand as a reference, the project compounds and your last round of designs. You can then select your favorites from the entire table and export these (for example for an upcoming team meeting).
- Defining the protein, SeeSAR decomposes the contents of a PDB file into chains, small molecules, waters and ions. Until now, users had to accept SeeSAR's default assignments, which is fine in the majority of cases. However, there is no rule without exception, e.g., the peptide inhibitor which is mistaken as a short chain, the small molecule which is actually a co-factor, or the solvent molecule that should be ignored. With this update, SeeSAR allows you to change these default assignments to better handle these exceptional cases, allowing you to categorize a short chain as a bound ligand, or re-assign a co-factor as a permanent part of the protein. You can also eliminate protein elements altogether.
- SMILES, PDB and MOL file support, SeeSAR now comes with with additional molecule readers that broaden the scope of the application. Aside from standard 3D molecule file formats (SDF and mol2), SeeSAR now supports 1D and 2D file formats as well as reading small molecules from PDB format. If no 3D coordinates are given, SeeSAR will calculate a clash-free, low energy conformation on the fly: with the SeeSAR positioning function you can then place such input molecules in the active site of interest. Amongst other things, this feature facilitates the importing of molecules straight from your favourite chemical drawing program and assessing such structures in in the context of your protein of interest.
There is a review of an earlier version of SeeSAR here, and a tutorial showing how to incorporate SeeSAR into a KNIME workflow.
3D printing improvements
3D printing has become a useful way to produce representations of scientific objects of interest, whether it be small molecules binding to a target protein to complete organisms.
Traditional 3D printing uses an additive process, where successive layers of material are laid down in different shapes to slowly build up the final 3 dimensional shape. This is a time-consuming process but a new process described in Science DOI aims to reduce production times considerably, at first examination this looks to be a real game changer.
We demonstrate the continuous generation of monolithic polymeric parts up to tens of centimeters in size with feature resolution below 100 micrometers. Continuous liquid interface production is achieved with an oxygen-permeable window below the ultraviolet image projection plane, which creates a “dead zone” (persistent liquid interface) where photopolymerization is inhibited between the window and the polymerizing part.
The authors have formed a company to exploit the new technology carbon3D, the website gives more details on the technology.
MyScript Calculator Updated
MyScript Calculator has been updated, MyScript Calculator performs mathematical calculations based on handwriting input.
Just write the mathematical expression on the screen then let MyScript technology perform its magic converting symbols and numbers to digital text and delivering the result in real time.
You might also be interested in Myscript MathPad which allows you to render complex handwritten mathematical expressions. The result can be shared as an image or as a LaTeX* or MathML* string for integration in your documents.
Substructure searching very large compound collections.
I described the use of the ability to script in Vortex 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. Whilst the script worked fine it was rather slow for larger datasets, in the latest tutorial you can see how to take advantage of some of the latest features in Vortex to substantially improve search speeds allowing searching of 70 million compound collections on a desktop.
Scripting Vortex 24:- Substructure searching very large compound collections.
There are many more scripts listed on the Hints and Tutorials Page.
ChemDoodle Web Components JCAMP Interpreter
Displaying spectra on the web is usually a pretty minimal experience, often simply an image file. Whilst there a number of desktop applications for viewing spectra, web-based tools were often limited to Java plugins which have now almost completely fallen out of favour.
(1) JCAMP-DX: A Standard Form for the Exchange of Infrared Spectra in Computer Readable Form ROBERT S. McDONALD and PAUL A. WILKS, JR. Appl. Spectrosc. 42(1), pp151-162, 1988
Chemistry Keyboard updated
The chemistry keyboard has been updated to improve appearance on the iPad and to correct missing greek letter. The Chemistry Keyboard is a specialized Keyboard Extension for anyone who needs to enter chemical formulae on iPad or iPhone.
Whilst I'm sure that the Apple Watch will be the major focus of todays Apple Event one thing that caught my eye was ResearchKit.
ResearchKit is a new open source framework intended to help researchers develop tools for medical research. This new framework takes advantage of the sensors and capabilities of iPhone to track movement, take measurements, and record data. There three modules to address the most common elements across different types of clinical studies: surveys, informed consent, and active tasks. These modules can be used as they are, or can be further built upon.
