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Neuronal dynamics: website and online book

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

Short film: Handmade (2015)

ICGenealogy: web application

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…

Weird SQLalchemy import bug: update ipython

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…

Article: Periodic versus Intermittent Adaptive Cycles in Quasispecies Coevolution

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…

Quick condor queueing from batch command files

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…

Fun with matplotlib pcolormesh: getting data&ticks to display in the right position

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,…

Using the migration assistant with a SMB/AFP/CIFS Time Machine sparsebundle on OSX 10.9 (Mavericks)

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…

Gephi plugin development on OSX 10.8

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…

Compiling NEST on OSX 10.8

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…

Useful bash commands

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…

Setting up SMB/AFP/CIFS network drive for Time Machine on OSX 10.8 (Mountain Lion)

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…

Le Smackoff: ad hoc python wrapping of R/smacof

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…

cProfile data visualization with Gprof2Dot & GraphVis

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…

Workaround for bits build error on MacPorts/OsX 10.7 Lion

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…

Import Evernote .enex files as Bookmarks into Delicious

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…

Evaluating Mathematica expressions in Python/Scipy

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…

Running Processing with OpenGL in Eclipse

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…

Useful Eclipse plugins

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,…