tag:blogger.com,1999:blog-194199782024-03-13T00:21:12.520+01:00BioclipseBlogA blog dedicated to Bioclipse - a workbench for life scienceOla Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.comBlogger79125tag:blogger.com,1999:blog-19419978.post-9839632511595002312012-12-22T00:45:00.000+01:002012-12-22T00:47:45.600+01:00Bioclipse 2.6 released<br />
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<a href="http://1.bp.blogspot.com/-coJoD7vU8X8/UNT02H-05EI/AAAAAAAAALk/rdVvcPI6A5k/s1600/bc26ishere.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="203" src="http://1.bp.blogspot.com/-coJoD7vU8X8/UNT02H-05EI/AAAAAAAAALk/rdVvcPI6A5k/s320/bc26ishere.png" width="320" /></a></div>
The Bioclipse team is proud to announce the release of <a href="http://www.bioclipse.net/">Bioclipse</a> version 2.6. The release contains new <a href="http://pubs.acs.org/doi/abs/10.1021/ci200242c">Decision Support</a> models (such as for <a href="http://bioclipse.blogspot.se/2012/04/chemical-decision-support-with.html">ChEMBL and Chemspider</a>), the latest <a href="http://sourceforge.net/apps/mediawiki/cdk/index.php?title=Main_Page">CDK</a> with e.g. improved aromaticity detection, and <a href="http://bioinformatics.oxfordjournals.org/content/early/2012/11/23/bioinformatics.bts681.long">Bioclipse-R</a> (including <a href="http://pele.farmbio.uu.se/bcr/predictive-modeling-Bioclipse-R.html">R-models for DS</a>), improved core stability based on Eclipse 3.8 and support for Java 1.7, new installation processes for Windows and Mac OS X, and numerous bug fixes.</div>
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Bioclipse 2.6 is available for Mac OS X, Linux, and Windows and can be <a href="https://sourceforge.net/projects/bioclipse/files/bioclipse2/bioclipse2.6.0/">downloaded from Sourceforge</a>. A <a href="http://pele.farmbio.uu.se/jenkins/job/Getting_Started/lastSuccessfulBuild/artifact/GettingStarted.pdf">getting started guide</a> is also available.</div>
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Thanks to everyone who has contributed to this version.</div>
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--</div>
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// The Bioclipse team</div>
Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com1tag:blogger.com,1999:blog-19419978.post-82100255940017783662012-12-13T23:38:00.000+01:002012-12-13T23:38:03.186+01:00Bioclipse 2.6.0 Release Candidate is out<br />
The Bioclipse team is proud to announce a release candidate for Bioclipse with version 2.6.0.RC1.<br />
We kindly ask from the community to put Bioclipse to the test and report bugs at <a href="http://bugs.bioclipse.net/">http://bugs.bioclipse.net</a>.<br />
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<a href="http://wiki.bioclipse.net/index.php?title=Bioclipse_2.6_Release">Download Bioclipse 2.6.0.RC1</a>.<br />
<a href="http://pele.farmbio.uu.se/jenkins/job/Getting_Started/lastSuccessfulBuild/artifact/GettingStarted.pdf">A getting-started guide is available</a>.<br />
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<i>Summarizing what's new (in no particular order):</i><br />
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<li>New Decision Support models (e.g. chemspider, daphnia, herg, opentox, SmartCyp)</li>
<li>Bioclipse-R, including R-models for DS</li>
<li>New online updates/installation</li>
<li>New user interface for downloading data and predictive models</li>
<li>Installer for Windows and Mac OS X</li>
<li>CDK version 1.4.15 including e.g. better double bond localization, more atom types, and speed improvements.</li>
<li>InChI (jni-inchi 0.8) supporting InChI v 1.0.3 (both standard and non-standard InChI).</li>
<li>Improved core stability (Eclipse 3.8)</li>
<li>Nightly build with Hudson and new provisioning system p2</li>
<li>Numerous bug fixes</li>
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Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-35575774918968611162012-04-19T08:48:00.005+02:002012-04-19T09:14:16.602+02:00Chemical decision support with Chemspider and ChEMBL-RDF<div style="text-align: center;"><br /></div><div style="font-family: Georgia, serif; font-size: 100%; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; "><a href="http://www.blogger.com/www.bioclipse.net/decision-support">Bioclipse Decision Support</a> is a system where users can draw or import chemical structures, execute multiple predictions or database lookups, and visually interpret results. This was previously demonstrated for <a href="http://pubs.acs.org/doi/abs/10.1021/ci200242c">chemical liability assessment</a>, and for running <a href="http://www.biomedcentral.com/1756-0500/4/487">OpenTox predictions</a>.</div><div style="text-align: center;font-family: Georgia, serif; font-size: 100%; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; "><br /></div><span ><span style="font-size: 100%;">In the recent days I have implemented a module for adding a </span></span><a href="http://www.chemspider.com/" style="font-family: Georgia, serif; font-size: 100%; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; ">ChemSpider</a><span ><span style="font-size: 100%;"> SimilaritySearch complemented by ChEMBL lookup via the </span></span><a href="https://github.com/egonw/chembl.rdf" style="font-family: Georgia, serif; font-size: 100%; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; ">ChEMBL-RDF</a><span ><span style="font-size: 100%;"> data maintained by Egon Willighagen. In short this is how it operates:</span></span><div><ol><li><span >Query ChemSpider using the SimilaritySearch via the <a href="http://www.chemspider.com/AboutServices.aspx?">Web API (SOAP)</a>.