Health is important to all of us, so we’ve made ResearchKit open source. Now anyone can contribute to the next big medical breakthrough, regardless of their platform. An open source framework is the best way to encourage researchers to collaborate and share their apps and methods. And most important, it’s the right thing to do
ResearchKit contains five Active Task modules developed in partnership with Stanford Medicine, University of Oxford, Sage Bionetworks, and University of Rochester. The four categories include motor activities (gait, tapping), fitness (timed walk), cognition (memory tasks using touch screen), and voice .
In addition of course for passive background data collection the APIs like HealthKit and CoreMotion can be included.
There are already an Asthma app, a breast cancer recovery monitor, Diabetes and Parkinson's tracker.
Mobile Molecular Datasheet updated
The Mobile Molecular Datasheet has been updated to version 1.6.0.
Property calculation now includes Bayesian models. For individual models, the results are shown as a probability estimate, and a molecular overlay showing the atoms that contributed (ECFP6) fingerprints to the better/worse features. For whole datasheets, probabilities are calculated and stored in a column for each row. In this version, models included are: Solubility, Lipinski Probelike, hERG, KCNQ1, Bubonic Plague, Chagas Disease, Malaria and Tuberculosis.
The ability to import and create new Bayesian models will be added in a followup release.
The app has also been extended to integrate with the iCloud document picker extensions: files can be imported or exported to iCloud folders, as well as other compatible file sharing services, like Dropbox
Round trip editing
Office for Mac Preview is the open beta version of the upcoming version of Office 2016. One of the issues that crops up everytime there is an update is round-trip editing, i.e. the ability to copy and paste from a chemical drawing package into Word for example and then be able to copy and paste the structure back from Word into the chemical drawing application.
I've not tested it myself but I am assured that ChemDoodle behaves as expected.
If anyone has tested any other chemical drawing packages please let me know.
Mobile Medical Applications
With the increased interest in mobile devices for health and medical indications it is perhaps not surprising that the FDA have updated their guidance for developers who might be creating applications for mobile devices.
The Food and Drug Administration (FDA) recognizes the extensive variety of actual and potential functions of mobile apps, the rapid pace of innovation in mobile apps, and the potential benefits and risks to public health represented by these apps. The FDA is issuing this guidance document to inform manufacturers, distributors, and other entities about how the FDA intends to apply its regulatory authorities to select software applications intended for use on mobile platforms (mobile applications or “mobile apps”). Given the rapid expansion and broad applicability of mobile apps, the FDA is issuing this guidance document to clarify the subset of mobile apps to which the FDA intends to apply its authority.
The focus is on mobile apps that are viewed as medical devices.
DOCK 6 is written in C++ and is functionally separated into independent components, allowing a high degree of program flexibility. Accessory programs are written in C and Fortran 77. Source code for all programs is provided. Read the FAQ for details of installation under MacOSX.
Allen, W. J.; Balius, T. E.; Mukherjee, S.; Brozell, S. R.; Moustakas, D. T.; Lang, P. T.; Case, D. A.; Kuntz, I. D.; Rizzo, R. C. DOCK 6: Impact of New Features and Current Docking Performance. J. Comput. Chem. Submitted.
Vulkan: New graphics API
The Khronos group have announced a series of lectures describing Vulcan the new cross-platform Graphics API Vulkan: High-Efficiency GPU Graphics and Compute. Also known as the Next Generation OpenGL Initiative.
There are more details on the Kronos website.
MathMagic is an equation editor application for editing any mathematical expressions and symbols with easy-to-use graphical interface and various powerful features. MathMagic Personal Edition works well with any word processors, presentation software like Keynote or PowerPoint, DTP layout software like Adobe InDesign or QuarkXPress.
There is a video showing it in action here
There is also a MathMagic for iOS
A review of Wizard Pro
When I first started the list of data analysis packages for Mac OS X it was a fairly short list, over the years the list has grown and the diversity of packages increased. From free packages like R to enterprise applications like IBM SPSS costing thousands. Some packages are enormously powerful but have a ferocious learning curve, whilst others are very easy to use but have only very limited capabilities. Wizard is an intuitive data analysis tool, designed from the ground up to be readily accessible but still retain the power of the sophisticated command line driven applications that only seem suitable for programmers. Wizard Pro allows the user to explore the data interactively without the need to learn a programming language. Read more here.
I should have added Wizard Pro runs under Yosemite and is on the list of Yosemite compatible applications, and has just been updated to version 1.6.7 (Feb 27th).
Sharing Molecules, Reactions and DataSheets
Strict sandboxing in the early version of iOS has caused issues with sharing molecular information between applications, chemists are very used to the idea of being able to copy and paste SMILES, or open sdf, mol files with multiple desktop applications. As iOS has evolved the strategies for sharing information have been implemented and this post on Molecular Materials Informatics has a brilliant summary of the current state of play.
