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| ==Research==
| | __NOTOC__ |
| [[Synthetic Biology:Semantic web ontology|Semantic Web Ontology]] for the [http://parts.mit.edu/ Registry of Standard Biological Parts]. | | Contact Ilya Sytchev (Илья Сычёв): |
| | *<math>\mbox{hackdna}</math>@<math>\mbox{gmail.com}</math> |
| | *[[Special:Emailuser/Ilya|send me an email via OpenWetWare]] |
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| ==OpenWetWare== | | ==Activities== |
| *[http://meta.wikimedia.org/wiki/Wikimania_2006 Wikimania 2006]: Boston, August 2006
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| *[[Wikipedia:Wikipedia:Tools/Editing_Tools|Editing tools]], including [http://diberri.dyndns.org/html2wiki.html html2wiki] converter based on HTML::WikiConverter Perl module
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| *[http://science.slashdot.org/article.pl?sid=05/03/28/054225 Slashdot article]: [http://www.alphaworks.ibm.com/tech/historyflow History Flow] shows how wiki articles evolve.
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| ===Ideas===
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| *[[Ideas_for_Wiki|Ideas for Wiki]] - local version
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| *[[Wikipedia:Journal_impact_factor|Journal impact factor]] is a measure of importance of scientific journals. Something like this could be used to measure the success of the OpenWetWare?
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| *[http://www.softwaregarden.com/wkcalpha/commonstarting.html Starting to use wikicalc]
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| ====Searching====
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| *[http://wiki.lumrix.net/en/ LuMriX Wikipedia Search] - dynamic search in style of Google Suggest
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| *[http://www.wikiwax.com/ WikiWax] - your quick index to Wikipedia (based on [http://lookahead.surfwax.com/ LookAhead by SurfWax])
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| *[http://ajaxpatterns.org/Suggestion Suggestion] - Ajax Patterns
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| ====Misc====
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| *[http://www.google.com/analytics/ Google Analytics]
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| * '''blacklist''' certain pages from public viewing and/or editing ([http://mail.wikipedia.org/pipermail/mediawiki-l/2004-August/000874.html Blacklist pages from viewing])
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| * use "endy members group" to restrict access to certain pages
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| *[http://martin.jambon.free.fr/biblio_php.html Biblio.php] - citation module
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| ===Resources=== | | ===Current=== |
| *[http://siphs.com/ Siphs] - a peer enabled search engine and online reference for the life sciences research community.
| | Developing an integrated data management and analysis system for the [http://winhide.wordpress.com/2011/04/13/setting-up-a-stem-cell-commons/ Stem Cell Commons] project. |
| *[http://collaboration.wikicities.com/ MetaCollab] - a collaboration on collaboration.
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| *[http://declanbutler.info/blog/ Declan Butler], [http://declanbutler.info/blog/?p=2 Nature on blogging in science]
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| *[http://wikiomics.org/ Wikinomics] - an open documentation initiative in the field of bioinformatics and systems biology.
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| *[http://www.biocrawler.com/ Biology Wiki]
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| *[http://nodalpoint.org/ Nodalpoint] - a bioinformatics weblog.
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| *[http://taqdot.org/ taqdot] - news for the open source and synthetic biology community.
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| ==Software== | | ===Previous=== |
| ===Firefox===
| | *Systems Engineer at [http://www.genstruct.com/ Genstruct] |
| *[http://biobar.mozdev.org/ Biobar] | | *[[User:Ilya/OpenWetWare|OpenWetWare]] |
| *[http://lsid.mozdev.org/ LSID] | | *Computing at the Endy Lab: |
| *[http://biofox.mozdev.org/ bioFOX] | | **[[User:Ilya/BioBrick aligner|BioBrick aligner]] |
| ===MySQL===
| | **[[Endy:Data storage|Data storage]] |
| *[http://www.cs.wcupa.edu/~rkline/mysql-java-lin.html Java/MySQL on Linux] | | **[[User:Ilya/Lab network|Lab network]] |
| *[http://www.kitebird.com/articles/mysql-xml.html Using XML with MySQL] | | **[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]] |
| *[http://turboajax.com/turbodbadmin.html TurboDbAdmin] - A single-page solution for exploring and editing databases from a browser.