</span></li><li><span >For a maximum of 15 nearest neighbors in Chemspider, query ChEMBL-RDF for interactions, and present information about assays, targets, and interaction values.</span></li></ol><div style="font-family: Georgia, serif; font-size: 100%; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; ">Below you can find a screenshot of how it looks like in action. <span style="font-size: 100%; ">Now, the ChemSpider similarity search is rather slow (>30 s) but then again it takes a while to query 27 M chemical structures.</span></div><div style="font-family: Georgia, serif; font-size: 100%; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; "><span style="font-size: 100%; "><br /></span></div><img src="http://4.bp.blogspot.com/-AQaqFj1ZFpw/T4-6QsrsAhI/AAAAAAAAAKw/uyJ82e-_iHE/s400/bioclipse-ds.png" border="0" alt="" id="BLOGGER_PHOTO_ID_5733005646701003282" style="font-family: Georgia, serif; font-size: 16px; display: block; margin-top: 0px; margin-right: auto; margin-bottom: 10px; margin-left: auto; text-align: center; cursor: pointer; width: 400px; height: 285px; " /><div style="font-family: Georgia, serif; font-size: 100%; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; "><br /></div><div style="font-family: Georgia, serif; font-size: 100%; font-variant: normal; line-height: normal; "><b>Note:</b><span style="font-weight: normal; font-style: normal; "> This work was done against a development version of Chemspider Web API. You also need a security token in order to be able to query Chemspider; it's free and can be obtained <a href="http://www.chemspider.com/Register.aspx">here</a>. When you have a security token, paste it into the Chemspider section of the Bioclipse preferences. </span><span style="font-weight: normal; font-size: 100%; ">The Chemspider + ChEMBL model for Bioclipse Decision Support will be part of the 2.6 release of </span><a href="http://www.bioclipse.net" style="font-weight: normal; font-size: 100%; ">Bioclipse</a><span style="font-weight: normal; font-size: 100%; ">, which we hope to have in place within a few weeks.</span></div><div style="font-family: Georgia, serif; font-size: 100%; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; "><br /></div><div style="font-family: Georgia, serif; font-size: 100%; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; ">Thanks to <a href="http://www.blogger.com/chem-bla-ics.blogspot.com">Egon Willighagen</a> (ChEMBL-RDF) and Valery Tkachenko (<a href="http://www.chemspider.com/" style="font-size: 100%; ">Chemspider</a><span style="font-size: 100%; ">)</span><span style="font-size: 100%; "> for aiding me in this work.</span></div></div>Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com1tag:blogger.com,1999:blog-19419978.post-13313284939507821792012-04-18T18:37:00.003+02:002012-04-18T18:38:18.216+02:00Postdoc position in predictive toxicology at Uppsala University<p class="p1" style="font-weight: normal; "><b style="font-size: 100%; ">Postdoc position in cheminformatics, bioinformatics, or computer science - applications in predictive toxicology</b></p> <p class="p1" style="font-weight: normal; ">We have an open postdoc position in the group of Pharmaceutical Bioinformatics at the Department of Pharmaceutical Biosciences, Uppsala University, Sweden.</p> <p class="p1" style="font-weight: normal; ">The successful applicant will conduct research on data interoperability for predictive toxicology, and especially design and implement an infrastructure consisting of a database and user interfaces for data and predictive models in toxicology. Of particular interest will be to merge chemical and biological data within a semantic framework, and link toxicity data to genomics and metabolomics data (toxicogenomics) with a connection to the Bioclipse framework (<a href="http://www.bioclipse.net/"><span class="s1">www.bioclipse.net</span></a>). PhD degree or equivalent scholarly competence in a relevant branch of chem/bioinformatics or computer science and a strong interest in informatics and data integration is required. Required competences include web programming, databases, and working knowledge in Java. Experience with linked data is desirable.</p> <p class="p1" style="font-weight: normal; ">Deadline for application: May 9th , 2012.</p> <p class="p3" style="font-weight: normal; "><span class="s2">Link to job ad and application form: <span class="s3"><a href="http://www.uu.se/jobb/others/annonsvisning?tarContentId=186211&languageId=1">http://www.uu.se/jobb/others/annonsvisning?tarContentId=186211&languageId=1</a></span></span></p>Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-71712297411634167082011-03-08T23:17:00.003+01:002011-03-08T23:24:16.208+01:00Bioclipse meets OpenToxBarry Hardy wrote a very nice post about when he encountered the <a href="http://en.wikipedia.org/wiki/Spirostachys_africana">Tamboti Tree</a>, a very toxic tree, and his experience when using <a href="http://www.bioclipse.net">Bioclipse</a> and <a href="http://www.opentox.org">OpenTox</a> to assess its toxicity. Read the full article and watch the movie here: <a