Methods for sharing chemical data are described: iOS apps have many different ways to pass data in and out. Making use of the numerous different ways to exchange data is essential to making cheminformatics functionality useful on mobile devices.
Developing Chemistry Apps in the Cloud
There is an interesting article in the latest issue of Bio IT World describing work to design and build applications for mobile devices.
The rapid incorporation of touch devices, such as smart phones and tablets, into our personal and business lives increases pressure on software providers to deliver technology via mobile apps.
ChemDoodle Mobile has been updated.
What's New in Version 1.5.0
- Added full 3D graphics support for 3D molecules!
- Full support for iOS8 and the new iPhone sizes
- Buttons are now larger on larger screens
- Various improvements to the sketcher
- Fixed clear button where it sometimes would not work
- Corrected bug where stereochemistry was inverted in 3D coordinate generation
- Resolved rare issue where the app would fail to load properly
- Significantly increased responsiveness
- Minor changes and fixes
ChemDoodle Mobile is the most highly rated App on the Mobile Science website and is accessed with your ChemDoodle account that is provided to you for free when you purchase ChemDoodle desktop.
CotEditor is an open source text editor
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 plain text/Markdown editors available for MacOSX and recently iOS so I’ve updated the listing of Markdown Editors.
MOSAIC is a modular toolbox for analyzing data from single molecule experiments
The interactions of single molecules with nanopores are observed by measuring changes to the ionic current that occurs when the pore changes from an unoccupied (i.e., an open channel) to an occupied state. The electrical nature of the measurement allows us to model components of the physical system with equivalent electrical elements, and describe system behaviour collectively with the circuit response.
MOSAIC is a modular toolbox for analyzing data from single molecule experiments. Primarily developed to analyze data from nanopore experiments. MOSAIC’s GUI greatly simplifies analyzing data from single-molecule nanopore experiments and provides easy access to most common algorithms and data types. MOSAIC can also be scripted using PYTHON to run multiple analyses in batch mode. It can also be integrated into Mathematica, MATLAB or IGOR Pro workflows.
Balijepalli, A. Ettedgui, J, Cornio, A. T., Robertson, J. W. F. Cheung, K. P., Kasianowicz, J. J. & Vaz, C., ACS Nano 2014, 8, 1547–1553
Datamate Numeric Processor
Datamate Numeric Processor allows you to Normalize, standardize, scale, and manage missing data and data outliers quickly and accurately.
There is a listing of data analysis tools for Mac OS X here.
OpenEye Toolkits v2015.Feb released
OpenEye have announced the release of OpenEye Toolkits v2015.Feb. These libraries include the usual support for C++, Python, C# and Java.
NEW FEATURES HIGHLIGHTS
- Depiction of protein-ligand interactions in Grapheme TK
- Improvements to matched pair analysis in OEMedChem TK
- Improved orientation options for images from OEDepict TK
- Better ring layout in OEDepict TK
- A major upgrade to the documentation system
I've just been sent details of a free open-source bioinformatics package Unipro UGENE first described in Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 2012 28: 1166-1167. doi:10.1093/bioinformatics/bts091. Commercial support is also available.
Papers for Mac updated
The popular reference management application Papers have been updated to version 3.2.7. This update includes improved syncing between multiple devices, Mendeley integration, when importing your Mendeley library, collections, annotations and keywords (tags) are now included.
Performance & Stability:
- App startup: Improvements to how the app accesses the user's library to reduce the likelihood of slow startup times, as well as improved performance during general app usage.
- Dropbox Sync: Improvements to reliability. Previously when syncing after launching the app, UI refreshes for subsequent sync operations that changed the metadata of library items that had been changed during the first sync would often not occur until relaunching the app.
- Reduces the likelihood of a crash during application startup.
- Reader: No longer crashes when closing all Reader tabs using Cmd+W after launching the app in Reader mode.
- Federated Search: No longer crashes when selecting "Others" when previously having one of the Favourite search engines selected.
- Citations: No longer crashes when generating an example citation of a single publication.
- Stability: Addressed the cause of a memory leak that could occur in certain scenarios.
- Smart Collections: Nested Smart Collections are no longer shown in the pop-over when using the "Add to collection" option. This was incorrect and improves app performance with large libraries with many Smart Collections.
