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| Graduate student in [http://www.bioinformatics.northeastern.edu/ Bioinformatics] at [http://www.northeastern.edu/ Northeastern University] working in [[Endy|Endy Lab]] at [http://mit.edu/ MIT].
| | __NOTOC__ |
| | 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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| Contact: <math>\mbox{ilyas}</math>@<math>\mbox{mit.edu}</math>
| | ==Activities== |
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| |
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| ==Research== | | ===Current=== |
| *Current: [[Synthetic Biology:Semantic web ontology|Semantic Web Ontology]] for the [http://parts.mit.edu/ Registry of Standard Biological Parts].
| | 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. |
| *Previous: [[Yeast:Mating_pheromone_response_pathway|Mating pheromone response pathway]] analysis across [[Yeast|yeast]] and [[Yeast:Phylogeny|related species]].
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| *Software
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| **[http://habanero.mit.edu/cgi-bin/biobricks.pl BioBricks aligner]
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| ***aligns sequence reads (fragments) to Biobrick sequence
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| ***based on [[doi:10.1101/gr.8.9.967|Sim4]] - program for aligning cDNA with genomic DNA sequence
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| ***uses [http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/sim4.html Bioperl sim4 module]
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| ==Bioinformatics== | | ===Previous=== |
| *[http://ds9a.nl/amazing-dna/ DNA seen through the eyes of a coder] | | *Systems Engineer at [http://www.genstruct.com/ Genstruct] |
| *[http://biology-pages.info/ Kimball's Biology Pages] | | *[[User:Ilya/OpenWetWare|OpenWetWare]] |
| | *Computing at the Endy Lab: |
| | **[[User:Ilya/BioBrick aligner|BioBrick aligner]] |
| | **[[Endy:Data storage|Data storage]] |
| | **[[User:Ilya/Lab network|Lab network]] |
| | **[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]] |
| | *[[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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| ===Online tools=== | | ==Miscellaneous== |
| *[http://weblogo.berkeley.edu/logo.cgi WebLogo] - create sequence logos
| | <html> |
| *[http://www.ch.embnet.org/software/TCoffee.html T-COFFEE server]
| | <a href="http://www2.clustrmaps.com/user/3e416041"> |
| *[http://bioinformatics.uams.edu/mafft/ MAFFT]: A Program for Multiple Sequence Alignment
| | <img style="float: right" src="http://www2.clustrmaps.com/stats/maps-no_clusters/openwetware.org-wiki-User-Ilya-thumb.jpg" /> |
| | </a> |
| | </html> |
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| |
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| ==Synthetic Biology==
| | *[[Synthetic Biology:Semantic web ontology|Semantic Web Ontology]] for [[Synthetic Biology]] ([[User:Ilya/Registry|Registry notes]]) |
| *[[SB:FAQ|Synth Bio FAQ]] | | *[[User:Ilya/Notes|Notes]] |
| *[http://www.dnahack.com/ DNA Hack] - The website for Amateur Genetic Engineering | | *[[User:Ilya/Todo|Todo]] |
| | *[[User:Ilya/Sandbox|Sandbox]] |
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| |
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| ===Misc===
| | [[Category:Steering Committee member]] [[Category:Bioinformaticians]] |
| using analog circuits/logic in synth bio
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| *digital design is modular and predictable (abstraction hierarchy)
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| *[[Reshma_Shetty/FAQ_and_thoughts|Reshma's thoughts]]
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| *[http://web.media.mit.edu/~vigoda/phd/phd.htm Analog Logic: Continuous-Time Analog Circuits for Statistical Signal Processing] by Ben Vigoda
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| *[[Wikipedia:Analog_circuit|Analog circuit]] Wikipedia article
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| *[http://kabuki.eecs.berkeley.edu/ Research in analog IC design]
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| *[http://www.falstad.com/circuit/ Circuit simulator applet]
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| *[http://www.circuitsage.com/ Analog design resources]
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| *[http://zone.ni.com/devzone/conceptd.nsf/webmain/D59654FA44D2F9FA86256F4A006064F3 Basic Analog Circuits - Tutorial]
| |
| | |
| ===Press===
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| *[http://www.economist.com/business/displaystory.cfm?story_id=7854314 Life 2.0]
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| | |
| ==OpenWetWare==
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| *[[In_the_News|Cool bio and engineering-related news]]
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| *[[OpenWetWare:Infrastructure]]
| |
| *[http://meta.wikimedia.org/wiki/Wikimania_2006 Wikimania 2006]: Boston, August 2006.
