Category: Code Page 1 of 2
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006928 Accompanying code: https://github.com/EPFL-LCN/pub-seeholzer2018 The ability to transiently memorize positions in the visual field is crucial for behavior. Models and experiments have shown that such memories can be…
This was published a while ago on Github. Langevin integrator for SDEs with constant drift and diffusion on continuous intervals with circular boundary conditions. CILES is written in…
After nearly three years, it’s finally out! https://elifesciences.org/content/6/e22152 Ion channel models are the building blocks of computational neuron models. Their biological fidelity is therefore crucial for the interpretation of…
Updated python exercises accompanying the book Neuronal Dynamics by Wulfram Gerstner, Werner M. Kistler, Richard Naud and Liam Paninski. http://neuronaldynamics-exercises.readthedocs.io https://github.com/EPFL-LCN/neuronaldynamics-exercises This version benefited mainly from the contributions…
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6041941 Excitatory synaptic connections in the adult neocortex consist of multiple synaptic contacts, almost exclusively formed on dendritic spines. Changes of dendritic spine shape and volume, a correlate…
Find the preprint on http://biorxiv.org Ion channel models are the building blocks of computational neuron models. Their biological fidelity is therefore crucial for the interpretability of simulations. However,…
https://github.com/zifeo/nest-stdpmodule This is a bachelor semester project carried out at the Laboratory of Computational Neuroscience from Swiss Institute of Technology in Lausanne. It was supervised by Alex Seeholzer…
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…
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…