href="http://barryhardy.blogs.com/theferryman/2011/03/the-tamboti-tree-use-case-bioclipse-meets-opentox.html">http://barryhardy.blogs.com/theferryman/2011/03/the-tamboti-tree-use-case-bioclipse-meets-opentox.html</a>Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-5753039646336215162011-03-07T05:12:00.003+01:002011-03-07T05:19:03.748+01:00Presenting at Society of Toxicology 2011Tomorrow I will present a poster at the <a href="http://www.toxicology.org/ai/meet/am2011/">Society of Toxicology Annual Meeting 2011</a> in Washington DC. With over 7,500 participants, this conference is rather large. My poster has the title: "A flexible method for building and using predictive models applied to safety endpoints" and mainly described the <a href="http://wiki.bioclipse.net/index.php?title=Bioclipse_Decision_Support">Decision Support</a> feature for <a href="http://www.bioclipse.net">Bioclipse</a>. Anyway, this is what my poster looks like:<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/-hMRV4nBuF6w/TXRcJcMdzpI/AAAAAAAAAHQ/en2p2VjVMSA/s1600/spjuth-SOT2011-poster.png"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 400px; height: 282px;" src="http://1.bp.blogspot.com/-hMRV4nBuF6w/TXRcJcMdzpI/AAAAAAAAAHQ/en2p2VjVMSA/s400/spjuth-SOT2011-poster.png" alt="" id="BLOGGER_PHOTO_ID_5581187155475943058" border="0" /></a>Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com2tag:blogger.com,1999:blog-19419978.post-72712994166883513502011-03-04T00:08:00.002+01:002011-03-04T00:11:01.223+01:00Web seminar on BioclipseOla Spjuth of the Bioclipse project will give a web seminar on Mar 29th 16:00 GMT entitled: <a href="http://bitesizebio.com/webinars/in-silico-prediction-of-drug-safety-and-metabolites-using-bioclipse/">In-Silico Prediction of Drug Safety and Metabolites Using Bioclipse</a>. The seminar is free of charge but requires registration.Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-44804385615512491992010-08-30T14:52:00.003+02:002010-08-30T15:00:45.679+02:00Bioclipse 2.4.1 now on update siteA new version can be found on the update site. The new versions of the features contain the latest fixes. New in this version is support for Jasper reports which are so far used by Bioclipse Decision Support and Bioclipse Brunn for generating printable reports.<br /><br />To update go to Help -> Software Updates... and select the features you want to install.<br /><br />Known problem: The splash screen erroneously shows version number to be 2.4.0 after update. (Technical information can be found at <a href="http://pele.farmbio.uu.se/cgi-bin/bugzilla/show_bug.cgi?id=2084">bug: 2084</a> in our Bugzilla)Jonalvhttp://www.blogger.com/profile/01302696904346930017noreply@blogger.com1tag:blogger.com,1999:blog-19419978.post-77450275900751185942010-07-09T15:28:00.001+02:002010-07-09T15:31:12.193+02:00Bioclipse 2.4 released<p>The Bioclipse team is proud to announce the release of Bioclipse version 2.4. The release contains various new features and bug fixes in cheminformatics and drug discovery, including improved QSAR functionality, site-of-metabolism prediction, semantic web functionality, browsing of large compound collections, editing of chemical structures, and numerous bug fixes.<br /></p><p>Bioclipse 2.4 is available for 32 and 64 bit versions of Mac OS X, Linux, and 32 bit version of Windows (Bioclipse for 64 bit Windows is currently unavailable, but will be provided as soon as a native Standard InChI is available for 64 bit Windows).</p><ul><li><a href="http://bioclipse.net/download">Download Bioclipse</a></li><li><a href="http://www.bioclipse.net/getting-started-with-bioclipse">Getting started guide</a></li><li><a href="http://planet.bioclipse.net/">Planet Bioclipse</a> integrates blogs related to Bioclipse.</li></ul><ul> </ul> <p> </p>Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-18055127250710216292010-07-06T19:21:00.002+02:002010-07-06T19:24:29.606+02:00Bioclipse 2.4.0.RC3 is hereA new release candidate is out and can be found at the usual site for release candidates:<br /><br /><a href="http://pele.farmbio.uu.se/bioclipse-devel/">http://pele.farmbio.uu.se/bioclipse-devel/</a><br /><br />I have a good feeling about this one. I think Bioclipse 2.4 is really close now.<br /><br />And as usual, if you download and try the release candidate of course you already know that we love to get bug reports in our <a href="http://bugs.bioclipse.net/">Bugzilla</a>. :)Jonalvhttp://www.blogger.com/profile/01302696904346930017noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-63092675278599549892010-06-01T11:25:00.004+02:002010-06-01T11:38:18.479+02:00Bioclipse 2.4.0.RC1 is outA new release candidate is out and can be found at the usual site for release candidates:<br /><br /><a href="http://pele.farmbio.uu.se/bioclipse-devel/">http://pele.farmbio.uu.se/bioclipse-devel/</a><br /><br /><span style="font-weight: bold;">What is new?</span><br />Among the main news are:<br /><ul><li>New molecules table.