| |
| | |
| *[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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| *[http://semapedia.org/ Semapedia] - connecting virtual and physical worlds
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| *[http://en.wikibooks.org/wiki/Wiki_Science Wiki Science] is the study of how the phenomenon of wikis, and free, open collaborative works in general (like free software and open source), are growing, changing and adapting.
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| *[http://www.wikimatrix.org/ WikiMatrix] - wiki software comparison
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| | |
| ===Tools===
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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://isaacnewton.princeton.edu/index.php/Help:Bulk_Uploads Bulk image uploads], [http://commons.wikimedia.org/w/index.php?title=Commons:File_upload_service/Script Perl script]
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| | |
| ====Editors====
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| *[http://wikiwyg.wikia.com/ Wikiwyg]
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| *[http://kupu.oscom.org/ Kupu]
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| **[http://www.onlamp.com/pub/a/onlamp/2005/04/28/kupu.html Rich web text editing with Kupu]
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| *[http://tinymce.moxiecode.com/ TinyMCE]
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| *[http://www.fckeditor.net/ FCKeditor]
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| *[http://wick.sourceforge.net/ WICK] web input completetion kit
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| | |
| ===CMS===
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| *arguments for using a [[Wikipedia:Content_management_system|content management system]]:
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| **there is some internal info that will not benefit from being world-writeable or even -readable
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| | |
| *[http://www.opensourcecms.com/ OpenSourceCMS] - demos
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| *[http://www.cmsmatrix.org/ The CMS Matrix] - CMS comparisons
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| *[http://www.infocopter.com/know-how/mediawiki-reference/other-cms.html a list of CMS]
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| | |
| *[http://drupal.org/node/13733 How does Drupal compare to Plone?]
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| *[http://www.drupal.org/ Drupal]
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| **PHP, MySQL, Apache
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| **easy install
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| **good for communities and hobbyst projects
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| **simple and clear internal structure, which requres minimum time for learning to use and administer it
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| **example site: [http://www.pharmer.org/ Pharmer.org]
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| **"all content is available as soon as it's written" model
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| | |
| *[http://plone.org/ Plone]
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| **Python, Zope (may use Apache)
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| **industrial, heavy-duty CMS system
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| **good for large corporate and intranet sites
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| **more powerfull permissions system
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| | |
| *[http://www.plos.org/cms/node/36 PLoS ONE] uses [http://www.topazproject.org/ TOPAZ] application framework
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| *[http://www.typo3.com/ TYPO3]
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| *[http://www.mamboserver.com/ Mambo Server]
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| *[http://mamboforge.net/ MamboForge]
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| *[http://lenya.apache.org/ Apache Lenya]- Java/XML
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| *[http://textpattern.com/ Textpattern]
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| *[http://www.magnolia.info/en/magnolia.html Magnolia]
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| *[http://www.metadot.com/ Metadot] - portal server and intranet
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| | |
| ===Development===
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| [http://meta.wikimedia.org/wiki/ParserFunctions Parser Functions]
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| | |
| ===Structure===
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| *[http://meta.wikimedia.org/wiki/Wikimedia Wikimedia]
