(bg:compneuro)= # Computational Neuroscience This document is intended to help newcomers to get into computational neuroscience. Note that this is a living document and it will regularly be updated. [Offers of help](https://github.com/OpenSourceBrain/Contribute/issues/3) to complete this are very welcome! ## Books 1. Neuroscience - [Cognitive Neuroscience][b_1.1], Michael S. Gazzaniga, Richard B. Ivry and George R. Mangun - [Principles of Neural Science][b_1.2], Eric Kandel 2. Computational modelling/theoretical neuroscience - [Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems][b_2.1], Peter Dayan and LF Abbott - [Methods in Neuronal Modeling: from Ions to Networks][kochsegev], C. Koch and I. Segev (eds.) - [Principles of Computational Modelling in Neuroscience][willshaw], David Sterratt, Bruce Graham, Andrew Gillies and David Willshaw (eds.) - [Neuronal Dynamics - from single neurons to networks and models of cognition][gerstner], Wulfram Gerstner, Werner M. Kistler, Richard Naud and Liam Paninski (**[freely available online!][gerstner]**) - [Computational Neuroscience: Realistic Modeling for Experimentalists][deschutter]. E. De Schutter (ed.) - [Introduction To The Theory Of Neural Computation][b_2.2], John A. Hertz, Anders S. Krogh and Richard G. Palmer - [Vision: A Computational Investigation into the Human Representation and Processing of Visual Information][b_2.3], David Marr - [The handbook of brain theory and neural networks][b_2.4], Michael A. Arbib (ed.) 3. Programming - [Matlab for Neuroscientists][b_3.1] - [SciPy and NumPy][b_3.2] - [Python for Data Analysis][b_3.3] - [Think Stats][b_3.4] - [Dive into Python][b_3.5] 4. Machine learning - [Pattern Recognition and Machine Learning][b_4.1], Christopher M Bishop - [Machine Learning, A Probabilistic perspective][b_4.2], Kevin P. Murphy [b_1.1]: http://www.amazon.com/Cognitive-Neuroscience-Biology-Mind-4th/dp/0393913481/ref=sr_1_1?s=books&ie=UTF8&qid=1457248826&sr=1-1&keywords=cognitive+neuroscience+gazzaniga [b_1.2]: http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 [b_2.1]: http://www.gatsby.ucl.ac.uk/~dayan/book/ [b_2.2]: http://www.amazon.com/Introduction-Theory-Neural-Computation-Institute/dp/0201515601 [b_2.3]: http://www.amazon.com/Vision-Computational-Investigation-Representation-Information/dp/0262514621 [b_2.4]: http://www.amazon.com/Handbook-Brain-Theory-Neural-Networks/dp/0262011972 [kochsegev]: https://mitpress.mit.edu/books/methods-neuronal-modeling [willshaw]: http://www.compneuroprinciples.org/ [gerstner]: http://neuronaldynamics.epfl.ch/ [deschutter]: http://www.amazon.co.uk/Computational-Neuroscience-Realistic-Experimentalists-Frontiers/dp/0849320682 [b_3.1]: http://www.amazon.com/MATLAB-Neuroscientists-Introduction-Scientific-Computing/dp/0123745519 [b_3.2]: http://shop.oreilly.com/product/0636920020219.do [b_3.3]: http://shop.oreilly.com/product/0636920023784.do [b_3.4]: http://greenteapress.com/thinkstats/ [b_3.5]: http://www.diveintopython.net/ [b_4.1]: http://www.amazon.com/Pattern-Recognition-Machine-Learning-Christopher/dp/8132209060/ref=pd_sim_14_4?ie=UTF8&dpID=51qDRMnf9LL&dpSrc=sims&preST=_AC_UL160_SR118%2C160_&refRID=1N99QG8VBWEBCHJ893BR [b_4.2]: https://mitpress.mit.edu/books/machine-learning-0 ## Publications 1. Review articles - Atick, J.J., 1992. [Could information theory provide an ecological theory of sensory processing?.][p_1.1] Network: Computation in neural systems, 