Bioclipse 2.6 released

The Bioclipse team is proud to announce the release of Bioclipse version 2.6. The release contains new Decision Support models (such as for ChEMBL and Chemspider), the latest CDK with e.g. improved aromaticity detection, and Bioclipse-R (including R-models for DS), 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.

Bioclipse 2.6 is available for Mac OS X, Linux, and Windows and can be downloaded from Sourceforge. A getting started guide is also available.

Thanks to everyone who has contributed to this version.

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// The Bioclipse team

Bioclipse 2.6.0 Release Candidate is out

The Bioclipse team is proud to announce a release candidate for Bioclipse with version 2.6.0.RC1.
We kindly ask from the community to put Bioclipse to the test and report bugs at http://bugs.bioclipse.net.

Download Bioclipse 2.6.0.RC1.
A getting-started guide is available.

Summarizing what's new (in no particular order):

• New Decision Support models (e.g. chemspider, daphnia, herg, opentox, SmartCyp)
• Bioclipse-R, including R-models for DS
• New online updates/installation
• New user interface for downloading data and predictive models
• Installer for Windows and Mac OS X
• CDK version 1.4.15 including e.g. better double bond localization, more atom types, and speed improvements.
• InChI (jni-inchi 0.8) supporting InChI v 1.0.3 (both standard and non-standard InChI).
• Improved core stability (Eclipse 3.8)
• Nightly build with Hudson and new provisioning system p2
• Numerous bug fixes

Chemical decision support with Chemspider and ChEMBL-RDF

Bioclipse Decision Support 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 chemical liability assessment, and for running OpenTox predictions.

In the recent days I have implemented a module for adding a ChemSpider SimilaritySearch complemented by ChEMBL lookup via the ChEMBL-RDF data maintained by Egon Willighagen. In short this is how it operates:

1. Query ChemSpider using the SimilaritySearch via the Web API (SOAP).
2. For a maximum of 15 nearest neighbors in Chemspider, query ChEMBL-RDF for interactions, and present information about assays, targets, and interaction values.

Below you can find a screenshot of how it looks like in action. Now, the ChemSpider similarity search is rather slow (>30 s) but then again it takes a while to query 27 M chemical structures.

Note: 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 here. When you have a security token, paste it into the Chemspider section of the Bioclipse preferences. The Chemspider + ChEMBL model for Bioclipse Decision Support will be part of the 2.6 release of Bioclipse, which we hope to have in place within a few weeks.

Thanks to Egon Willighagen (ChEMBL-RDF) and Valery Tkachenko (Chemspider) for aiding me in this work.

Postdoc position in predictive toxicology at Uppsala University

Postdoc position in cheminformatics, bioinformatics, or computer science - applications in predictive toxicology

We have an open postdoc position in the group of Pharmaceutical Bioinformatics at the Department of Pharmaceutical Biosciences, Uppsala University, Sweden.

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 (www.bioclipse.net). 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.

Deadline for application: May 9th , 2012.

Link to job ad and application form: http://www.uu.se/jobb/others/annonsvisning?tarContentId=186211&languageId=1

Bioclipse meets OpenTox

Barry Hardy wrote a very nice post about when he encountered the Tamboti Tree, a very toxic tree, and his experience when using Bioclipse and OpenTox to assess its toxicity. Read the full article and watch the movie here: http://barryhardy.blogs.com/theferryman/2011/03/the-tamboti-tree-use-case-bioclipse-meets-opentox.html

Presenting at Society of Toxicology 2011

Tomorrow I will present a poster at the Society of Toxicology Annual Meeting 2011 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 Decision Support feature for Bioclipse. Anyway, this is what my poster looks like:

Web seminar on Bioclipse

Ola Spjuth of the Bioclipse project will give a web seminar on Mar 29th 16:00 GMT entitled: In-Silico Prediction of Drug Safety and Metabolites Using Bioclipse. The seminar is free of charge but requires registration.

Bioclipse 2.4.1 now on update site

A 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.

To update go to Help -> Software Updates... and select the features you want to install.

Known problem: The splash screen erroneously shows version number to be 2.4.0 after update. (Technical information can be found at bug: 2084 in our Bugzilla)

Bioclipse 2.4 released

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.

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).

• Download Bioclipse
• Getting started guide
• Planet Bioclipse integrates blogs related to Bioclipse.

Bioclipse 2.4.0.RC3 is here

A new release candidate is out and can be found at the usual site for release candidates:

http://pele.farmbio.uu.se/bioclipse-devel/

I have a good feeling about this one. I think Bioclipse 2.4 is really close now.

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 Bugzilla. :)

Bioclipse 2.4.0.RC1 is out

A new release candidate is out and can be found at the usual site for release candidates:

http://pele.farmbio.uu.se/bioclipse-devel/

What is new?
Among the main news are:

• New molecules table.
• We are now using Java 1.6
• Eclipse 3.5.2
• CDK 1.3.5

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 Bugzilla.

Bioclipse is finalist for the Eclipse Community Awards 2010

Bioclipse is one of three Finalists for the Eclipse Community Awards 2010 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 submission abstract). UPDATED: My poster is now accepted!

Below is the screencast which I constructed for the Community Awards submission:

Bioclipse 2.2 released

The 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:

* Cheminformatics, with a pure SWT-based chemical 2D editor (JChemPaint) and a lazy-loading molecules table.
* QSAR, supporting local, REST, and XMPP services
* MetaPrint2D for interactive site-of-metabolism prediction for chemical structures
* StructureDB and VScreen: A chemical database with virtual screening functionality
* The new Decision Support feature with graphical reports using BIRT
* Semantic web features
* Bioinformatics, with the new Sequence Editor and sequence alignments via the Kalign Web service (Experimental)

A screenshot from Bioclipse with the MetaPrint2D feature showing predicted sites of metabolsim for a set of drugs in the MoleculesTable.

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 installation guide is also provided, but the main documentation for Bioclipse is available from help.bioclipse.net; the same information is also available from within Bioclipse from the menu Help > Help Contents. For general questions there is the bioclipse-users and bioclipse.devel mailing lists.

Links:

• Download Bioclipse 2.2.0.
• Bioclipse help (online version)
• Bioclipse website
• Bioclipse 2.0 announcement
• Installation guide
• Report a bug
• Mailing lists

Congratulations doctor Ola Spjuth

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 here and more importantly I have it all documented in pictures on flickr.