BioclipseBlog

Bioclipse meets OpenTox

2011-03-08T23:17:00.003+01:00

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

2011-03-07T05:12:00.003+01:00

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

2011-03-04T00:08:00.002+01:00

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

2010-08-30T14:52:00.003+02:00

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

2010-07-09T15:28:00.001+02:00

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

2010-07-06T19:21:00.002+02:00

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

2010-06-01T11:25:00.004+02:00

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

2010-03-07T14:00:00.004+01:00

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

2010-01-28T17:12:00.008+01:00

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:

Congratulations doctor Ola Spjuth

2009-11-30T11:21:00.003+01:00

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.

Download PDBs with Bioclipse

2009-11-03T14:34:00.006+01:00

It is easy to download bioinformatics resources into Bioclipse using the WSDbfetch Web service at the European Bioinformatics Institute (EBI). From console you can use the method:

ws.downloadDbEntry(String db, String query, String format)

From the GUI you can use menu: File > New... and select the Wizard Download > Query WSDbfetch at EBI. Click next and see the many available databases in the dropdown list Supported databases:

Try for example to download the sequence "NM_210721" from the "refseq" database.

If you'd like to download proteins in PDB format, there is a convenience wizard available in the New Wizards dialog available from the menu File > New...

Clicking Next 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.

Align sequences with the Kalign Web service

2009-11-03T14:24:00.005+01:00

A recent feature addition to Bioclipse is the ability to align protein sequences using the Kalign Web service available from the European Bioinformatics Institute (EBI). 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 Align > Align using Kalign.

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 SequenceEditor (note the new Wrap feature available from the toolbar).

The feature is available from the latest development version of Bioclipse.

Bioclipse 2.1.1 devel release

2009-10-03T14:02:00.004+02:00

A new development release is now available for download at http://pele.farmbio.uu.se/bioclipse-devel/. Highlights of the development update site (http://update2-devel.bioclipse.net) are:

Bioinformatics, with the new Sequence Editor now capable of wrapping sequences
Bioclipse Reporting (BIRT)
QSAR, supporting local, REST, and XMPP services
Semantic web features (RDF and Pellet)
StructureDB: A chemical database for Bioclipse
The new VScreen feature for Virtual Screening
The new Decision Support feature
The new MetaPrint2D feature

Note that the development versions are not compatible with the stable 2.0.x release branch which is available from Sourceforge. This update replaces the 2.1.0 devel release, and the devel update site is only compatible with the 2.1.1 release.

Figure: Screenshot teaser from the Bioclipse 2.1.1 devel release showing the Decision Support feature in action for a collection of molecules.

Virtual Screening for Bioclipse

2009-10-03T13:47:00.004+02:00

I recently created a Bioclipse feature to filter chemical structures in a StructureDB database (the new database for chemical structures in Bioclipse). The new plugin is called VScreen, 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.

Currently, the only way of interacting with the plugin is via Bioclipse scripts. A sample usage is available below in a Gist:

A screenshot from Bioclipse is shown below:

Bioclipse 2.1.0 development release

2009-08-07T14:34:00.002+02:00

Today 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 Sourceforge.

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

Bioclipse 2.0 released

2009-07-09T11:19:00.015+02:00

On behalf of all Bioclipse 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 (Jmol), a Molecules Table capable of reading large files, and a powerful backbone in cheminformatics provided by the Chemistry Development Kit (CDK) library.

Figure 1: Screenshot of Bioclipse showing editing of a chemical structure using the new JChemPaint editor.

Bioclipse is a Rich Client 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 Eclipse framework, Bioclipse delivers a state-of-the-art plugin architecture which makes it possible to extend it in any direction.

Figure 2: Screenshot of the interactive 3D visualization of a protein using the integrated component Jmol.

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.

Figure 3: All functionality in Bioclipse is available from an integrated scripting language based on Javascript.

Bioclipse 2 can be downloaded from Sourceforge, releases are available for all major platforms. There is an update site where users can install additional functionality (such as Speclipse) and data collections; this is available from the Bioclipse workbench under menu Help > Software updates.

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 mailing list.

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 bugs.bioclipse.net. There is a list of intractable bugs on the Bioclipse development wiki, and also a convenience list for tracking known major bugs.

Bioclipse is an open development that welcome new developers with varying backgrounds. Developers hang out on daily basis on IRC (irc.freenode.net, channel #bioclipse), and can also be reached via the mailing list bioclipse-devel.

Thanks to all contributors who made this release possible!

Working with large SDFiles in Bioclipse

2009-07-03T16:04:00.006+02:00

I 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 ChEBI (Chemical Entities of Biological Interest) 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.