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| *[http://meta.wikimedia.org/wiki/Board_of_Trustees Board of Trustees]
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| *[http://meta.wikimedia.org/wiki/Wikipedia_policies Wikipedia policies]
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| | |
| ===Quality===
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| [http://slashdot.org/articles/05/10/18/2135219.shtml?tid=95 Wikipedia Founder Sees Serious Quality Problems]
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| | |
| ===Ideas===
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| *[[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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| *OpenID
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| **[http://videntity.org/ Videntity] is an OpenID registrar
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| | |
| ====Semantics====
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| *[[Wikipedia:Semantic_Wiki|Semantic Wiki]] - Wikipedia article
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| *[http://www.semwiki.org/ SemWiki] - The Semantic Wiki Community
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| *[http://meta.wikimedia.org/wiki/Category:Wikidata Category:Wikidata]
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| *[http://meta.wikimedia.org/wiki/Del.icio.us-style_Tags_for_MediaWiki Del.icio.us-style Tags for MediaWiki]
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| *[http://sw.deri.org/2005/04/wikipedia/wikiont.html WikiOnt] is an an ontology to model that aims at integrating MediaWiki-based sites into the Semantic Web framework and making them machine-processable and -understandable
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| *[http://meta.wikimedia.org/wiki/RDF RDF] interface to MediaWiki
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| **[http://meta.wikimedia.org/wiki/RDF_metadata RDF metadata]
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| **[http://www.communitywiki.org/cw/DublinCoreForWiki DublinCoreForWiki] - a suggested implementation for providing DublinCore metadata in WikiEngines.
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| **A sample implementation of [http://svn.wikimedia.org/svnroot/mediawiki/trunk/extensions/RDF/ RDF extension] is in production at [[Wikitravel:Wikitravel:RDF|Wikitravel]]:
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| **[[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/ Ontoworld] - wiki for semantic web community, also a [http://wiki.ontoworld.org/index.php/Semantic_MediaWiki demo] of the [http://sourceforge.net/projects/semediawiki Semantic MediaWiki extension]
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| **[http://meta.wikimedia.org/wiki/Transwiki:Wikimania05/Paper-MK2 Wikipedia and the Semantic Web - The Missing Links] - Wikimania 2005 paper
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| **[http://wikimania2006.wikimedia.org/wiki/Proceedings:DV1 Wikipedia and the Semantic Web - Part II] - Wikimania 2006 presentation
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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/index.php/Special:Categories Special:Categories]: a complete list of all categories
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| **[http://wiki.ontoworld.org/index.php/Special:Relations Special:Relations]: a complete list of all relations; [http://wiki.ontoworld.org/wiki/Category:Relation Category:Relation] is deprecated
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| **[http://wiki.ontoworld.org/wiki/Special:Attributes Special:Attributes]: a complete list of all attributes (not just the ones with articles); [http://wiki.ontoworld.org/wiki/Category:Attribute Category:Attribute] is deprecated
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| **[http://wiki.ontoworld.org/index.php/Special:Types Special:Types]: a complete list of all datatypes; [http://wiki.ontoworld.org/wiki/Category:Datatype Category:Datatype] is deprecated
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| **[http://wiki.ontoworld.org/wiki/Semantic_Wiki_Use_Cases Semantic Wiki Use Cases]
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| **[http://wiki.ontoworld.org/index.php/Help:Inline_queries Inline queries]
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| **[http://wiki.ontoworld.org/index.php/Semantic_Wiki_State_Of_The_Art Semantic Wiki State Of The Art] - a list of existing Semantic Wiki Prototypes
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| **Knowledge structure (from [http://wiki.ontoworld.org/index.php/Help:Semantics Semantics page] @ ontoworld.org)
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| ***Categories are a means to ''classify'' articles according to certain criteria. For example, by adding <nowiki>[[Category:City]]</nowiki> to an article, the page is ''tagged'' as describing a city.
