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| ==Research==
| | __NOTOC__ |
| Current: [[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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| [[Yeast:Mating_pheromone_response_pathway|Mating pheromone response pathway]] analysis across [[Yeast|yeast]] and [[Yeast:Phylogeny|related species]].
| | ==Activities== |
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| ==Bioinformatics== | | ===Current=== |
| *[http://ds9a.nl/amazing-dna/ DNA seen through the eyes of a coder]
| | 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://biology-pages.info/ Kimball's Biology Pages]
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| ==Synthetic Biology== | | ===Previous=== |
| using analog circuits/logic in synth bio
| | *Systems Engineer at [http://www.genstruct.com/ Genstruct] |
| *digital design is modular and predictable (abstraction hierarchy)
| | *[[User:Ilya/OpenWetWare|OpenWetWare]] |
| *[[Reshma_Shetty/FAQ_and_thoughts|Reshma's thoughts]] | | *Computing at the Endy Lab: |
| *[[SB:FAQ|Synth Bio FAQ]] | | **[[User:Ilya/BioBrick aligner|BioBrick aligner]] |
| *[http://web.media.mit.edu/~vigoda/phd/phd.htm Analog Logic: Continuous-Time Analog Circuits for Statistical Signal Processing] by Ben Vigoda | | **[[Endy:Data storage|Data storage]] |
| *[[Wikipedia:Analog_circuit|Analog circuit]] Wikipedia article | | **[[User:Ilya/Lab network|Lab network]] |
| *[http://kabuki.eecs.berkeley.edu/ Research in analog IC design] | | **[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]] |
| *[http://www.falstad.com/circuit/ Circuit simulator applet] | | *[[User:Ilya/Yeast/Mating_pheromone_response_pathway|Mating pheromone response pathway]] analysis across [[User:Ilya/Yeast|yeast]] and [[User:Ilya/Yeast/Phylogeny|related species]] |
| *[http://www.circuitsage.com/ Analog design resources]
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| *[http://zone.ni.com/devzone/conceptd.nsf/webmain/D59654FA44D2F9FA86256F4A006064F3 Basic Analog Circuits - Tutorial]
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| ==OpenWetWare== | | ==Miscellaneous== |
| *[[In_the_News|Cool bio and engineering-related news]]
| | <html> |
| *[http://meta.wikimedia.org/wiki/Wikimania_2006 Wikimania 2006]: Boston, August 2006
| | <a href="http://www2.clustrmaps.com/user/3e416041"> |
| *[[Wikipedia:Wikipedia:Tools/Editing_Tools|Editing tools]], including [http://diberri.dyndns.org/html2wiki.html html2wiki] converter based on HTML::WikiConverter Perl module
| | <img style="float: right" src="http://www2.clustrmaps.com/stats/maps-no_clusters/openwetware.org-wiki-User-Ilya-thumb.jpg" /> |
| *[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.
| | </a> |
| ===Ideas===
| | </html> |
| *[[OpenWetWare:Ideas|Ideas discussion area]] - "the goal is some flexible framework where it is easy to create and modify databases on the fly, with nice user interfaces for database entry"
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| *[[OpenWetWare:Software|Software]] - flexible science databases, etc
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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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| *online spreadsheet
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| **[http://www.softwaregarden.com/wkcalpha/commonstarting.html Starting to use wikicalc]
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| **[http://irows.com/ iRows]
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| ====Semantics====
| | *[[Synthetic Biology:Semantic web ontology|Semantic Web Ontology]] for [[Synthetic Biology]] ([[User:Ilya/Registry|Registry notes]]) |
| *[http://meta.wikimedia.org/wiki/Del.icio.us-style_Tags_for_MediaWiki Del.icio.us-style Tags for MediaWiki] | | *[[User:Ilya/Notes|Notes]] |
| *[http://meta.wikimedia.org/wiki/RDF RDF] interface to MediaWiki
| | *[[User:Ilya/Todo|Todo]] |
| **A sample implementation of [http://svn.wikimedia.org/svnroot/mediawiki/trunk/extensions/RDF/ RDF extension] is in production at [[Wikitravel:Wikitravel:RDF|Wikitravel]]:
| | *[[User:Ilya/Sandbox|Sandbox]] |
| **[[Wikitravel:Wikitravel:RDF|RDF]]
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| **[[Wikitravel:Wikitravel:RDF_Expedition|RDF Expedition]]
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| *[[Wikipedia:Semantic_MediaWiki|Semantic MediaWiki]]
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| **[http://wiki.ontoworld.org/wiki/Special:Specialpages Specialpages]
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| **[http://wiki.ontoworld.org/wiki/Special:SearchTriple SearchTriple]
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| **[http://wiki.ontoworld.org/wiki/Special:SMWRelations SMWRelations]
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| **[http://wiki.ontoworld.org/wiki/Relation Relation]
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| **[http://wiki.ontoworld.org/wiki/Attribute Attribute]
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| **[http://wiki.ontoworld.org/wiki/Category:Attribute Category:Attribute]
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| **[http://wiki.ontoworld.org/wiki/Category:Datatype Category:Datatype]
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| **[http://wiki.ontoworld.org/wiki/Semantic_Wiki_Use_Cases Semantic Wiki Use Cases]
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| *[[Wikipedia:Semantic_Wiki|Semantic Wiki]]
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| *[http://meta.wikimedia.org/wiki/Flexible_Fields_for_MediaWiki Flexible Fields for MediaWiki] | |
| *[http://wiki.ontoworld.org/ Live demo 1], [http://semanticwiki.jp/jabionpedia/ live demo 2] and [http://semantic.nodix.net/2005/09/semantic-mediawiki-demo.html live demo 3]
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| *[http://platypuswiki.sourceforge.net/ Platypus Wiki] - a Semantic Wiki WikiWeb. It uses RDF (Resource Description Framework), RDF Schema and OWL (Web Ontology Language) to create ontologies and manage metadata. | |
| *[http://wiki.ontoworld.org/wiki/Built_in_Types Built in Types]
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| *[http://labs.systemone.at/wikipedia3 Wikipedia³] is a conversion of the English Wikipedia into RDF.