3(2), pp.213-251. - Oztop, E., Kawato, M. and Arbib, M., 2006. [Mirror neurons and imitation: A computationally guided review.][p_1.5] Neural Networks, 19(3), pp.254-271. - Bower, J.M., 2013. [20 years of computational neuroscience.][p_1.3] New York: Springer. - Brette, R., Rudolph, M., Carnevale, T., Hines, M., Beeman, D., Bower, J.M., Diesmann, M., Morrison, A., Goodman, P.H., Harris Jr, F.C. and Zirpe, M., 2007. [Simulation of networks of spiking neurons: a review of tools and strategies.][p_1.4] Journal of computational neuroscience, 23(3), pp.349-398. 2. Classic papers - Hodgkin, A.L. and Huxley, A.F., 1952. [A quantitative description of membrane current and its application to conduction and excitation in nerve.][p_2.1] The Journal of physiology, 117(4), p.500. - McCulloch, W.S. and Pitts, W., 1943. [A logical calculus of the ideas immanent in nervous activity.][p_2.2] The bulletin of mathematical biophysics, 5(4), pp.115-133. - Donald O.Hebb, [The Organization of Behavior,][p_2.3] New York: Wiley, Introduction and Chapter 4, "The first stage of perception: growth of the assembly," pp. xi-xix, 60-78. - Lashley, K.S., 1950. [In search of the engram.][p_2.4] - Von Neumann, J. and Kurzweil, R., 2012. [The computer and the brain.][p_2.5] Yale University Press. - Rosenblatt, F., 1958. [The perceptron: a probabilistic model for information storage and organization in the brain.][p_2.6] Psychological review, 65(6), p.386 - Marr, D. and Poggio, T., 1976. [Cooperative computation of stereo disparity.][p_2.7] Science, 194(4262), pp.283-287. - Grossberg, S., 1982. [How does a brain build a cognitive code?][p_2.8] In Studies of mind and brain (pp. 1-52). Springer Netherlands. - Ackley, D.H., Hinton, G.E. and Sejnowski, T.J., 1985. [A learning algorithm for Boltzmann machines.][p_2.9] Cognitive science, 9(1), pp.147-169. [p_1.1]: http://invibe.net/biblio_database_dyva/woda/data/att/0b79.file.pdf [p_1.2]: ftp://134.76.12.4/pub/misc2/neuron/papers/nsimenv.pdf [p_1.3]: http://link.springer.com/book/10.1007/978-1-4614-1424-7 [p_1.4]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638500/ [p_1.5]: http://www.sciencedirect.com/science/article/pii/S0893608006000268 [p_2.1]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1392413/ [p_2.2]: http://www.minicomplexity.org/pubs/1943-mcculloch-pitts-bmb.pdf [p_2.3]: http://www.cs.cmu.edu/~bhiksha/courses/deeplearning/Fall.2013/slides.2014/3.Srivaths.Hebb.pdf [p_2.4]: http://gureckislab.org/courses/fall13/learnmem/papers/Lashley1950.pdf [p_2.5]: https://books.google.co.in/books/about/The_Computer_and_the_Brain.html?id=Q30MqJjRv1gC&redir_esc=y [p_2.6]: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.335.3398 [p_2.7]: http://www.dtic.mil/dtic/tr/fulltext/u2/a030748.pdf [p_2.8]: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.228.3623&rep=rep1&type=pdf [p_2.9]: http://onlinelibrary.wiley.com/doi/10.1207/s15516709cog0901_7/pdf ## Open Source Brain projects See [here](http://www.opensourcebrain.org/search_custom_field?f[]=43&op[43]=~&v[43][]=Tutorial) for a list of OSB projects which contain tutorials, exercises, etc. in computational neuroscience. ## Software 1. Modelling An overview of the main target simulators for models in Open Source Brain can be found [here](https://github.com/OpenSourceBrain/OSB_Documentation/blob/master/contents/Help/08_Simulators.md). 