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| ***[http://wiki.ontoworld.org/wiki/Relation Relations] can be viewed as "categories for links". An article on Berlin contains a link to "Germany" that has a special meaning: it was put there since Berlin is the capital of Germany. To make this knowledge available to computer programs, one would like to "tag" the link. This is done by writing <nowiki>[[is capital of::Germany]]</nowiki>.
| |
| ***[http://wiki.ontoworld.org/wiki/Attribute Attribute]: a special type of relations/categories: <nowiki>[[population:=3,396,990]]</nowiki>
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| ***Datatypes: the prefix "Type:" is again a separate namespace that distinguishes descriptive articles about types from normal pages: <nowiki>[[has type::Type:integer]]</nowiki> to say that the special relation "has type" holds between Attribute:population and Type:integer.
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| ***Semantic templates can be used to support the consistent usage of annotations
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| *[http://www.wiktionaryz.org/ WikitionaryZ] - a universal dictionary and thesaurus that can be queried by machines and humans.
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| *[http://meta.wikimedia.org/wiki/Flexible_Fields_for_MediaWiki Flexible Fields for MediaWiki]
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| *[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://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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| *[http://www2006.org/wiki/w/Semantic_Wiki_Features Semantic Wiki features] used for WWW2006 conference: [http://wiki.ontoworld.org/index.php/Help:Semantics Creating semantic data] and [http://wiki.ontoworld.org/index.php/Help:Inline_queries Using semantic data in queries].
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| *[http://wikimodel.sourceforge.net/ RDF-compatible WikiModel]
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| *Other implementations:
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| **[http://wiksar.sf.net/ WikSAR]
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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.
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| **[http://rx4rdf.liminalzone.org/ Rx4RDF] is a set of technologies designed to make W3C's RDF more accessible and easier to use. [http://rx4rdf.liminalzone.org/Rhizome Rhizome] is a general purpose content management and delivery system that runs on [http://rx4rdf.liminalzone.org/Raccoon Raccoon]. It is dynamic and self-editable like a Wiki but uses ZML and RxML to enable structured content and editable metadata.
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| *[http://collaborate.extension.org/wiki/BettaMeta BettaMeta] - allows users to specify the available metadata in an easy to use form
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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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| | |
| ====Wiki database====
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| *[http://meta.wikimedia.org/wiki/User:HappyDog/WikiDB HappyDog/WikiDB]
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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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| *[http://collaborate.extension.org/wiki/WikiSpeller WikiSpeller] - spellcheck extension
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| | |
| ===Resources===
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| *[http://thesynapticleap.org/ The Synaptic Leap] - Open Source Biomedical Research for the 21st Century
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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]
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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://wikiomics.org/ Wikinomics] - an open documentation initiative in the field of bioinformatics and systems biology.
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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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| *[http://www.syntheticpages.org/ Synthetic Pages] - is a freely available interactive database of synthetic chemistry.
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| *[http://www.bio.net/ BIOSCI/Bionet] is a set of electronic communication forums - the bionet USENET newsgroups and parallel e-mail lists - promotes communication between professionals in the biological sciences
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| *[http://www.bioresearchonline.com/ BioResearch Online] is an online community that serves the product-sourcing and information-seeking needs of bioresearch professionals working on biopharm manufacturing, RNA, enzymatic reactions, biopharm contract manufacturing, as well as fermentation, pathogens, filtration, research and biopharm testing
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| *[http://www.nature.com/news/2006/060703/multimedia/50_science_blogs.html 50 popular science blogs] from 2006
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| *[http://biohacker.com/ Biohackers] News for life science Nerds. Biology that matters.
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| *[http://www.protocol-online.org/ Protocol Online] - your lab's reference book
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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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| *[http://www.siphs.com/ SIPHS] is a peer support network for researchers in the biological and biomedical sciences
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| *[http://cbio.mskcc.org/~hoffmann/iHOP/index.html iHOP] - a gene network for navigating the literature
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| | |
| ====Science wikis====
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| [http://en.wikibooks.org/wiki/WikiSci Wiki Sci] is an attempt for researchers to organize research efforts in a task-oriented manner, facilitating much better idea exchange.
