Whilst this website is aimed at providing a resource for Mac using chemists regular readers will know that much of the content is platform agnostic and includes much code/software that will be of interest to all scientists.
I recently got a rather sad email
It seems that Third Street Software quietly disappeared, breaking the syncing for Sente (reference management).
I've also heard about a couple of other smaller software developers who are finding life very tough and it started me thinking about the status of scientific software, after exchanging emails with a number of people in the industry (many thanks for their input) I thought I'd collect a few thoughts on my blog.
You can read it here https://www.macinchem.org/reviews/scientificsoftware/software.php.
The SCINDR project aims to develop a way to connect, in real time, globally disparate researchers who are doing similar science so that they can work better and faster towards the development of new medicines
Once a researcher has their data stored on the ELN, or on any similar open database, for that matter, SCINDR would be able to detect if similar molecules, chemical reactions, biological assays or other features of importance in health research have been entered by someone else. If the robot identifies another scientist looking into similar features, it will suggest introducing the two to each other, so that they could start working together and combine their efforts and knowledge for the good of both science and the public.
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".
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
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 184.108.40.206 and this seems to fix the problem.
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
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.
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