Computational biology

From Biohack

• Compneurosci
  • Compartmental modeling
    • http://www.strout.net/conical/
    • http://www.cam.cornell.edu/~rclewley/cgi-bin/moin.cgi/
    • http://vlsi.eecs.harvard.edu/research/nans.html
    • http://retina.anatomy.upenn.edu/~rob/neuronc.html
    • http://snnap.uth.tmc.edu/
    • http://www.neurophys.biomedicale.univ-paris5.fr/~graham/surf-hippo.html
    • http://www.math.pitt.edu/~bard/xpp/xpp.html
  • Compneurosci db sites
    • http://www.cerebellum.org/
    • http://www.modelersworkspace.org/channeldb/ChannelDB.html
    • http://cocomac.org/home.asp
    • http://flybrain.neurobio.arizona.edu/
    • http://leonserver.bio.uci.edu//
    • http://microcircuit.epfl.ch/
    • http://neurodatabase.org/dataserver/goto.do;jsessionid=E1ADE2F4EC3DC76803174D9F1BDE361C?page=.home
    • http://www.neurobiologie.fu-berlin.de/beebrain/default.html
    • http://neurosys.cns.montana.edu/
  • Data acquisition and control
    • http://inls.ucsd.edu/~rpinto/dynclamp.html
    • http://www.neuro.gatech.edu/mrci/
    • http://inls.ucsd.edu/~nowotny/dynclamp.html
    • http://www.bu.edu/ndl/dynamicclamp.html
  • Data analysis and visualization
    • Time series data
      • http://datathief.org/
      • http://www.cam.cornell.edu/~rclewley/DSSRT.html
      • http://klustakwik.sourceforge.net/
      • http://klusters.sourceforge.net/
      • http://neuralc.sourceforge.net/
      • http://inls.ucsd.edu/~nowotny/neuranim.html
      • http://www.uoguelph.ca/~awillms/neurofit/
      • http://sourceforge.net/projects/neurofitter/
      • http://www.neuromatic.thinkrandom.com/
      • http://keck.ucsf.edu/projects/spiff/
      • http://millerlab.ucsf.edu/Software/Spiker/spiker.html
    • http://brainmap.wustl.edu/resources/caretnew.html
    • http://www.mssm.edu/cnic/tools-neurogl.html
    • http://www.mssm.edu/cnic/tools-ns.html
    • http://neuron.duke.edu/cells/usage.html
    • http://krasnow.gmu.edu/cn3/L-Neuron/index.htm
    • http://www.neugen.org/
    • http://www.rdg.ac.uk/neuromantic/
    • http://www.imagescience.org/meijering/software/neuronj/index.html
    • http://www.personal.soton.ac.uk/dales/morpho/
    • http://cns.iaf.cnrs-gif.fr/alain_demos.html#ntscable
  • Interoperability
    • http://brainml.org/goto.do;jsessionid=91425CAD140A7D8F8D3528DFA53012B4?page=.home
    • http://www.morphml.org/
    • http://www.neuralensemble.org/trac/PyNN/
    • http://www.neuroml.org/
  • Misc
    • http://www.neuroscholar.org/
  • Realistic network modeling
    • http://askja.bu.edu/catacomb/
    • http://compneuro.uwaterloo.ca/codelibrary/codelibrary.html#NESim
    • http://www.lsm.tugraz.at/csim/
    • http://www.kinness.net/
    • http://www.nest-initiative.org/index.php/Main_Page
    • http://www-sop.inria.fr/odyssee/software/mvaspike/
    • http://brain.cse.unr.edu/ncsDocs/
    • http://neuralsimulationlanguage.org/
    • http://www.physiol.ucl.ac.uk/research/silver_a/neuroConstruct/
    • http://www.cs.usfca.edu/neurosys/
    • http://sourceforge.net/projects/pcsim/
    • http://www.sccn.ucsd.edu/~arno/spikenet/
    • http://topographica.org/Home/index.html
    • http://sourceforge.net/projects/xnbc/
  • http://home.earthlink.net/~perlewitz/sftwr.html
  • http://www.copasi.org/tiki-index.php
  • http://128.125.37.80:8080/
  • http://www.qub.buffalo.edu/wiki/index.php/Main_Page
  • http://senselab.med.yale.edu/modeldb/
  • http://www.neurogems.org/
  • http://www.neuroml.org/index.html
  • http://senselab.med.yale.edu/NeuronDB/
  • http://neuron.duke.edu/
  • http://neurospaces.sourceforge.net/
  • http://www.psics.org/
  • http://www.ebi.ac.uk/compneur-srv/meredys.html
  • http://web.njit.edu/~matveev/calc.html
  • http://www.genesis-sim.org/GENESIS/
• Model databases
  • http://doqcs.ncbs.res.in/
• http://arep.med.harvard.edu/moma/
• http://x.amath.unc.edu:16080/BioNetS/
• http://www.chemengr.ucsb.edu/~ceweb/faculty/doyle/biosens/BioSens.htm
• http://biospice.sourceforge.net/
• http://biowarehouse.ai.sri.com/
• http://www.bioinformaticsservices.com/bis/resources/cybertext/IBcont.html
• http://www.cellml.org/
• http://discov.cs.kent.edu/resources/cell/cell_modeling.html
• http://biodynamics.indiana.edu/CellModeling/AboutCellX.html
• http://rtg.cis.upenn.edu/mobies/charon/
• http://www.dbi.tju.edu/tools/biospice/dbi_tju_feb_23/
• http://www.dbi.tju.edu/dbi/mod.php?mod=forum&menu=6
• http://dev.e-cell.org/
• http://arep.med.harvard.edu/gmc/fba.html
• http://www.ee.ucla.edu/~riccardo/GeneScreen/genescreen.html
• http://geneways.genomecenter.columbia.edu/
• http://www.gepasi.org/
• http://gfit.sourceforge.net/
• http://ftp.bioinformatics.org/pub/wrair/genecite/
• http://jdesigner.org/
• http://jigcell.biol.vt.edu/parameter.html
• http://jigcell.biol.vt.edu/index.html
• http://textmine.cu-genome.org/html/index.html
• http://biodynamics.indiana.edu/CellModeling/AboutKaryote.html
• http://receptor.seas.ucla.edu/lcDNA/
• http://www.mcell.psc.edu/
• http://www.mcell.cnl.salk.edu/
• http://monod.molsci.org/
• http://bioinformatics.nyu.edu/Projects/DARPA-BioComp/index.shtml
• http://bioinformatics.nyu.edu/Projects/Simpathica/
• http://oscill8.sourceforge.net/
• http://www.dbi.tju.edu/dbi/tools/paint/
• http://www.quantumii.com/qi/qisd2.html
• http://www.sbml.org/Forums/index.php?t=register&rid=0&reg_coppa=N
• http://icb.med.cornell.edu/crt/SigPath/DetailedInformation.xml
• http://www.cds.caltech.edu/sostools/
• http://www.ebi.ac.uk/~lenov/stochsim.html
• http://sbml.org/index.php/Main_Page
• http://www.sys-bio.org/