Macs in Chemistry

Insanely Great Science

SpeckTackle

 

The latest issue of Journal of Cheminformatics has a paper that might be of interest to a variety of people involved in spectroscopy or data visualsation. SpeckTackle: JavaScript charts for spectroscopy.

We present SpeckTackle, a custom-tailored JavaScript charting library for spectroscopy in life sciences. SpeckTackle is cross-browser compatible and easy to integrate into existing resources, as we demonstrate for the MetaboLights database. Its default chart types cover common visualisation tasks following the de facto ‘look and feel’ standards for spectra visualisation.

SpeckTackle is an open-source JavaScript library to create custom-tailored charts for spectroscopy in life sciences. Implemented charts exist for mass spectrometry, one- and two-dimensional NMR, UV/VIS, IR, and general continuous data use cases such as chromatograms.

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


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DataWarrior Update

 

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.

DataWarrior2

There is a review of DataWarrior here.


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Scientific Applications under Yosemite (Update 25)

 

This will probably be the last update, the page has been viewed by over 11,000 people so it looks like it was a very worthwhile effort. Many thanks to all those who contributed.

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

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

If you do use Homebrew then it is worth updating

brew update
brew upgrade

Aabel 3 appears to be working fine

BBEdit version 10.5.13 and newer are compatible with Yosemite

Beaker all seems OK

Brainsight 2.2.12 is best used under 10.10.2

Ch Professional offers numerical computing and plotting which works for Yosemite.

ChemBioDraw versions 12, 13 and 14 all function as before. In particular round-trip editing still works! There are a couple of issues emerging * Sometimes it becomes "almost" unresponsive. Quiting and reopening the application usually fix the problem. * There is a frequent crash on quit. * Sometimes the popup window for "save as" is too large and the "save" and "cancel" buttons get outside the screen.

Update. Cambridgesoft have released a new version, ChemDraw 15.0 supports Mac OS X 10.10 (Yosemite) and supports the retina display.

ChemDoodle all seems to work fine

Chenomx NMR Suite latest version developed under Yosemite but website not yet updated.

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

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

COMSOL 5.0 works out of the box on Mac OS X 10.10 Yosemite. We now have instructions and a patch for installing and running COMSOL 4.4 Update 2 on Mac OS X 10.10 Yosemite. You can find the instructions at www.comsol.com/support/updates/comsol44p3 COMSOL 5.0 works out of the box on Mac OS X 10.10 Yosemite.

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

Cytoscape 3.1.1 seems to be working fine

DataWarrior 4.1.1 no issues

EndNote X7.2 works well with Yosemite.

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

Graph Builder has been updated to support Yosemite, the movies at http://www.vvidget.org show Graph Builder on Yosemite and also show how to build a custom data visualization application using Xcode, the Swift programming language and Graph Builder and a link to the Xcode project files to build the app.

Gravity Lab updated to allow printing under Yosemite.

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

Igor Pro version 6.3.5.5 works fine

iNMR A minor problem has been reported just once, only with the latest version of Mac OS Yosemite. When the the user opens the dialog that adds experiments to a Cross Peaks Manager, the list therein contained does not show the first item. It reappears after manual scrolling. The solution has been found and the problem will disappear completely with the next version of iNMR for Mac. If you have seen the same kind of problem in another dialog, please report it.

KaleidaGraph all OK.

LabQuest Viewer has preliminary support for Yosemite.

MacVector 13.0.6 No significant issues reported

Maestro 10.10 and the rest of Schrödinger Release 2014-4 are all Yosemite-compatible

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

Mathematica no issues reported

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

MOE works fine but you may need to reinstall Quartz (see below), no problems reported with running the license server under Yosemite, MOE 2014.0901 update runs fine.

Molden I just got this message from the developers, “I just got round to compiling molden on yosemite and everything worked as expected”

OpenBabel no issues so far

Opsin all works fine

OSRA no issues

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

Pro Fit 6.2 appears to work fine.

PhySyCalc - The only scientific and engineering calculator on the app store with units just updated.

Pybel no issues reported

PyCharm works fine

Pymol All these are confirmed to work:

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

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

PyRx 0.8 for docking works fine

RDkit no issues reported

RMN - multi-dimensional signal processing for Bruker NMR, Varian/Agilent NMR, JEOL NMR, Tecmag NMR, Chemagnetics Spinsight, and one-dimensional JCAMP datasets.

SeeSAR all seems to be working fine

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

SMARTCyp downloaded app runs fine.

Spartan 14 does not work because the Sentinel drivers are broken in Yosemite. The problem is NOT with Spartan, it is with the SafeNet developed Sentinel Run-Time Environment driver (the license manager). SafeNet has not given a definitive date when they will release an updated driver with Yosemite compatibility, but they are working on this. Best advice is to not upgrade but if you have to then contact support@wavefun.com for a temporary alternative license procedure. UPDATE Spartan’14 version 1.1.9 includes the new Yosemite supported driver from SafeNet. (http://www.wavefun.com/support/spmac/supportmacLV.html)

Torch no issues

VarSeq no issues

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

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

VMD no issues reported

WHICHCyp downloaded app runs fine

Wizard Pro is fully Yosemite compatible

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

Updated 20 May 2015

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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.

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You can read the full review here.


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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.


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