Figure 1: Screenshot from Bioclipse with the entire Chebi SDF open.

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!

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.

As a side note: Handling large SDFiles is generally not a recommended solution. When StructureDB (a relational database for chemistry) is released for Bioclipse, we will see a dramatic performance boost when dealing with large collections of molecules.

Bioclipse 2.0 Release Candidate 5

2009-07-02T17:09:00.005+02:00

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 Bioclipse help is also available as standalone. The release requires a fresh download from Sourceforge, and we kindly ask beta-testers for bug reports on the bugs.bioclipse.net.

Bioclipse 2.0 Release Candidate 4

2009-06-29T16:44:00.001+02:00

Today, Bioclipse 2.0 Release Candidate 4 (versioned 2.0.0.RC4) was released. The release requires a fresh download from Sourceforge, and we kindly ask beta-testers for bug reports on the bugs.bioclipse.net.

Hopefully this will be the candidate for the 2.0 release.

Bioclipse 2.0 Release Candidate 3

2009-06-24T09:44:00.001+02:00

Today, Bioclipse 2.0 Release Candidate 3 (versioned 2.0.0.RC3) was released. The release requires a fresh download from Sourceforge, and we kindly ask beta-testers for bug reports on the bugs.bioclipse.net.

Bioclipse 2.0 Release Candidate 2

2009-06-15T13:22:00.001+02:00

Today, Bioclipse 2.0 Release Candidate 2 (versioned 2.0.0.RC2) was released. The release requires a fresh download from Sourceforge, and we kindly ask beta-testers for bug reports on the bugs.bioclipse.net.

Bioclipse 2.0 Release Candidate 1

2009-06-05T17:21:00.003+02:00

Today, Bioclipse 2.0 Release Candidate 1 (versioned 2.0.0.RC1) was released. This constitutes a big step towards the Bioclipse 2.0 release and also implies a feature freeze. The release is available from Sourceforge, and we kindly ask beta-testers for bug reports on the bugs.bioclipse.net.

Figure: Screenshot from Bioclipse showing the drug Reserpine with
a SMARTS hit highlighted as substructure.

Bioclipse 2.0RC1 includes the core, chemoinformatics, and balloon features as well as extended sample data, the Blue Obelisk Data Repository, and the Drugbank collection. On the main update site are the Bioclipse SDK, CDK Power tools, XWS4J, and hivpred features. The Experimental update site contains the experimental feature (with R support), the QSAR, RDF, and XML feature. See www.bioclipse.net and the Bioclipse Wiki for more information about the features.

Bioclipse 2.0-beta5 released

2009-05-21T14:44:00.002+02:00

Due to a major update in the Bioclipse managers, Bioclipse2.0 beta5 was released today (versioned 2.0.0.B20090520). Grab your download from Sourceforge (unfortunately this release cannot be updated from the update site). This IS the last beta release before Release Candidate 1, and contains numerous bug fixes to JCP, SDFEditor. Please report any bugs to http://bugs.bioclipse.net.

Bioclipse 2.0-beta4 released

2009-04-09T15:09:00.003+02:00

Today, Bioclipse2.0 beta4 was released (versioned 2.0.0.B20090409). Grab your download from Sourceforge (unfortunately this release cannot be updated from the update site). This is (hopefully) the last beta release before Release Candidate 1, and contains numerous bug fixes, Balloon for 3D conformer generation, and a SmartsView for testing out SMARTS on your chemical structure. Please report any bugs to http://bugs.bioclipse.net.

Screenshot: Bioclipse 2.0beta4 with all Features installed from update site. From left to right: Eclipse RCP, XWS4J, CDK Extras, Sample Data, Blue Obelisk Data Collection, Balloon, QSAR, HIVPred, and Chemoinformatics.

To learn more about the features and projects in Bioclipse, see the Bioclipse Wiki.

Bioclipse 2.0-beta3 released

2009-02-28T14:40:00.005+01:00

Today, Bioclipse2.0 beta3 was released with id 2.0.0.B20090227. Grab your download from Sourceforge. The major updates in this release are many bug fixes for JChemPaint for 2D editing, and a new MoleculesTable with resizable columns and rows (see Figure 1) for working with collections of molecules.

Figure 1: Screenshot showing the new MoleculesTable with resizable columns and rows (middle), the selected molecule in the 2DView (top right) and molecular properties of the selected molecule (bottom right).

Also added is a new update site for experimental features, including an early version of the Bioclipse QSAR package (see Figure 2). Experimental site will be used extensively in the future to give users the ability to test new features that are in development.