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| *[http://species.wikimedia.org Wikispecies] is meant to become an open, free directory of species.
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| *[http://www.biocrawler.com/ Biocrawler]
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| *[http://www.fluwikie.com/ Flu Wiki]
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| *[http://www.biodirectory.com/wiki/ BioWiki]
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| *[http://isaacnewton.princeton.edu/ QED wiki], aka TigerWeb; data analysis and calendar extensions
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| *[http://microbewiki.kenyon.edu/ MicrobeWiki] is a free wiki resource on microbes and microbiology, edited by students at Kenyon College
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| | |
| ====Wikis in education====
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| *[http://wikimania2006.wikimedia.org/wiki/Category:Wikis_in_Education Wikis in Education] - proceedings of Wikimania 2006
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| *[http://cs.marlboro.edu/courses/home Wikiacademia] - a web application which manages course wikis with a markup syntax and feel similar to MediaWiki but with the addition of assignments, grades, and access rights.
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| | |
| ====Wiki hosting====
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| *[http://www.wikia.com/ a collection of communities with websites that you can edit
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| *[http://pbwiki.com/ PBwiki] - free collaborative editing
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| *[http://projectforum.com/ ProjectForum] is software that makes it easy for a team of people to work together
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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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| *[http://libraries.mit.edu/help/libx.html MIT LibX] is a toolbar that allows you to quickly search the Barton catalog, Vera, Google Scholar, the SFX FullText Finder and other search tools
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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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| *[http://www.nodalpoint.org/node/1644 Freezer management LIMS?]
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| *[http://slims.sourceforge.net/ SLIMS] Small Laboratory Informatics Management System is geared toward chemoinformatics and biological assays but can be extended with new datatypes
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| *[http://www.gnosislims.org/ GnosisLIMS] is a project to create a fully functional Open Source Laboratory Information Management System
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| | |
| ===Application servers===
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| *[http://www.whitebeam.org/ Whitebeam] - open source; applications are written as a set of XML pages that contain embedded JavaScript
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| | |
| ===Miscellaneous===
| |
| *[http://wwwhomes.uni-bielefeld.de/chase/biotool2web/ Biotool2Web]: Creating Simple Web Interfaces for Bioinformatics Applications
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| *[http://modis.ispras.ru/sedna/index.htm Sedna] is an open source XML-native database management system developed from scratch in C/C++ and Scheme
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| *[http://www.aggregatedata.com/ Aggregate Data] utilizes AJAX-based "sliders" so survey takers can choose anywhere along a spectrum of opinion
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| *CHM file viewers for non-Windows platforms
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| **[http://gnochm.sourceforge.net/ GnoCHM]
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| **[http://xchm.sourceforge.net/ xchm]
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| | |
| ==Web 2.0==
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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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| *JSON (JavaScript Object Notation) is a data interchange format that can be trivially parsed by JavaScript, with JavaScript's built in eval() procedure.
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| **[[Wikipedia:JSON|JSON]] Wikipedia article
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| **[http://www.json.org/ Introducing JSON]
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| **[http://www.theurer.cc/blog/2005/12/15/web-services-json-dump-your-proxy/ Web services + JSON]
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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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| ===AJAX===
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| *[http://www.xml.com/pub/a/2005/02/09/xml-http-request.html Very Dynamic Web Interfaces]
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| *[http://haxe.org/intro haXe] - web oriented universal language
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| *[http://jackbe.reddit.com/ Ajax news]
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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.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://www.ajaxpatterns.org/ Ajax Patterns]
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| *[http://microformats.org/wiki/rest/ahah AHAH: Asychronous HTML and HTTP]
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| *[http://ajaxphp.packtpub.com/ajax_whiteboard.htm AJAX Whiteboard] - free minibook
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| ====Specifications====
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| *[http://www.w3.org/TR/XMLHttpRequest/ The XMLHttpRequest object]: W3C Working Draft
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| *[http://www.whatwg.org/specs/web-apps/current-work/ Web Applications 1.0] This specification introduces features to HTML and the DOM that ease the authoring of Web-based applications. Additions include the context menus, a direct-mode graphics canvas, inline popup windows, server-sent events, and more.
