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Instructional video for https://icg.neurotheory.ox.ac.uk. Editing and screen recording: Alex Seeholzer Writing: Alex Seeholzer, William Podlaski Voice-over: GavinVoice (Fiverr)
Static website and conversion of the Neuroscience Textbook Neuronal Dynamics by Wulfram Gerstner, Werner M. Kistler, Richard Naud and Liam Paninski. http://neuronaldynamics.epfl.ch
Web application at https://icg.neurotheory.ox.ac.uk, built on linux, mysql, nginx, Python, uwsgi and Django. The D3js based javascript graphical viewer was developed in tight collaboration with phyramid.com. The backend runs analyses in NEURON, through a task-queue implemented…
After migrating to SQLalchemy 0.9.8 (python 2.7.6) I had an hour of bugfixing fun: Running this little test script below in ipython 1.2.1 with autoreload magic on, I…
http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.128101 We study an abstract model for the coevolution between mutating viruses and the adaptive immune system. In sequence space, these two populations are localized around transiently dominant…
This takes a file cmds.batch and submits every line as a shell command to the condor queue. cmds.batch [code lang=”bash”] cd working_dir;python /exec_path/script.py -param1 > logfile.log 2>&1; cd…
This is not the first time I try to get this done correctly, hopefully it will be the last. I do not like the indirect control of matplotlib’s imshow,…
Following up to this article on how to set up time machine backups to a sparsebundle located on an arbitrary SMB/AFP/CIFS network share on OSX, there came a time…
If you’re trying to follow http://wiki.gephi.org/index.php/Plugin_Quick_Start_(5_minutes) to setup a basic Gephi plugin environment in Netbeans on OSX 10.8 with JDK 1.7 you might run into some of these nice…
Trying to install NEST on a OSX 10.8 machine and getting a [code] sed: RE error: illegal byte sequence[/code] error on make install? It seems OSX Lion has some issues with…
Add several commands to queue at once [code lang=”bash”] echo “call0;call1;” | at -q b -m now [/code] Delete all queued jobs [code lang=”bash”] atrm $(atq | cut…
This took a short while to figure out, since most guides out there are written for pre OSX 10.7. I guess this should work for 10.7 and 10.8…
Since I had to use the R package smacof, yet the rest of my code usually is in python, I thought the fastest thing to do would be…
While looking for a straightforward way to visualize python cProfile profiling data I stumbled over the nice tool Gprof2Dot which uses GraphVis to generate nice graphics. I am just writing…
Just in case anybody encounters this as well, I just had a build error while trying to build gwPython though MacPorts. It seems the OSX 10.6 SDK is…
Today I decided to switch back to delicious bookmarks from Evernote, which I’ve been using a while now, but turned out to be just too slow for quick…
In my research I am currently using both Python/Scipy and Mathematica, the former for data evaluation and the latter for symbolic computations. I currently have to transfer symbolic…
As i found several descriptions on the web how to do this, and only a mixture of them worked, here’s the a guide on setting up processing with…
As michael asked for it, here it is (links to repositories for update/install in Eclipse itself – i.e. Help/Software Updates) CDT – C++ developer tools, incl code completion,…