</li><li>We are now using Java 1.6</li><li>Eclipse 3.5.2</li><li>CDK 1.3.5 </li></ul>And of course bug fixes and probably a lot of other stuff which I don't know about. If you download and try the release candidate of course you already know that we love to get bug reports in our <a href="http://bugs.bioclipse.net">Bugzilla</a>.Jonalvhttp://www.blogger.com/profile/01302696904346930017noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-16495315567206431572010-03-07T14:00:00.004+01:002010-03-12T10:46:52.716+01:00Bioclipse is finalist for the Eclipse Community Awards 2010<a href="http://www.bioclipse.net/">Bioclipse</a> is one of three <a href="http://www.eclipse.org/org/press-release/20100305_awardsfinalists.php">Finalists for the Eclipse Community Awards 2010</a> in the category Best RCP Application. I am looking forward to going to EclipseCon, it will be my first visit. I have also submitted a poster, and hope it will be among the selected ones (see below or the <a href="https://www.eclipsecon.org/submissions/2010/view_talk.php?id=1627&search=*">submission abstract</a>). <span style="color: rgb(153, 0, 0);">UPDATED: My poster is now accepted!</span><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.bioclipse.net/dl/eclipseCon2010poster.pdf"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 320px; height: 266px;" src="http://3.bp.blogspot.com/_h6tAVZXYvfs/S5OnQd8QtdI/AAAAAAAAAGw/Sknz4NpC-yk/s320/eclipseCon2010poster_thumb.png" alt="" id="BLOGGER_PHOTO_ID_5445880275778188754" border="0" /></a><br /><br /><div style="text-align: center;">Below is the screencast which I constructed for the Community Awards submission:<br /></div><div style="text-align: center;"><br /><embed src="http://blip.tv/play/AYHBs04C" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" height="300" width="480"></embed><br /></div>Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com6tag:blogger.com,1999:blog-19419978.post-1142304327282473682010-01-28T17:12:00.008+01:002010-01-29T17:47:24.053+01:00Bioclipse 2.2 releasedThe Bioclipse Team is proud to announce the release of Bioclipse 2.2.0. The new version includes, apart from numerous bug fixes, the following highlights:<br /><br /> * Cheminformatics, with a pure SWT-based chemical 2D editor (<a href="http://wiki.bioclipse.net/index.php?title=JChemPaint">JChemPaint</a>) and a <a href="http://wiki.bioclipse.net/index.php?title=MolTable">lazy-loading molecules table</a>.<br /> * <a href="http://wiki.bioclipse.net/index.php?title=QSAR_Project_with_automated_builds">QSAR</a>, supporting local, REST, and <a href="http://www.biomedcentral.com/1471-2105/10/279">XMPP services</a><br /> * <a href="http://wiki.bioclipse.net/index.php?title=MetaPrint2D">MetaPrint2D</a> for interactive site-of-metabolism prediction for chemical structures<br /> * <a href="http://wiki.bioclipse.net/index.php?title=Structure_DB">StructureDB</a> and <a href="http://bioclipse.blogspot.com/2009/10/virtual-screening-for-bioclipse.html">VScreen</a>: A chemical database with <a href="http://bioclipse.blogspot.com/2009/10/virtual-screening-for-bioclipse.html">virtual screening</a> functionality<br /> * The new <a href="http://wiki.bioclipse.net/index.php?title=Bioclipse_Decision_Support">Decision Support</a> feature with graphical reports using <a href="http://www.eclipse.org/birt/phoenix/">BIRT</a><br /> * <a href="http://chem-bla-ics.blogspot.com/2010/01/semantic-web-features-in-bioclipse-22.html">Semantic web features</a><br /> * Bioinformatics, with the new Sequence Editor and sequence alignments via the <a href="http://bioclipse.blogspot.com/2009/11/align-sequences-with-kalign-web-service.html">Kalign Web service</a> (Experimental)<br /><br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/_h6tAVZXYvfs/S2HXQPxJNYI/AAAAAAAAAF0/_7y6Kb1-44Q/s1600-h/m2d_multi.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 370px;" src="http://1.bp.blogspot.com/_h6tAVZXYvfs/S2HXQPxJNYI/AAAAAAAAAF0/_7y6Kb1-44Q/s400/m2d_multi.png" alt="" id="BLOGGER_PHOTO_ID_5431859299696063874" border="0" /></a>A screenshot from Bioclipse with the <a href="http://wiki.bioclipse.net/index.php?title=MetaPrint2D">MetaPrint2D</a> feature showing predicted sites of metabolsim for a set of drugs in the <a href="http://wiki.bioclipse.net/index.php?title=MolTable">MoleculesTable</a>.<br /></div><br />Note that Bioclipse 2.2.0 requires a fresh download, i.e. it can not be upgraded to by using the software update functionality. A small <a href="http://wiki.bioclipse.net/index.php?title=Installing_Bioclipse2">installation guide</a> is also provided, but the main documentation for Bioclipse is available from <a href="http://help.bioclipse.net/">help.bioclipse.net</a>; the same information is also available from within Bioclipse from the menu <span style="font-weight: bold;">Help > Help Contents</span>. For general questions there is the <a href="http://sourceforge.net/projects/bioclipse/support">bioclipse-users</a><a href="http://sourceforge.net/projects/bioclipse/support"> and bioclipse.devel</a> mailing lists.<br /><br />Links:<br /><ul><li><a href="http://sourceforge.net/projects/bioclipse/files">Download Bioclipse 2.2.0</a>.</li><li><a href="http://help.bioclipse.net/">Bioclipse help (online version)</a></li><li><a href="http://www.bioclipse.net/">Bioclipse website</a></li><li><a href="http://bioclipse.blogspot.com/2009/07/biocipse-20-released.html">Bioclipse 2.0 announcement</a></li><li> <a href="http://wiki.bioclipse.net/index.php?title=Installing_Bioclipse2">Installation guide</a></li><li><a href="http://bugs.bioclipse.net/">Report a bug</a></li><li><a href="http://sourceforge.net/projects/bioclipse/support">Mailing lists</a> </li></ul>Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com1tag:blogger.com,1999:blog-19419978.post-47741725194636764812009-11-30T11:21:00.003+01:002009-11-30T11:35:26.791+01:00Congratulations doctor Ola Spjuth<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/_dIdeUAuGktA/SxOfre3vm4I/AAAAAAAAALg/oOmOzJnmkyc/s1600/4143359899_45e651875d.jpg"><img style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 213px; height: 320px;" src="http://2.bp.blogspot.com/_dIdeUAuGktA/SxOfre3vm4I/AAAAAAAAALg/oOmOzJnmkyc/s320/4143359899_45e651875d.