Publication: Mapping the function of neuronal ion channels in model and experiment

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…

Neuronal Dynamics: Python Exercises 0.2.0

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…

Preprint: Multi-contact synapses for stable networks: a spike-timing dependent model of dendritic spine plasticity and turnover

https://arxiv.org/abs/1609.05730 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…

CatCave9: “Winner” merch design

Paper: Algorithmic Composition of Melodies with Deep Recurrent Neural Networks

https://arxiv.org/abs/1606.07251 Published in the Proceedings of 1st Conference on Computer Simulation of Musical Creativity . A big challenge in algorithmic composition is to devise a model that is both easily…

Preprint: ICGenealogy: Mapping the function of neuronal ion channels in model and experiment

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,…

CatCave9: Science Monologue & Longform

Nichola Plowman (https://scholar.google.co.uk/citation…) in the CatCave9 science guest spot in CC9E03 on March 17, 2016 @ Cinema Oblo, Lausanne. Edited by: Alex Seeholzer  

Short film: Fed Up (2016)

A generalizable model of spike-timing dependent plasticity for the Neural Simulation Tool (NEST)

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…

ICGenealogy: Instructional video

Instructional video for https://icg.neurotheory.ox.ac.uk. Editing and screen recording: Alex Seeholzer Writing: Alex Seeholzer, William Podlaski Voice-over: GavinVoice (Fiverr)

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 cd working_dir;python /exec_path/script.py -param1 > logfile.log 2>&1; cd working_dir;python /exec_path/script.py…

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,…