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| ====Software development kits====
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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://cows-ajax.sourceforge.net/ COWS Ajax] makes cross-site, asynchronous, tri-directional communication (the user, your site, the application host) a no-brainer
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| *[http://developer.yahoo.com/yui/ Yahoo! UI Library] is a set of utilities and controls, written in JavaScript, for building richly interactive web applications using techniques such as DOM scripting, DHTML and AJAX.
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| *[http://www.modernmethod.com/sajax/ SAJAX]: Simple Ajax Toolkit
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| *[http://dojotoolkit.com/ Dojo toolkit]
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| *[http://twilightuniverse.com/2005/05/sack-of-ajax/ SACK]: Simple AJAX Code Kit
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| *[http://www.bindows.net/ Bindows]: desktop web applications framework
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| *[http://spaces.msn.com/editorial/rayozzie/demo/liveclip/liveclipsample/clipboardexample.html Live Clipboard]
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| *[http://www.onlinetools.org/articles/unobtrusivejavascript/ Unobtrusive Javascript]
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| *[http://helma.org/ Helma project] - Javascript application framework
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| *[http://www.mochikit.com/ Mochikit] - a lightweight Javascript library
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| *Sarissa
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| **[http://sarissa.sourceforge.net/ Sarissa API reference]
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| **[http://www.xml.com/pub/a/2005/02/23/sarissa.html Sarissa to the Rescue]
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| ===XML Data Islands===
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| [http://ajaxpatterns.org/XML_Data_Island XML Data Islands] @ AjaxPatterns
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| ===Applications===
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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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| *[http://lazybase.com/ Lazybase] - easy online databases
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| *[http://infogami.com/ infogami] lets anyone build good-looking, easily-editable web sites
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| *[http://googlepages.com Google Pages]
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| *[http://www.meebo.com/ Meebo]: Web 2.0 IM client
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| *[http://ajaxSketch.com/ ajaxSketch] is a web-based drawing tool that provides a familiar environment for diagramming, creating flow charts, free hand drawing and more
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| *[http://www.writeboard.com/ Writeboard] - shareable, web-based text documents
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| *Terminal
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| **[http://anyterm.org/ Anyterm]
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| **[http://antony.lesuisse.org/qweb/trac/wiki/AjaxTerm AjaxTerm]
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| ====Mashups====
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| *[http://www.programmableweb.com/ PorgrammableWeb] - directory of mashups, APIs, tagging, etc
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| *[http://www.frappr.com/ Frappr] - create your own custom map
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| *[http://gotapi.com/ gotAPI] - AJAX-based documentation resource for HTML, PHP, MySQL, Perl, Ruby, etc.
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| ====Office====
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| *[http://slashdot.org/article.pl?sid=05/09/29/000223&tid=126 Early AJAX Office Apps]
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| *[[Web_resources#Office_applications|Office 2.0 applications]]
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| *[http://www.goffice.com/ gOffice]
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| *Word processors
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| **[http://www.writely.com/ Writely] (part of Google)
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| *Spreadsheets
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| **[http://www.editgrid.com/ EditGrid]
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| **[http://spreadsheets.google.com/ Google Spreadsheets]
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| **[http://ajaxxls.com/ ajaxXLS Viewer] is a web-based spreadsheet viewer that allows you to easily open any .xls file within your Firefox browser
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| **[http://numsum.com/ NumSum]
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| **[http://www.irows.com/ iRows]
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