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5409843146772159362" /></a><br />Ola Spjuth, the mastermind behind the realization of Bioclipse is now a doctor. These last days he and his best friend Martin Eklund went through the process. Olas thesis can be found <a href="http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-109305">here</a> and more importantly I have it all documented in pictures on <a href="http://www.flickr.com/photos/jonathanalvarsson/sets/72157622774569663/">flickr</a>.Jonalvhttp://www.blogger.com/profile/01302696904346930017noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-14299561100262604382009-11-03T14:34:00.006+01:002009-11-03T15:00:47.284+01:00Download PDBs with BioclipseIt is easy to download bioinformatics resources into Bioclipse using the<a href="http://www.ebi.ac.uk/Tools/webservices/services/dbfetch"> WSDbfetch Web service </a>at the <a href="http://www.ebi.ac.uk">European Bioinformatics Institute (EBI)</a>. From console you can use the method:<br /><br /> <span style="font-family:courier new;">ws.downloadDbEntry(String db, String query, String format)</span><br /><br />From the GUI you can use menu: <span style="font-weight: bold;">File > New...</span> and select the <span style="font-weight: bold;">Wizard Download > Query WSDbfetch at EBI</span>. Click next and see the many available databases in the dropdown list Supported databases:<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/_h6tAVZXYvfs/SvAzKXX9HuI/AAAAAAAAAFU/ASShycXPCJ0/s1600-h/wsdbfetch_dbs.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 365px; height: 400px;" src="http://1.bp.blogspot.com/_h6tAVZXYvfs/SvAzKXX9HuI/AAAAAAAAAFU/ASShycXPCJ0/s400/wsdbfetch_dbs.png" alt="" id="BLOGGER_PHOTO_ID_5399872206383423202" border="0" /></a>Try for example to download the sequence "NM_210721" from the <a href="http://www.ncbi.nlm.nih.gov/RefSeq/">"refseq" database</a>.<br /><br />If you'd like to download proteins in <a href="http://en.wikipedia.org/wiki/Protein_Data_Bank">PDB format</a>, there is a convenience wizard available in the New Wizards dialog available from the menu <span style="font-weight: bold;">File > New...</span><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/_h6tAVZXYvfs/SvA1Q4gu88I/AAAAAAAAAFc/FSbCfUyyWvk/s1600-h/NewPDBWizard.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 324px; height: 308px;" src="http://4.bp.blogspot.com/_h6tAVZXYvfs/SvA1Q4gu88I/AAAAAAAAAFc/FSbCfUyyWvk/s400/NewPDBWizard.png" alt="" id="BLOGGER_PHOTO_ID_5399874517381084098" border="0" /></a><br />Clicking <span style="font-weight: bold;">Next</span> allows for inputting a comma-separated list of PDB IDs, try for example "1ale,2pdz". Clicking next downloads the file to the selected folder in the Navigator, or to the Virtual project if nothing is selected. Below is visualized 2PDZ in the Jmol Editor.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/_h6tAVZXYvfs/SvA24xV8ifI/AAAAAAAAAFs/Ij8fvtemhiA/s1600-h/res_jmol_2pdz.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 304px;" src="http://2.bp.blogspot.com/_h6tAVZXYvfs/SvA24xV8ifI/AAAAAAAAAFs/Ij8fvtemhiA/s400/res_jmol_2pdz.png" alt="" id="BLOGGER_PHOTO_ID_5399876302163184114" border="0" /></a>Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-81826945575320690022009-11-03T14:24:00.005+01:002009-11-03T14:34:03.921+01:00Align sequences with the Kalign Web serviceA recent feature addition to <a href="http://www.bioclipse.net">Bioclipse</a> is the ability to align protein sequences using the <a href="http://www.ebi.ac.uk/Tools/webservices/services/kalign">Kalign Web service</a> available from the <a href="http://www.ebi.ac.uk">European Bioinformatics Institute (EBI)</a>. Simply select two protein sequences in the Navigator (currently the FASTA format is only supported but more formats are in the pipe), right-click, and select <span style="font-weight: bold;">Align > Align using Kalign</span>.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/_h6tAVZXYvfs/SvAvyHCQpKI/AAAAAAAAAFE/4X3_E4XzA58/s1600-h/align_context.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 315px; height: 275px;" src="http://3.bp.blogspot.com/_h6tAVZXYvfs/SvAvyHCQpKI/AAAAAAAAAFE/4X3_E4XzA58/s400/align_context.png" alt="" id="BLOGGER_PHOTO_ID_5399868491145716898" border="0" /></a><br />This compiles the sequences into the input format that Kalign expects, and sends it via SOAP to the Kalign Web service at EBI. The results is stored as a file in the same folder as the aligned resources, and opened in the <a href="http://wiki.bioclipse.net/index.php?title=Sequence_editor">SequenceEditor</a> (note the new Wrap feature available from the toolbar).<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/_h6tAVZXYvfs/SvAwQ-i8tgI/AAAAAAAAAFM/mXtuDBdrUpg/s1600-h/kaligned_wrap.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 323px;" src="http://2.bp.blogspot.com/_h6tAVZXYvfs/SvAwQ-i8tgI/AAAAAAAAAFM/mXtuDBdrUpg/s400/kaligned_wrap.png" alt="" id="BLOGGER_PHOTO_ID_5399869021442848258" border="0" /></a><br />The feature is available from the latest <a href="http://pele.farmbio.uu.se/bioclipse-devel">development version</a> of Bioclipse.Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-37233082902308640102009-10-03T14:02:00.004+02:002009-10-03T14:37:51.885+02:00Bioclipse 2.1.1 devel releaseA new development release is now available for download at <a href="http://pele.farmbio.uu.se/bioclipse-devel/">http://pele.farmbio.uu.se/bioclipse-devel/</a>. Highlights of the development update site (http://update2-devel.bioclipse.net) are:<br /><br /><ul><li>Bioinformatics, with the new Sequence Editor now capable of wrapping sequences</li><li>Bioclipse Reporting (BIRT)</li><li><a href="http://wiki.bioclipse.net/index.php?title=QSAR_Project_with_automated_builds">QSAR</a>, supporting local, REST, and XMPP services</li><li><a href="http://chem-bla-ics.blogspot.com/2009/08/bioclipse-and-sparql-end-points.html">Semantic web features</a> (RDF and Pellet)</li><li><a href="http://wiki.bioclipse.net/index.php?title=Structure_DB">StructureDB</a>: A chemical database for Bioclipse</li><li>The new <a href="http://bioclipse.blogspot.com/2009/10/virtual-screening-for-bioclipse.html">VScreen</a> feature for Virtual Screening</li><li>The new <a href="http://wiki.bioclipse.net/index.php?title=Bioclipse_Decision_Support">Decision Support</a> feature</li><li>The new <a href="http://wiki.bioclipse.net/index.php?title=MetaPrint2D">MetaPrint2D</a> feature</li></ul><br />Note that the development versions are not compatible with the stable 2.0.x release branch which is available from <a href="https://sourceforge.net/projects/bioclipse/files/">Sourceforge</a>. This update replaces the 2.1.0 devel release, and the devel update site is only compatible with the 2.1.1 release.<br /><br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/_h6tAVZXYvfs/SsdFSfqSOzI/AAAAAAAAAE8/e4sI_oNhaOY/s1600-h/ds_multimol.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 251px;" src="http://1.bp.blogspot.com/_h6tAVZXYvfs/SsdFSfqSOzI/AAAAAAAAAE8/e4sI_oNhaOY/s400/ds_multimol.png" alt="" id="BLOGGER_PHOTO_ID_5388351663210904370" border="0" /></a><br /><span style="font-size:85%;"><span style="font-weight: bold;">Figure:</span> Screenshot teaser from the Bioclipse 2.1.1 devel release showing the Decision Support feature in action for a collection of molecules.<br /></span></div>Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-47718209599767236272009-10-03T13:47:00.004+02:002009-10-03T14:01:39.134+02:00Virtual Screening for BioclipseI recently created a <a href="http://www.bioclipse.net">Bioclipse</a> feature to filter chemical structures in a <a href="http://wiki.bioclipse.net/index.php?title=Structure_DB">StructureDB</a> database (the new database for chemical structures in Bioclipse). The new plugin is called <a href="http://wiki.bioclipse.net/index.php?title=VScreen">VScreen</a>, and aims at being a future Virtual Screening feature. Currently the feature is in very early proof-of-concept state with only two simple filters, Molecular Weight and XlogP. Plans include to create an extension point for filters that plugin can extend to contribute new filters.<br /><br />Currently, the only way of interacting with the plugin is via Bioclipse scripts. A sample usage is available below in a Gist:<br /><br /><script src="http://gist.github.com/200556.js"></script><br /><br />A screenshot from Bioclipse is shown below:<span style="text-decoration: underline;"><br /><br /></span><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/_h6tAVZXYvfs/Ssc8TEwmujI/AAAAAAAAAE0/N_IYdYgPcZ0/s1600-h/vscreen2000.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 241px;" src="http://4.bp.blogspot.com/_h6tAVZXYvfs/Ssc8TEwmujI/AAAAAAAAAE0/N_IYdYgPcZ0/s400/vscreen2000.png" alt="" id="BLOGGER_PHOTO_ID_5388341777564875314" border="0" /></a>Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com3tag:blogger.com,1999:blog-19419978.post-73794077744866985492009-08-07T14:34:00.002+02:002009-08-07T14:46:30.085+02:00Bioclipse 2.1.0 development releaseToday the first Bioclipse development version (versioned 2.1.0.v20090807) was released. A development update site (http://update2-devel.bioclipse.net) is packed with features to test (for example the new Bioinformatics feature, early versions of the StructureDB, QSAR, and RDF features). Note that the development versions are not compatible with the stable 2.0.x release branch which is available from <a href="https://sourceforge.net/projects/bioclipse/files/">Sourceforge</a>.<br /><br />There will be frequent updates to the update site for this, towards the next stable version 2.2.0. For more information and downloads of this development release, see <a href="http://pele.farmbio.uu.se/bioclipse-devel/">http://pele.farmbio.uu.se/bioclipse-devel/</a>.Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-88986070343318257212009-07-09T11:19:00.015+02:002010-02-19T11:35:35.311+01:00Bioclipse 2.0 released<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/_h6tAVZXYvfs/SlXkrWA2ryI/AAAAAAAAAEk/vJ27t17GilI/s1600-h/bioclipse-banner_300w.png"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 200px; height: 60px;" src="http://3.bp.blogspot.com/_h6tAVZXYvfs/SlXkrWA2ryI/AAAAAAAAAEk/vJ27t17GilI/s200/bioclipse-banner_300w.png" alt="" id="BLOGGER_PHOTO_ID_5356438765121744674" border="0" /></a><br /><br /><br /><br /><br />On behalf of all <a href="http://bioclipse.net/">Bioclipse</a> developers I am happy to announce the release of Bioclipse 2.0. Bioclipse is a free, open source workbench for the life sciences that provides advanced functionality mainly in cheminformatics (bioinformatics is planned for version 2.1 later this summer). Some major components include a brand new chemical editor for SWT (JChemPaint), interactive 3D visualization of molecules (<a href="http://www.jmol.org/">Jmol</a>), a Molecules Table <a href="http://bioclipse.blogspot.com/2009/07/working-with-large-sdfiles-in-bioclipse.html">capable of reading large files</a>, and a powerful backbone in cheminformatics provided by the <a href="http://cdk.sourceforge.net/">Chemistry Development Kit (CDK)</a> library.