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| ====Searching====
| | [[Category:Steering Committee member]] [[Category:Bioinformaticians]] |
| *[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===
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| *[http://siphs.com/ Siphs] - a peer enabled search engine and online reference for the life sciences research community.
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| *[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==
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| ===Eclipse===
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| *[http://eclipse.org/webtools/index.html Eclipse Web Tools Platform (WTP)]:
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| **source editors for HTML, Javascript, CSS, JSP, SQL, XML, DTD, XSD, and WSDL
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| **graphical editors for XSD and WSDL
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| **J2EE project natures, builders, and models and a J2EE navigator
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| **a Web service wizard and explorer, and WS-I Test Tools
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| **database access and query tools and models
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| *[http://www.bioclipse.net/ Bioclipse] - an integrated biochemistry workbench
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| *[http://www.eclipse.org/jdt Java Development Tools (JDT)] subproject
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| ===Firefox===
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| *[http://biobar.mozdev.org/ Biobar]
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| *[http://lsid.mozdev.org/ LSID]
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| *[http://biofox.mozdev.org/ bioFOX]
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| ===MySQL===
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| *[http://www.cs.wcupa.edu/~rkline/mysql-java-lin.html Java/MySQL on Linux]
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| *[http://www.kitebird.com/articles/mysql-xml.html Using XML with MySQL]
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| *[http://turboajax.com/turbodbadmin.html TurboDbAdmin] - A single-page solution for exploring and editing databases from a browser.
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| *[http://dev.mysql.com/usingmysql/java/ Using MySQL with Java]
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| ===LIMS===
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| *[http://rescentris.com/ CERF Notebook] by Rescentris Ltd
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| **Capture and share files, notes, data - your entire research record
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| **21CFR11 compliant - role-based access, digital signatures, audit trails, and more
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| **Extensible - Customizable - integrate with existing solutions & databases
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| **Custom templates ensure uniform recordkeeping across your organization
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| **Windows, Mac, Linux
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| *[http://www.waters.com/WatersDivision/ContentD.asp?watersit=KHAS-5YRRYX eLab Notebook] by Waters Corp
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| *[http://www.waters.com/WatersDivision/ContentD.asp?watersit=JDRS-5WJQ2W&WT.svl=1 NuGenesis SDMS] "Information Management Platform" by Waters Corp
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| *[http://starlims.com/solutions/ STARLIMS] web-based LIMS
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| ==Web 2.0==
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| *[http://www.programmableweb.com/ PorgrammableWeb] - directory of mashups, APIs, tagging, etc
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| *[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."
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| *[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
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| *[[Wikipedia:JSON|JSON]] is a data interchange format that can be trivially parsed by JavaScript, with JavaScript's built in eval() procedure.
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| *[[Wikipedia:YAML|YAML]] is a data serialization and lightweight markup language that takes concepts from languages such as XML, C, Python, and Perl.
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| *[http://www.onlinetools.org/articles/unobtrusivejavascript/ Unobtrusive Javascript]
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| *[http://reddit.com/ reddit] - what's new online
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| *[http://wufoo.com/ Wufoo] - making forms easy
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| ===Life Sciences===
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| *[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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| *[http://www.citeulike.org/ CiteULike] is a free service to help academics to share, store, and organise the academic papers they are reading
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| *[http://www.connotea.org/ Connotea] is a free website to help researchers and clinicians manage and share information.
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| *[http://postgenomic.com/ Postgenomic] collates posts from life science blogs.
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| *[http://iSpecies.org/ iSpecies] - the mashup returns a page with NCBI genomics information, Yahoo images of the species, and articles culled from Google Scholar.
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| ===XMLHTTP===
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| *Google software
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| **[http://code.google.com/webtoolkit/ Google Web Toolkit (GWT)] is a Java software development framework that makes writing AJAX applications easy. With GWT, you can develop and debug AJAX applications in the Java language using the Java development tools of your choice. When you deploy your application to production, the GWT compiler translates your Java application to browser-compliant JavaScript and HTML.
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| **[http://goog-ajaxslt.sourceforge.net/ AJAXSLT] is an implementation of XSL-T in JavaScript
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| *[http://jackbe.reddit.com/ Ajax news]
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| *[http://www.w3.org/TR/XMLHttpRequest/ The XMLHttpRequest object]: W3C Working Draft
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| *[http://www.ibm.com/developerworks/opensource/library/os-ecl-ajax Two tools bring Ajax to Eclipse's Ajax Toolkit Framework]: Dojo and Zimbra
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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://goog-ajaxslt.sourceforge.net/ Google AJAXSLT] is an implementation of XSL-T in JavaScript
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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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| ===Applications===
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| *[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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| *[[Web_resources#Office_applications|Office 2.0 applications]]
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| *[http://spaces.msn.com/editorial/rayozzie/demo/liveclip/liveclipsample/clipboardexample.html Live Clipboard]
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| *[http://gotapi.com/ gotAPI] - AJAX-based documentation resource for HTML, PHP, MySQL, Perl, Ruby, etc.
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