Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Given that this seems to be such a major upgrade I thought I’d set up a spare machine to test applications before I update my main machine. I’ll update the list regularly and feel free to send in information.
I have a number of applications/libraries/toolkits installed using Homebrew and installed in usr/local, this is known to cause extended installation times for Yosemite. So don’t worry if it appears the install is stuck at 1 min remaining.
If you do use Homebrew then it is worth updating
brew update brew upgrade
Aabel 3 appears to be working fine
BBEdit version 10.5.13 and newer are compatible with Yosemite
Beaker all seems OK
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.
ChemDoodle all seems to work fine
Chimera aka UCSF Chimera versions 1.10 and higher are working on Yosemite.
Conquest and Mercury from CCDC works fine but you may need to reinstall Quartz (see below)
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.
Cytoscape 3.1.1 seems to be working fine
DataWarrior no issues
EndNote X7.2 works well with Yosemite.
Findings Electronic Notebook no issues, only small issue is that the ‘+’ button of the window does not trigger full-screen, though it can still be done via the Window menu.
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 220.127.116.11 works fine
iNMR no problems reported
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
Mathematica no issues reported
MOE works fine but you may need to reinstall Quartz (see below), no problems reported with running the license server under Yosemite.
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 18.104.22.168
- MacPyMOLX11Hybrid 22.214.171.124 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 email@example.com for a temporary alternative license procedure.
Torch no issues
VarSeq no issues
Vortex Upgraded when the developer preview came out. All works fine
The VVI products work well enough on Yosemite, but I'd like to achieve a higher level of quality for Yosemite (and iOS/iPad). There is an ongoing beta program for this product: https://itunes.apple.com/us/app/graph-ide/id904733611?mt=8 which is Graph Builder reincarnated on the iPad. There is also a beta program ramping for Graph Builder on Yosemite: https://itunes.apple.com/us/app/graph-builder/id470597599?mt=12 but a last minute interaction bug with Yosemite has delayed that for perhaps a few days. Please feel free to broadcast this information as you see fit. Beta program participation should be directed to firstname.lastname@example.org
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 25 November 2014
Another very useful features for scientific programming is the NumPy array viewer to easily get a graphical view of a NumPy array and support for matplotlib.
There is a really comprehensive support section that includes demos and screencasts .
With iOS 8 Apple now support third party custom keyboards
A custom keyboard replaces the system keyboard for users who want capabilities such as a novel text input method or the ability to enter text in a language not otherwise supported in iOS.
The Chemistry Keyboard allows users to enter chemical formulae, equations etc without having to struggle entering subscripts etc. Whilst the chemistry keyboard is an app in itself it also allows you to use the custom keyboard with other applications.
You can read more details here.