- Keywords: When in the Labels mode, filtering now works correctly in the Keywords search bar.
- Dropbox Sync: Author metadata for papers newly imported on another device is now display correctly in the Info Inspector without needing to relaunch the app.
- Finder integration: Several improvements to the Finder Spotlight search feature.
- Spotlight Search: Improvements to index rebuilding to prevent a crash in rare circumstances.
- Papers 2 Import: Improvements to reliability during the import operation.
- Author editing: Resolves a bug in the Authors screen where it was possible for the "Me" author to become un-editable.
- Collections: Correct identation style for nested collections when viewed in the "Add to collection" pop-over from the Overview Inspector.
- Freehand annotations: Improvements to the selection of previously drawn freehand annotations.
There is a comprehensive listing of reference management applications for Mac here.
Chenomx NMR Suite
The latest update to the Chenomx NMR Suite has just been released, this includes a new batch processing wizard and several improvements. I checked with the developers and this update was built on a machine under Mac OS X 10.10 although the website had not yet been updated to include Yosemite compatibility.
There is a listing of spectroscopy applications here, and a comprehensive summary of compatibility of Scientific Applications under Yosemite here.
Chemistry Keyboard updated
The Chemistry Keyboard has been updated.
What's New in Version 1.0.2
- Period had been inaccessible in portrait mode.
- Split the elements flyout into 2 and filled in missing elements.
- Worked around rendering
The Chemistry Keyboard is a specialised Keyboard Extension for anyone who needs to enter chemical formulae on their iPad or iPhone.
iOS 8 hits 75%
BioBlender is now opensource
BioBlender, the molecular visualization and animation tool based on Blender, is now an Open Program on GitHub. You can find it here: https://github.com/MonZop/BioBlender.
BioBlender is an addon for Blender, aimed at providing tools for the import and elaboration of biological molecules. It consists of several functions, some executed by Blender and/or its Game Engine, and some others performed by external programs, such as PyMOL, APBS etc.
It was developed by the Scientific Visualization Unit of the Institute of Cliniclal Physiology of the CNR of Italy in Pisa, with the contribution of several colleagues.
Swift course on iTunes U
I just noticed that there is are new Swift programming courses available on iTunes U.
The outstanding Stanford University iOS development courses on iTunes U has been updated to use Swift. The first two lectures from the new “Developing iOS 8 Apps with Swift” class are now live and additional lessons will be added as they are taught. In addition there is also a new course from Plymouth University in the UK.
Data Extractor has been updated
Data Extractor has been updated to version 1.4. Data Extractor allows to extract data in a sparse format contained inside various files and collect the data you need in an internal structured table. Collected data can be exported at any time in various format (CSV, TSV, HTML, Custom). Data extractor can parse thousands and thousands of file in few seconds and collect the data inside. It uses simple smart instructions about how to recognize the data you need, how to extract them and where to put these data inside a structured table, ready to be exported.
- Usage of prefix to identify a data with data on a newline (prefix with newline at end)
- More resilient extraction algorithm
- Faster algorithm, often 10x time faster of the previous release
- Improved multithreading capabilities
- Fast adding of DataBase fields during 'Extraction Rules' editing and adding
- Extraction of data based on position (example: 3th element of a tab separated values row) at popular demand
- Solved a bug causing crash during extractions under certain circumstances
- Solved a bug with double newline at the end of files
- Solved a bug under other specific text characteristic of files to extract
- Other generic bug fixes
There are more data analysis tools here
ChEMBL 20 released
ChEMBL 20 has been released.
The updated database contains
- * 1,715,135 compound records
- * 1,463,270 compounds (of which 1,456,020 have mol files)
- * 13,520,737 activities
- * 1,148,942 assays
- * 10,774 targets
- * 59,610 source documents
A number of structural alerts have now been added these include Pfizer LINT filters, Glaxo Wellcome Hard Filters, Bristol-Myers Squibb HTS Deck Filters, NIH MLSMR Excluded Functionality Filters, University of Dundee NTD Screening Library Filters and Pan Assay Interference Compounds (PAINS) Filters. The PAINS annotation was created using the Vortex script described here.
Mobile Science Updates
Findings Lab Notebook Updated.