Figure 2: Screenshot showing the experimental QSAR editor (bottom), the Matrix editor (top) and a Plot (bottom left) of two descriptors against each other.

Please note that you need to download a fresh version from Sourceforge, it is not possible to upgrade from Software Updates inside Bioclipse.

Links:

Bioclipse 2.0-beta2 released

2009-02-13T16:08:00.004+01:00

Today, Bioclipse2.0 beta2 was released. The status was unfortunately not good enough so that a release candidate could be made available this week. Anyway, the beta2 version is packed with new features, like a completely new Welcome page, SMILES files support, and numerous updates to JChemPaint for 2D editing.

Figure: A topic in the new Welcome page of Bioclipse

Existing users cannot upgrade to Bioclipse 2.0beta2 via online updates; the version requires a fresh download from Sourceforge.

Figure: A drug visualized in 3D using the isoSurface command in Jmol.

Links:

Bioclipse 2.0beta released

2009-01-23T17:16:00.004+01:00

Today, the beta version of Bioclipse (versioned 2.0.0B20090123) was released. This release features, among others, the new JChemPaint, a new SDFEditor capable of parsing large files (tested >1Gb), a rewritten welcome page, a new console for command line access, a new Javascript editor to run scripts, etc. It also features (via online updates) optional installation of the XMPP plugin for accessing web services based on XMPP, etc.

Existing users cannot upgrade to Bioclipse 2.0beta via online updates; the version requires a fresh download from Sourceforge and read the installation guide.

More information: See the Bioclipse website and the Bioclipse development wiki.

Bioclipse 2.0.0A20081028 released

2008-10-29T11:12:00.003+01:00

Today, Bioclipse 2.0.0A20081028 was released. For existing users: Bioclipse should pick this up and ask for upgrade automatically, but you can always choose menu "Search for extensions..." to manually start the upgrade.

The upgrade brings numerous bug fixes to Bioclipse, but the new JChemPaint and CDK1.2 rendering are not included yet. Bioclipse 2.0.0 is preliminary scheduled for release in mid December, and will contain a new 2D-editor for chemical structures (JChemPaint 3), a new MoleculesTable (for editing large lists of molecules like SDFiles, database queries etc), a new Jmol feature with stable Jmol interaction, search/retrieval/editing/upload of various spectra, and a plugin for local chemical databases (StructureDB). More features (QSAR, Pharmacophores etc) will be available in early 2009.

Get Bioclipse 2.0.0 alpha02 at Sourceforge and read the installation guide.

The Bioclipse Team

Bioclipse 2.0-alpha02 released

2008-08-08T11:23:00.003+02:00

To fix some things in the core Bioclipse plugins of Bioclipse, the 2.0.0.alpha02 version was released today (new versioning: 2.0.0.A20080808 where A stands for alpha). You are not able to upgrade to this version from the update site, and any new updates from that site will not work in alpha01 version. This is an inconvenience that we hope not will be repeated, but was necessary at this point.

Get Bioclipse 2.0.0 alpha02 at Sourceforge and read the installation guide.

Bioclipse 2.0-alpha01 released

2008-08-01T19:06:00.007+02:00

The Bioclipse Team is proud to present the first alpha release of Bioclipse2. Note that this is a release targeted towards developers. We are extremely happy for all sorts of feedback, please read here about how to submit bug reports or feature requests.

Fig: Screenshot of SDFile editing in Bioclipse2.

Bioclipse2 is released for Windows (win32_32, win32_64), Mac OS X (x86, ppc), and Linux (x86_32, x86_64), and downloads are available from the Sourceforge download page.

Fig: Screenshot of 2D editing in Bioclipse2.

On first startup, Bioclipse will search for updates to currently installed features but will not install extra features. To do this, simply go to the menu Help > Search for updates...

Fig: Screenshot of 3D visualization in Bioclipse2.

Links:

/The Bioclipse Team

Threading and Javascript

2008-05-21T13:33:00.014+02:00

The Javascript console is slowly acquiring features that the other two consoles (ruby and groovy) don't have. The latest addition to this line of features is threading. Here's what we learned from adding threading:

We still think threading is tricky. Basically, we kept adding synchronized to places until everything worked. Effective Java says that you shouldn't add synchronized everywhere.

The basic problem was this: when executing long commands, the js interpreter grabbed the main thread, and things locked up.

We solved this by replacing the js environment with a js thread, which in turn initialized the environment.

After that change, commands were executed, but couldn't print things back to the js console.