| | *[[User:Ilya/Yeast/Mating_pheromone_response_pathway|Mating pheromone response pathway]] analysis across [[User:Ilya/Yeast|yeast]] and [[User:Ilya/Yeast/Phylogeny|related species]] |
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| ==Web 2.0== | | ==Miscellaneous== |
| *[http://www.paulgraham.com/web20.html Web 2.0] by Paul Graham: "Web 2.0 means using the web the way it's meant to be used. The "trends" we're seeing now are simply the inherent nature of the web emerging from under the broken models that got imposed on it during the Bubble."
| | <html> |
| *[http://www.oreillynet.com/pub/a/oreilly/tim/news/2005/09/30/what-is-web-20.html What Is Web 2.0] by Tim O'Reilly
| | <a href="http://www2.clustrmaps.com/user/3e416041"> |
| *[[Wikipedia:JSON|JSON]] is a data interchange format that can be trivially parsed by JavaScript, with JavaScript's built in eval() procedure.
| | <img style="float: right" src="http://www2.clustrmaps.com/stats/maps-no_clusters/openwetware.org-wiki-User-Ilya-thumb.jpg" /> |
| *[[Wikipedia:YAML|YAML]] is a data serialization and lightweight markup language that takes concepts from languages such as XML, C, Python, and Perl.
| | </a> |
| *[http://www.onlinetools.org/articles/unobtrusivejavascript/ Unobtrusive Javascript]
| | </html> |
| *[http://reddit.com/ reddit] - what's new online
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| ===Life Sciences=== | |
| *[http://declanbutler.info/blog/?p=2 Nature on blogging in science]
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| **From [http://www.nature.com/nature/journal/v438/n7068/full/438547a.html Science in the web age: Science in the web age: The expanding electronic universe]: "Young scientists are often '''reluctant to express their thoughts online''' out of fear that it is somehow inappropriate, or even possibly damaging to their careers."
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| **From [http://www.nature.com/nature/journal/v438/n7068/full/438548a.html Science in the web age: Joint efforts]: "...younger researchers, in particular, are '''concerned that scientists are missing out on new ways to communicate''' with each other and the public."
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| *[http://www.biolicious.com/ Biolicious] - tagging for biology
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| ===XMLHTTP===
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| *[[Wikipedia:XMLHTTP|XMLHTTP]] is a set of APIs that can be used by JavaScript and other web browser scripting languages to transfer XML to and from a web server using HTTP.
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| *[http://adaptivepath.com/publications/essays/archives/000385.php Ajax: A New Approach to Web Applications]
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| *[http://www.modernmethod.com/sajax/ SAJAX]: Simple Ajax Toolkit
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| *[http://dojotoolkit.com/ Dojo]
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| *[http://www.intertwingly.net/blog/2005/03/16/AJAX-Considered-Harmful AJAX-Considered-Harmful]
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| *[http://www.xml.com/pub/a/2005/11/09/fixing-ajax-xmlhttprequest-considered-harmful.html Fixing AJAX]
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| *[http://twilightuniverse.com/2005/05/sack-of-ajax/ SACK]: Simple AJAX Code Kit
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| *[http://www.ajaxpatterns.org/ Ajax Patterns]
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| *[http://www.whatwg.org/specs/web-apps/current-work/ Web Applications 1.0]
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| *[http://microformats.org/wiki/rest/ahah AHAH: Asychronous HTML and HTTP]
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| ===Web Services===
| | *[[Synthetic Biology:Semantic web ontology|Semantic Web Ontology]] for [[Synthetic Biology]] ([[User:Ilya/Registry|Registry notes]]) |
| *[http://webservices.xml.com/pub/a/ws/2003/09/30/soa.html Service-Oriented Architecture] | | *[[User:Ilya/Notes|Notes]] |
| *[http://www.ebi.ac.uk/xembl/index.html EMBL in XML] | | *[[User:Ilya/Todo|Todo]] |
| | *[[User:Ilya/Sandbox|Sandbox]] |
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| ===Applications===
| | [[Category:Steering Committee member]] [[Category:Bioinformaticians]] |
| *[http://www.meebo.com/ Meebo]: Web 2.0 IM client
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| *[http://slashdot.org/article.pl?sid=05/09/29/000223&tid=126 Early AJAX Office Apps]
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| *[http://www.bindows.net/ Bindows]: desktop web applications framework
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| ===REST===
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| *[http://www.xml.com/pub/at/34 The RESTful Web] - articles from xml.com
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