<br /><br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/_h6tAVZXYvfs/SlW2doIhPOI/AAAAAAAAAEM/PfRyscUxB0c/s1600-h/jcpfull_atp.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 320px; height: 204px;" src="http://3.bp.blogspot.com/_h6tAVZXYvfs/SlW2doIhPOI/AAAAAAAAAEM/PfRyscUxB0c/s320/jcpfull_atp.png" alt="" id="BLOGGER_PHOTO_ID_5356387951932685538" border="0" /></a><span style="font-size:85%;"><span style="font-style: italic;"><span style="font-weight: bold;">Figure 1:</span> Screenshot of Bioclipse showing editing of a chemical structure using the new JChemPaint editor.</span></span> </div><br />Bioclipse is a <a href="http://www.eclipse.org/rcp">Rich Client</a> for the life sciences that provides the means to run and integrate algorithms and tools in disconnected state, while still taking advantage of remote services if a network connection is available. Built on the famous <a href="http://www.eclipse.org/">Eclipse</a> framework, Bioclipse delivers a state-of-the-art plugin architecture which makes it possible to extend it in any direction.<br /><br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/_h6tAVZXYvfs/SlW21mmWo4I/AAAAAAAAAEU/arG2Y-ZGnpc/s1600-h/jmolClose.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 320px; height: 225px;" src="http://4.bp.blogspot.com/_h6tAVZXYvfs/SlW21mmWo4I/AAAAAAAAAEU/arG2Y-ZGnpc/s320/jmolClose.png" alt="" id="BLOGGER_PHOTO_ID_5356388363837809538" border="0" /></a><span style="font-size:85%;"><span style="font-style: italic;"><span style="font-weight: bold;">Figure 2:</span> Screenshot of the interactive 3D visualization of a protein using the integrated component Jmol.</span></span> </div><br />All functionality in Bioclipse 2 is available from the GUI as well as a new scripting language based on Javascript. This allows for complete control of the workbench and functionality from scripts, which can be used to automate tasks or reproduce and validate scientific analyses.<br /><br /><br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/_h6tAVZXYvfs/SlW3YIUm2tI/AAAAAAAAAEc/cVBhFEtu9wI/s1600-h/js_gen2d_open.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 204px; height: 320px;" src="http://2.bp.blogspot.com/_h6tAVZXYvfs/SlW3YIUm2tI/AAAAAAAAAEc/cVBhFEtu9wI/s320/js_gen2d_open.png" alt="" id="BLOGGER_PHOTO_ID_5356388957005732562" border="0" /></a><span style="font-size:85%;"><span style="font-style: italic;"><span style="font-weight: bold;">Figure 3:</span> All functionality in Bioclipse is available from an integrated scripting language based on Javascript.</span></span> </div><br />Bioclipse 2 can be downloaded from <a href="http://sourceforge.net/projects/bioclipse/files/">Sourceforge</a>, releases are available for all major platforms. There is an update site where users can install additional functionality (such as <a href="http://wiki.bioclipse.net/index.php?title=Speclipse">Speclipse</a>) and data collections; this is available from the Bioclipse workbench under menu <span style="font-weight: bold;">Help > Software updates</span>.<br /><br />A small <a href="http://wiki.bioclipse.net/index.php?title=Installing_Bioclipse2">installation guide</a> is also provided, but the main documentation for Bioclipse is available from <a href="http://help.bioclipse.net/">help.bioclipse.net</a>; the same information is also available from within Bioclipse from the menu <span style="font-weight: bold;">Help > Help Contents</span>. For general questions there is the <a href="https://lists.sourceforge.net/mailman/listinfo/bioclipse-users">bioclipse-users</a> mailing list.<br /><br />All software contains bugs, and Bioclipse is no exception. However, in contrast to many commercial and closed source initiatives, open source projects generally have a faster bug fixing rate as well as more frequent releases. If you find bugs in Bioclipse, please report them on <a href="http://bugs.bioclipse.net/">bugs.bioclipse.net</a>. There is a list of <a href="http://wiki.bioclipse.net/index.php?title=Intractable_Bugs">intractable bugs</a> on the <a href="http://wiki.bioclipse.net/">Bioclipse development wiki</a>, and also a convenience list for tracking <a href="http://wiki.bioclipse.net/index.php?title=Known_Major_Bugs">known major bugs</a>.<br /><br />Bioclipse is an open development that welcome new developers with varying backgrounds. Developers hang out on daily basis on IRC (irc.freenode.net, channel <span style="font-style: italic;">#bioclipse</span>), and can also be reached via the mailing list <a href="https://lists.sourceforge.net/mailman/listinfo/bioclipse-devel">bioclipse-devel</a>.<br /><br />Thanks to all contributors who made this release possible!Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com3tag:blogger.com,1999:blog-19419978.post-23406394013954173902009-07-03T16:04:00.006+02:002009-07-07T16:31:21.216+02:00Working with large SDFiles in BioclipseI decided to test the performance of Bioclipse 2 (current release 2.0.0RC5) for working with large structural files (SDFiles). I first loaded in the complete <a href="http://www.ebi.ac.uk/chebi">ChEBI</a> (<b>Ch</b>emical <b>E</b>ntities of <b>B</b>iological <b>I</b>nterest) which consisted of 13.486 chemical structures and has a file size of 54 MB on disk. This was very fast, Bioclipse indexed and opened the file in less than 4 seconds, and then continued to parse the properties in the background for another 4 seconds (but during this time it is possible to browse and work with the structures). The MolTable editor was very responsive and scrolls nicely.<br /><br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/_h6tAVZXYvfs/SlNap1ktU-I/AAAAAAAAAEE/OtuBs30u3iI/s1600-h/moltable_chebi.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 211px;" src="http://2.bp.blogspot.com/_h6tAVZXYvfs/SlNap1ktU-I/AAAAAAAAAEE/OtuBs30u3iI/s400/moltable_chebi.png" alt="" id="BLOGGER_PHOTO_ID_5355724056675832802" border="0" /></a><br /><span style="font-size:85%;"><span style="font-style: italic;">Figure 1: Screenshot from Bioclipse with the entire Chebi SDF open.</span></span><br /></div><br />To really push Bioclipse, a test file of the first 225.000 compounds in Pubchem were concatenated, resulting in an SDFile of size 1.1 Gb. Bioclipse creates an index of the file and opens it in 66 seconds. It then continues parsing the properties in the background, which takes another 78 seconds. The MolTable editor was still very responsive and scrolls nicely. Not bad for such a large file!<br /><br />Calculating InChI on the >1Gb file on the open file in MoleculesTable (resulting in all InChI properties kept in memory) took 13.20 min. Trying to save the resulting file took 2 min 49 seconds for the first 20Mb, extrapolated to 2h and 20 minutes for the total (this forces a complete save of all chemical structures and a lot of swapping in and out from disc). Calculating the same InChi and saving to file but not opening it in MolTable first (avoiding keeping all properties in memory) took 20 minutes. What do we learn from this? Browse large files is fine, but if you want to manipulate them then, do this on the file directly without visual inspection.<br /><br />As a side note: Handling large SDFiles is generally not a recommended solution. When <a href="http://wiki.bioclipse.net/index.php?title=Structure_DB">StructureDB</a> (a relational database for chemistry) is released for Bioclipse, we will see a dramatic performance boost when dealing with large collections of molecules.Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com2tag:blogger.com,1999:blog-19419978.post-21505372044363106002009-07-02T17:09:00.005+02:002009-07-03T13:30:40.104+02:00Bioclipse 2.0 Release Candidate 5<div style="text-align: left;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/_h6tAVZXYvfs/SkzOKiZsOJI/AAAAAAAAAD0/_7cXzQoP0VE/s1600-h/bioclipse-banner_300w.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 300px; height: 90px;" src="http://1.bp.blogspot.com/_h6tAVZXYvfs/SkzOKiZsOJI/AAAAAAAAAD0/_7cXzQoP0VE/s320/bioclipse-banner_300w.png" alt="" id="BLOGGER_PHOTO_ID_5353880737465251986" border="0" /></a><br /></div>Today, Bioclipse 2.0 Release Candidate 5 (versioned 2.0.0.RC5) was released with primarily a fix in the atom typing done when editing chemical structures, and a less stricter handling of SDFiles. The <a href="http://pele.farmbio.uu.se/bioclipse/help/2.0beta5/index.jsp">Bioclipse help</a> is also available as standalone. The release requires a fresh download from <a href="http://sourceforge.net/projects/bioclipse">Sourceforge</a>, and we kindly ask beta-testers for bug reports on the <a href="http://bugs.bioclipse.net/">bugs.bioclipse.net</a>.<br /><p><br /></p>Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-26301849359246653322009-06-29T16:44:00.001+02:002009-06-29T16:46:09.678+02:00Bioclipse 2.0 Release Candidate 4Today, Bioclipse 2.0 Release Candidate 4 (versioned 2.0.0.RC4) was released. The release requires a fresh download from <a href="http://sourceforge.net/projects/bioclipse">Sourceforge</a>, and we kindly ask beta-testers for bug reports on the <a href="http://bugs.bioclipse.net/">bugs.bioclipse.net</a>.<br /><p><br />Hopefully this will be the candidate for the 2.0 release.Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-75522700741763544962009-06-24T09:44:00.001+02:002009-06-24T09:46:07.925+02:00Bioclipse 2.0 Release Candidate 3Today, Bioclipse 2.0 Release Candidate 3 (versioned 2.0.0.RC3) was released. The release requires a fresh download from <a href="http://sourceforge.net/projects/bioclipse">Sourceforge</a>, and we kindly ask beta-testers for bug reports on the <a href="http://bugs.bioclipse.net/">bugs.bioclipse.net</a>.Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0tag:blogger.com,1999:blog-19419978.post-68422643357016819112009-06-15T13:22:00.001+02:002009-06-15T13:24:52.385+02:00Bioclipse 2.0 Release Candidate 2Today, Bioclipse 2.0 Release Candidate 2 (versioned 2.0.0.RC2) was released. The release requires a fresh download from <a href="http://sourceforge.net/project/showfiles.php?group_id=150681&package_id=286282&release_id=687593">Sourceforge</a>, and we kindly ask beta-testers for bug reports on the <a href="http://bugs.bioclipse.net/">bugs.bioclipse.net</a>.Ola Spjuthhttp://www.blogger.com/profile/10379047094508592338noreply@blogger.com0