So, we devised a mechanism for sending the js thread a "post-command hook" along with the js command. The post-command hook is a piece of code that the js thread executes after it has executed the js command. Sending code as parameters is exciting!

Normally, one puts such code into an anonymous Runnable subclass, but we couldn't do that, since Runnable.run() doesn't take a parameter, and we needed to send a parameter to our hook. So we invented our own class, Hook.

Overall, the Javascript console hasn't really recovered after this set of changes. Some of the additions required excessive scoping, and there are probably refactorings to be made. But overall, our first adventure into the land of threading has paid off: if you run a long, heavy job on the Javascript console, the Bioclipse GUI no longer locks up and stops responding until the job is done.

JChemPaint with highligting in Bioclipse2

2008-05-07T14:45:00.002+02:00

Following up on the recently added MDLEditor using JChemPaint in Bioclipse2, I created and added an Outline with selections properly highlighted in the structure in JChemPaint. Also added are basic properties available in the Properties View. They are currently read-only, but could easily be extended for editing properties of the selected entity.

Editor for SDFiles in Bioclipse

2008-04-28T14:46:00.002+02:00

Based on Egon's new StructureWidget, I constructed an Editor to browse SDFiles in Bioclipse. It uses lazy UI rendering and is shows very promising performance. Apart from reading and rendering the structure, it also reads and displays properties in a table. Indeed a very important feature-addition towards open source QSAR in Bioclipse!

Jnanotube - a nanotube plugin for Bioclipse

2008-04-17T10:35:00.004+02:00

I'm delighted to announce the addition of a new Bioclispe plugin entitled 'Jnanotube'. The plugin makes it possible to easily create nanotube structures in Bioclipse. The plugin adds a new view, 'Jnanotube' which consists of GUI components that are able to generate virtual XYZ files that easily can be displayed in the JmolView. The plugin was contributed for the Bioclipse 1.2.x branch by Joe and Sam, and I hope they will continue to support the plugin for Bioclipse2 as well, and are looking forward to other additions from them (they have hinted that they are building a peptide-builder plugin). So far the plugin is not part of a Bioclipse release, but we will include it in the next 1.2.x release.

General service infrastructure in Bioclipse

2008-03-14T16:47:00.006+01:00

The last week I have worked on a general service infrastructure for Bioclipse, or more specifically for Bioclipse2. the thought is to be able to easily add new services and service implementations via extension points in Bioclipse. The installed services can be displayed in the ServiceView (see figure to the right), and the aim is to add filters and hence only display the currently interesting services (based on user preference of course). Double-click the service to invoke it with a dialog or drag a resource (a sequence or a molecule) and drop it on a service to invoke it directly.

For a more detailed explanation about the extension points and examples for using it can be found on the Bioclipse wiki. Below is a sample screenshot for how this integrates into Bioclipse2.

A fully working use case with recording

2008-03-07T17:21:00.005+01:00

Much hard work has finally paid off and now there is some cool recording features in bioclipse 2. Since I know how you all would love to try it out I am now gonna explain how you can do that. The plugins needed for this example is net.bioclipse.biojava.ui and all it's dependencies. First of all we need a sequence file containing a couple of sequences. I called my file "a.fasta". Something looking like this would suffice:

>a
ACT

>b
ACG

You can create such a file in Bioclipse by right clicking in a project and creating a new file.

Now for the interesting part. This sequence file contains two sequences. If we want to translate one of them we can open the children of the sequence file by clicking on the arrow in the left of it in the bioclipse explorer. Right clicking any of the sequences brings up a context menu where biojava.ui has contributed a few actions. We can for example translate our sequence to a protein sequence. After having done that, bring up the Action History view. It is under the Scripting category in the show view dialog.

The actions history view shows a view of the recording that has been taken place while we have clicked around in the gui. Select the actions you are intrested in, right click and choose Generate JavaScript. The JsScriptGenerator will now do it's best to build a javascript out how the selected actions. That isn't always so easy but I hope it performs quite good and I know that it succeeds with the sequence translation example I have described here. Try it out and please report any problems that you might find.

The 5000th commit to Bioclipse

2008-03-04T16:30:00.000+01:00

The Bioclipse project team is delighted to announce the 5000th commit to Bioclipse made by Egon Willighagen when performing an SVN reorganization for Bioclipse2. Great job, Egon!

Swedish Bioinformatics Workshop

2008-03-01T13:07:00.000+01:00

The Bioclipse team was present during the Swedish Bioinformatics Workshop in Uppsala on February 28th-29th. Ola Spjuth held a well-received talk about Bioclipse data integration in bioinformatics, and a poster detailing the workings of Bioclipse drew both interested parties in the hallway track, and a price for best poster. Overall, the reception of Bioclipse felt very positive, and many new contacts were made, possibly leading to further collaborations.