2. Markup Languages - A Model Description Language for Computational Neuroscience [(NeuroML)][s_1.2.1] - Systems Biology Markup Language [(SBML)][s_1.2.2] - [CellML][s_1.2.3] [s_1.2.1]: http://www.neuroml.org/home [s_1.2.2]: http://sbml.org/Main_Page [s_1.2.3]: http://www.cellml.org/ 3. Libraries: Data analysis and scientific computing - [Pandas, python][s_2.1] - [NumPy, python][s_2.2] - [SciPy, python][s_2.3] 4. Libraries: Data visualization - [matplotlib, python][s_3.1] - [prettyplotlib, python][s_3.2] - [bokeh, python][s_3.3] - [ggplot, R][s_3.4] 3. Libraries: Machine learning - [PyBrain, python][s_4.1] - [SciKit, python][s_4.2] - [Pylearn2, python][s_4.3] - [Theano, python][s_4.4] - [Nilearn, python][s_4.5] [s_2.1]: http://pandas.pydata.org [s_2.2]: http://www.numpy.org [s_2.3]: http://scipy.org/index.html [s_3.1]: http://matplotlib.org/ [s_3.2]: http://blog.olgabotvinnik.com/prettyplotlib/ [s_3.3]: http://bokeh.pydata.org/en/latest/ [s_3.4]: http://ggplot2.org/ [s_4.1]: http://pybrain.org [s_4.2]: http://scikit-learn.org/stable/ [s_4.3]: http://deeplearning.net/software/pylearn2/ [s_4.4]: http://deeplearning.net/software/theano/ [s_4.5]: http://nilearn.github.io/ ## Databases - ModelDB: model database for computational neuroscience [(ModelDB)][d_1] - Open Source Brain [(OSB)][d_2] - Digitally Reconstructed Neuron Database [(NeuroMorpho)][d_3] - Neuroscience Information Framework [(NIF)][d_4] - Brain Operation Database System [(BODB)][d_5] - BioModels Database [(BioModels)][d_6] [d_1]: https://senselab.med.yale.edu/ModelDB/ [d_2]: http://opensourcebrain.org/ [d_3]: http://neuromorpho.org/neuroMorpho/index.jsp [d_4]: http://www.neuinfo.org/about/index.shtm [d_5]: http://bodb.usc.edu/bodb/ [d_6]: http://www.ebi.ac.uk/biomodels-main/ ## Organisations - Organization for Computational Neurosciences [(OCNS)][o_1] - International Neuroinformatics Coordinating Facility [(INCF)][o_2] [o_1]: http://www.cnsorg.org/ [o_2]: http://www.incf.org/ ## Institutions, Laboratories and Research Groups 1. Asia - [Computational Neuroscience Laboratories, ATR][larg_1.1] - [RIKEN Brain Science Institute (BSI)][larg_1.2] - [Neural Computation Unit, OIST][larg_1.3] - [Computational Neuroscience Unit, OIST][larg_1.4] - [Neurophysics lab, Hebrew University of Jerusalem, Israel][larg_1.5] - [Prof. Upinder S. Bhalla, NCBS, India][larg_1.6] 2. Europe - [National Bernstein Network Computational Neuroscience][larg_2.1] - [Gatsby Computational Neuroscience Unit][larg_2.2] - [Centre for Computational Neuroscience and Cognitive Robotics (CNCR)][larg_2.3] - [Prof. Wolfgang Maass, Institute for Theoretical Computer Science, TU Graz][larg_2.4] 3. USA - [Allen Institute of Brain Science][larg_3.1] - [Swartz Center for Computational Neuroscience, UCSD, CA][larg_3.2] - [Center for the Neural Basis of Cognition][larg_3.3] - [Seung Lab, Priceton, NY][larg_3.4] - [Neural Dynamics and Computation Lab, Stanford, CA][larg_3.5] - [Center for Theoretical Neuroscience, Columbia University, NY][larg_3.6] - [Sejnowski Lab, UCSD, CA][larg_3.7] A more comprehensive list of labs, centers and researchers can be found [here](https://compneuroweb.com/labs.html). [larg_1.1]: http://www.cns.atr.jp/en/home-3/cns/ [larg_1.2]: http://www.brain.riken.jp/en/ [larg_1.3]: https://groups.oist.jp/ncu/research [larg_1.4]: https://groups.oist.jp/cnu/ [larg_1.5]: http://neurophysics.huji.ac.il/ [larg_1.6]: https://www.ncbs.res.in/faculty/bhalla-research [larg_2.1]: http://www.nncn.de/en [larg_2.2]: http://www.gatsby.ucl.ac.uk/ [larg_2.3]: http://www.birmingham.ac.uk/research/activity/cncr/index.aspx [larg_2.4]: http://www.igi.tugraz.at/maass/#Research [larg_3.1]: http://www.alleninstitute.org/our-science/brain-science/research/open-science-resources/ [larg_3.2]: http://sccn.ucsd.edu/ [larg_3.3]: http://www.cnbc.cmu.edu/computational-neuroscience [larg_3.4]: http://seunglab.org/ [larg_3.5]: http://ganguli-gang.stanford.edu/ [larg_3.6]: http://www.neurotheory.columbia.edu/index.html [larg_3.7]: http://cnl.salk.edu/ ## Mailing Lists, Blogs and News 1. Mailing lists - Computational Neuroscience [(Comp-neuro)][mlbn_1.1] - Computational and Systems Neuroscience [(Cosyne)][mlbn_1.2] - The Connectionists mailing list [(connectionists)][mlbn_1.3] 2. Blogs - [Neuroskeptic][mlbn_2.1] - [Oscillatory Thoughts][mlbn_2.2] - [The Scicurious Brain][mlbn_2.3] - [xcorr : comp neuro][mlbn_2.4] - [PLoS Neuro][mlbn_2.5] - [Brain Box][mlbn_2.6] 3. News - [Science Daily][mlbn_3.1] - [Neuroscience News][mlbn_3.2] [mlbn_1.1]: http://www.neuroinf.org/mailman/listinfo/comp-neuro [mlbn_1.2]: https://groups.google.com/forum/#!forum/cosyne-announce [mlbn_1.3]: http://www.cnbc.cmu.edu/connectionists [mlbn_2.1]: http://blogs.discovermagazine.com/neuroskeptic/#.Vt59D5x9600 [mlbn_2.2]: http://blog.ketyov.com/ [mlbn_2.3]: http://blogs.scientificamerican.com/scicurious-brain/ [mlbn_2.4]: https://xcorr.net/ [mlbn_2.5]: http://blogs.plos.org/neuro/ [mlbn_2.6]: http://the-brain-box.blogspot.in/ [mlbn_3.1]: http://www.sciencedaily.com/articles/c/computational_neuroscience.htm [mlbn_3.2]: http://neurosciencenews.com/neuroscience-terms/computational-neuroscience/ ## Online courses 1. Coursera - [Computational Neuroscience][oc_1.1] - [Machine Learning][oc_1.3] - [Synapses, Neurons and Brains][oc_1.4] 2. edX - [Fundamentals of Neuroscience, Part I][oc_2.1] - [Fundamentals of Neuroscience, Part II][oc_2.2] 3. Wulfram Gerstner - [Neuronal Dynamics - Computational Neuroscience of Single Neurons][oc_3.1] - [Modeling of Biological Neurons and Neural Networks][oc_3.2] 4. OCW MIT - [Introduction to Computational Neuroscience][oc_4.1] - [Computational Cognitive Science][oc_4.2] [oc_1.1]: https://www.coursera.org/course/compneuro [oc_1.2]: https://www.coursera.org/course/neuraldata [oc_1.3]: https://www.coursera.org/learn/machine-learning [oc_1.4]: https://www.coursera.org/course/bluebrain [oc_2.1]: https://www.edx.org/course/fundamentals-neuroscience-part-i-harvardx-mcb80-1x#.VRv8q8svD0o [oc_2.2]: https://www.edx.org/course/fundamentals-neuroscience-part-2-neurons-harvardx-mcb80-2x#.VRv9qMsvD0o [oc_3.1]: http://lcn.epfl.ch/~gerstner/NeuronalDynamics-MOOC1.html [oc_3.2]: http://lcn.epfl.ch/~gerstner/VideoLecturesGerstner.html [oc_4.1]: http://ocw.mit.edu/courses/brain-and-cognitive-sciences/9-29j-introduction-to-computational-neuroscience-spring-2004 [oc_4.2]: http://ocw.mit.edu/courses/brain-and-cognitive-sciences/9-66j-computational-cognitive-science-fall-2004/ ## Other resources - [Computational Neuroscience on the web][or_1] - [Interesting (Computational) Neuroscience papers ][or_2] - [Comments on Theoretical Neuroscience Books][or_3] - [Introductory lectures on computational neuroscience][or_4] [or_1]: https://compneuroweb.com [or_2]: http://compneuropapers.tumblr.com/ [or_3]: http://compneuro.uwaterloo.ca/research/theoretical-neuroscience/comments-on-theoretical-neuroscience-books.html [or_4]: http://www.genesis-sim.org/cnslecs/cnslecs.html