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BioWikis removed from the list

I don't want to delete this information, but it isn't so important to have it in the main list, especially when we can refer to the comprehensive list of BioWikis. Add it back if you like --Dan 04:13, 21 August 2011 (EDT)

More BioWikis

SubtiWiki 

Bacillus subtilis annotation the "wiki" way!

DictyWiki 

The database of the model organism Dictyostelium discoideum. Users can add comments and annotations about Dictyostelium genes, gene products, and other features available through dictyBase.

MicrobeWiki 

The student-edited microbiology resource.

Wikiomics 

A collection of questions and answers about bioinformatics. Wikiomics has recently been absorbed into OpenWetWare. More information.

BioWiki 

Used mostly as an online lab notebook by the Holmes lab at UC Berkeley.

WikiData 

A proposed wiki-like database for various types of structured content. See also the OmegaWiki project and WikiProteins.

Open Bioinformatics Foundation 

A non profit, volunteer run organization focused on supporting open source programming in bioinformatics.

BiNCO-wiki (Dead?)

A wiki system that stores information related to biological networks and allows all users to add or modify this information in an easy way. More information...

Link dump

http://biowiki.net/index.php/All_the_BioWiki_contest_sites http://biome.info/index.php/Main_Page http://biopedia.org/index.php/Main_Page http://bioprograms.net/ http://biocafe.net/index.php/Main_Page http://biodenmark.org/index.php/Main_Page http://bioindonesia.org/index.php/Main_Page http://bioinformatist.org/index.php/Main_Page http://biolive.org/index.php/Main_Page http://biopicture.net/index.php/Main_Page http://biosingapore.org/index.php/Main_Page http://biostructure.org/index.php/Main_Page http://web.archive.org/web/20070302150127rn_1/biotip.org/index.php/Main_Page http://biovideo.org/index.php/Main_Page http://biozine.org/index.php/Main_Page http://contactome.org/index.php/Main_Page http://diseasepedia.net/index.php/Main_Page http://ethnome.org/index.php/Main_Page http://evolomics.net/index.php/Main_Page http://expressome.org/index.php/Main_Page http://introductome.org/index.php/Main_Page http://koreansnp.org/index.php/Main_Page http://mitogenome.org/index.php/Main_Page http://mybio.net/biowiki/Main_Page http://networkbiology.org/index.php/Main_Page http://pharmanome.org/index.php/Main_Page http://primatome.org/index.php/Main_Page http://stemcellbiology.net/index.php/Main_Page http://proteinfunction.net/index.php/Main_Page http://www.bioforge.net/forge/index.jspa http://tech.groups.yahoo.com/group/biohacking/ http://biowaredb.org/site/ http://kk.org/cooltools/archives/000582.php http://ecolihub.org/ http://en.wikibooks.org/wiki/Future/Biotechnology http://en.wikibooks.org/wiki/General_Biology/Genetics/Recombinant_DNA_Technology http://www.nexusresearchgroup.com/technical_data/carter.htm http://openwetware.org/wiki/Main_Page http://rsss.anu.edu.au/~janeth/home.html http://biohackery.com/ http://web.archive.org/web/20070420204234/http://www.dnahack.com/ http://biobricks.org/ (Endy just added some new mailing lists!)

Some other stuff.

http://openprosthetics.org/ http://obofoundry.org/ http://www.open-bio.org/wiki/Main_Page http://www.bioconductor.org/ http://www.openehr.org/home.html http://openeeg.sourceforge.net/ http://open-rtms.sourceforge.net/ http://transcenmentalism.org/OpenStim/tiki-index.php http://biocyc.org/open-compounds.shtml http://opendoar.org/ http://www.opensearch.org/Home http://www.howtoforge.com/ http://www.openhardwarefoundation.org/ http://www.ohloh.net/ http://www.earlham.edu/~peters/

-- Kanzure 04:53, 28 January 2008 (KST)

Oops. Do not forget

http://en.wikipedia.org/wiki/Synthetic_biology http://syntheticbiology.org/ http://www.syntheticgenomics.com/ http://heybryan.org/forums.html <-- the list of forums that I monitor (inc. many bio related sites) -- Kanzure 04:58, 28 January 2008 (KST)

http://bionumbers.org/ ( http://bionumbers.hms.harvard.edu/ )

What do we do with those ?? Should we create a categoy and start to order them ? --Pingou 00:27, 29 January 2008 (KST)

Second round (Return of the Linkdump)

Hey, I'd like to offer reactome.org and the following from the hplusroadmap wiki on computational biology:

• 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/

-- Kanzure 05:56, 16 March 2008 (KST)

Letter to 'BioWiki' practitioners ...

Something along these lines to be sent to each 'BioWiki' listed on the 'related resources' page. Also to be listed in the Nature Network 'BioWiki' group as a community hub for the BioWiki practitioners.

Dear 'BioWiki' practitioners,

nature network group - shared issues - shared goals - more communication.

Gathering information was the goal of MetaBase. For this reason information on BioWikis is particularly important... Please review your page in MetaBase.

No doubt there are other resouces that you know of that should be added to teh list on MetaBase...

Each page has been created with a minimum on content, namely, a short description, contact details and link to the homepage additionally at least one link has been provided to some other content of interest on your site.

Please review your pages entry in metabase.

Please

Please