New: Quicklook for attachments, allowing to view images at full resolution and any type of files supported by Quicklook (Numbers, Excel, Keynote, Powerpoint, Illustrator, etc); you can enter quicklook by double-tapping on an attachment, or using the Quicklook icon in the toolbar that appears after tapping on an attachment
New: support for viewing tables (no editing yet), which can now be created in the beta version of Findings for Mac
New: improveed navigation in the app, by using a different tint color when browsing experiments (blue) and protocols (orange)
Fix: proper scrolling within the metadata view
Fix: insertion of notes or pictures now properly happens at the selected paragraph when using the paragraph toolbar (insertion using the bottom toolbar is still done at the end of the current day)
Wolfram|Alpha updated to with bug fixes.
ChemDoodle Web Components 7 is Available
iChemLabs have just announced an update to ChemDoodle Web Components. This is a major update to the ChemDoodle Web Components with new additions to the 3D features, most notably Pipe and Plank models for proteins and support for high DPI displays, such as the Apple Retina display.
The following pages show off some of the new features:
Cheminformatics on a Mac
A little while back I wrote a detailed tutorial for getting a wide variety of cheminformatics tools running on a Mac.
Someone just let me know about an issue with OSRA a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES
It turns out that OSRA requires ghostscript to process pdf images, this can be installed using brew.
brew install ghostscript
MedChem Wizard KNIME workflow
The MedChemWizard is a KNIME workflow designed to assist medicinal chemists with idea generation, ligand design and lead optimization using a number of common functional group transformations and medchem rules-of-thumb, this tutorial provided by Dr. Alastair Donald gives a detailed description of it's use.
Mobile Molecular DataSheet
The Mobile Molecular DataSheet has been updated, this is an important update and adds a number of exciting new features. There is now the ability to calculate a variety of chemical properties and add these to the data sheet. Importantly these are calculated locally on the mobile device rather than via an internet service.
The properties that are now available include:
- Molecular formula/weight, # heavy atoms, H-acceptors/donors, # rotatable bonds.
- Log P & molar refractivity: both calculated by an atom contribution method (S. A. Wildman and G. M. Crippen JCICS 39 868-873 1999), which requires implementation of substructure searching.
- Bad valences: reviews the valence counts for each of the main group atoms and reports egregious mistakes (e.g. pentavalent carbon).
- Stereochemistry: sites for R/S and E/Z stereochemistry are identified and their labels calculated, with unspecified or known ambiguous cases classified appropriately.
- Tautomers: common H-shifts are identified and the complete list of tautomeric forms are enumerated, with duplicate equivalent molecules removed, and racemised stereocentres labelled accordingly.
- PAINS filters: the original set of queries for identifying frequent hitters and other high throughput screening problem compounds is applied, and any matches are identified.
- Mass distribution: the isotope distribution is calculated for integral masses, as well as the exact mass for the base peak.
The results are also displayed on the individual molecules with bad valencies highlighted, stereochemistry labeled, and PAINS substructures highlighted.
This update really demonstrates the computing power of the mobile devices (Requires iOS8).
I have three printers and have to order three different sets of printer cartridges, why?
Swift's unprecendented growth
he latest RedMonk Programming Language Rankings are now available, these rankings have been run since 2010 using essentially the same methodology so we can compare with historical data. The plot below compares popularity of Stack Overflow and GitHub.
Whilst the top ten is pretty much as expected
Perhaps the most important change is just outside the top 20.
the growth that Swift experienced is essentially unprecedented in the history of these rankings. When we see dramatic growth from a language it typically has jumped somewhere between 5 and 10 spots, and the closer the language gets to the Top 20 or within it, the more difficult growth is to come by. And yet Swift has gone from our 68th ranked language during Q3 to number 22 this quarter, a jump of 46 spots.
Swift is an innovative new programming language for Cocoa and Cocoa Touch and you can find out more about Swift on the Apple Developer site,
Wolfram|Alpha has been updated, the release notes simply state "Design Updates".
Parts of Wolfram|Alpha are used in the Apple Siri Assistant; this app gives you access to the full power of the Wolfram|Alpha computational knowledge engine.
There is a comprehensive collection of science applications for iOS on the MobileScience site.
Alternative to OriginLab for Mac
A reader has contacted me asking for suggestions for alternatives to OriginLab that run on a Mac. Whilst you can run OriginLab under virtualisation there are many Data Analysis Packages that run under Mac OS X natively but I don't know enough about OriginLab to suggest which has similar capabilities. Any suggestions?
Data Creator updated
Data Creator has been updated to version 1.4.
Data Creator is an advanced data generator that can create table filled with pseudo-random custom content in just few clicks, absolutely invaluable when you need data to test a database of data analysis tool.
What's New in Version 1.4
- New (faster) algorithm for records creation
- Better handling of creation of a higher number of records in a single command
- Improved more informative progress toolbar for longer operations
- More commands to add, delete and set number of records
- Improved menus
- Bug fix regarding the fields table
- Bug fix regarding the record table
- Other bug fixes
- Improved general stability using a more resilient code
There is a review of Data Creator here.
SeeSAR Updated to 2.0
SeeSAR has been updated to version 2.0. SeeSAR is a really interesting tool for ligand design, it enables users to explore lingered interactions in a real-time manner. There is a review of SeeSAR here. BioSolveIT have taken a strategic decision to provide rapid and regular incremental updates which means it is always worth checking to get the latest version. However this looks to be a rather more significant update.
This update of SeeSAR qualifies as a major release, since it covers a milestone in its development. So far SeeSAR was able to assess given poses of small molecules in a protein structure. Starting with release 2.0 SeeSAR can also generate poses. Also note that the Hyde affinity assessment behind the scenes has been further improved by a variety of fixes and small changes for the benefit of more stability of the calculations. These changes may have an effect on the computed scores. If you rely on the scores resulting from a scecific version of the tool, we recommend to keep such older versions of the tool in an archive.
Pose generation SeeSAR assesses the binding affinity based on the given position of the ligand in the active site. New in major release number 2 is the introduction of ligand pose generation directly within SeeSAR. So now you can draw and save a molecule in 2D, load it and have SeeSAR predict both binding poses and the related affinity for those poses. Similarly, if you make a substantial modification to the ligand in the editor, you can now validate the original position by generating new binding poses followed by the affinity assessment.
Ring conformation sampling Significant conformational changes occasionally occurred when ring atoms were modified, reducing confidence in the Hyde estimated binding affinity. We have overcome this by implementing a conformational sampling of ring systems to identify the closest of all energetically favorable ring-conformations.
Stay focused Sometimes, the “big picture” can get lost while browsing and inspecting poses in 3D – users can now reset to a standard orientation by hitting "Space" on the keyboard or with a click on the center view button in the toolbox (located in the lower right corner).
Versions of iOS in use
Before Christmas a couple of developers contacted me about which versions of Mac OS X were used by scientists, based on website statistics and a poll I posted it looks like >80% of users have migrated to Mac OS X 10.9 or higher. There were a couple of scientists still using 10.6 because of the need for gfortran but several people pointed out that this is now compatible with the newer Mac OS X versions.
I've now been asked a similar question about mobile devices, according to Google analytics for this site for the last month, 75% of the visitors using an identified mobile device are using an iPad or iPhone. Looking at the version of operating system on those iOS devices 80% are running 8.x.x, around 15% are using 7.x.x with the remainder running earlier versions. This seems to be supported by the latest data from https://mixpanel.com/trends/ shown below, which shows >70% iOS adoption.
From a developers point of view it really underlines the need to support the latest versions of Mac OS X and iOS.
Macs in chemistry Annual site review
It is interesting to look at the Google Analytics data for the website at the end of each year to see what was popular.
Overall there were nearly 200,000 page views with around 70% of the visitors being new to the site. The visitors come from 186 different countries and spent an average of 2 mins on the site.
Around 86% are using a desktop or laptop and 14% using a mobile device (Phone or tablet). 60% of the visitors are using Mac OS, 23% Windows and 10% iOS, with remainder split between Linux, Android and a variety of alternative mobile OS. Safari, Chrome and Firefox are the most popular browsers.
As might have been expected the most popular blog entry was the Scientific Applications under Yosemite, followed by the instructions for installing Molden and 3D stereo viewing on a Mac.
Looking at the blog categories the top 3 were Chemical Drawing, Molecular Modelling and Computational Chemistry.
The most popular review articles were Comparison of clipboard managers, Fortran on a Mac and the review of the metabolism prediction software FAME.
In the Hints and Tutorials section the most popular was the tutorial describing How to create Safari Extensions, Setting up a Mac for Cheminformatics and the ChemDoodle Reviews.
In the AppleScript Section the Curl script was the most popular, followed by the Print clipboard script.
Other popular pages include Data Analysis tools, Spectroscopy and Reference Management.
Science Apps under Yosemite
I've just updated the page detailing compatibility of science applications under Yosemite of particular note is the update of Spartan’14 version 1.1.9 that includes the new Yosemite supported driver from SafeNet.
Full details are here http://www.wavefun.com/support/spmac/supportmacLV.html