DAS workshop 2008 - day 1

2008-02-25T14:48:00.000+01:00

Today was the first day of the DAS workshop 2008 that I visited on behalf of the Bioclipse project. It was held at EBI and had some interesting presentations and discussions. Apart from introducing the Distributed Annotation System (DAS), the first day consisted of presentations of many client implementations. DAS is basically a set of Web services for annotation of biological sequences with the goal to split data and presentation. This means that a DAS client can request info from many DAS servers and integrate the info in a single view or analysis. The technology behind is simple HTTP requests that return XML responses. Uniprot is the reference server and provides the sequences.

Jim Procter presented Jalview and VAMSAS, an exchange format to combine Topali, Jalview, and AstexViewer.

Rob Finn talked about the new Pfam website with nice feature visualization that incorporated DAS. He talked about their REST web services and how they are superior to SOAP-based implementations for resource-providers like themselves.

Rafael Jimenez demonstrated Dasty2, which is a DAS web-client using AJAX.

Thomas Down talked about Dastard and the problem of firewalls. He also interestingly brought up the question weather DAS clients should be Web-based. He himself preferred desktop apps to get better interaction with other local programs (excel etc). He also recommended the Java database Derby over HSQLDB.

Andreas Prlic talked about DAS registries and the SPICE viewer for connecting genomes with structural data and visualize SNPs and multiple alignments on 3D.

Asja Grzibovska described the DAS Writeback project that extends read-only DAS model by adding possibilities to write data back to the server.

Hagen Blankenburg described molecular interactions with DAS, called DASMI. They have extended DAS servers with support for protein-protein interactions. He also showed the DASMIweb client which is able to integrate a lot of data from interaction databases. I wonder why people keep calling it molecular interactions instead of protein-protein interaction?

Jose Ramon Macias talked about their extension of DAS to cope with 3D Electron Microscopy, called 3D-EM DAS. They had built a client, Pepper, but as they required more responsive functionality they were discussing building yet another client for DAS based on the Netbeans Rich Client Platform. He was familiar with Bioclipse but had decided to use Netbeans because he was familiar with it. Let's hope they'll honor MVC to full extent!

Syed Haider presented Biomart which basically is a convenient way of joining databases together by visualizing original tables and generating the SQL for the mart construction. They are close to having an incremental-update function. We really should build a Biomart plugin for Bioclipse!

Several people mentioned OpenID for single sign-in. This is maybe something that we should consider for Bioclipse in the long run.

Well, this ends day 1. Tomorrow we will get hands-on instructions for coding a DAS client, but first it's dinner in Cambridge.

Multiple alignments in Bioclipse

2008-01-21T13:33:00.000+01:00

I have talked a lot about about integrating Jalview into Bioclipse for visualization and editing of multiple sequence alignments. I spent some hours on the problem and it was not too hard to get things going. It's now possible to double-click an alignment in any of the formats supported by Jalview (fasta, msf, clustalw, pileup, pir, blc, pfam) and Bioclipse opens an Alignment Editor with Jalview on one tab and the source file on the second.

It is currently not possible to interact with Jalview via the mouse, this needs some wrapping of functionality into SWT actions and menus. But it's a good start :-). See the wiki page net.bioclipse.jalview for progress.

Complete

2008-01-08T18:04:00.000+01:00

Go to the Javascript Console, type rhi and press <Tab>. The command line now says rhino.

If you now type a . (after the rhino) and then <Tab> twice. The first time around, there'll be a beep, and the second time, there'll be a list of possible completions.

People seem happy about this feature when I show it to them. Myself, I'm even happier because I got to implement the (top secret) mechanism that does this under the hood. I could tell you more, but I would have to kill you.

Update: I forgot to say that this goes for Bioclipse 2 only, but I've now backported the feature to Bioclipse 1 too.

Update²: Tab completion now in the Ruby Console, too.

Subversion in Bioclipse2

2008-01-02T13:32:00.000+01:00

Since Bioclipse2 is more Eclipse-like, it is quite easy to make use of external Eclipse plugins. Here I demonstrate this by adding the Subclipse plugin for Subversion and making use of it from the Bioclipse2 workbench.

Figure: A local project shared on a Subversion repository. The editor shows compare of the local and remote version of the same document with changes highlighted.

Having version control inside the Bioclispe workbench opens up many new possibilities for collaborative work. It allows e.g. for shared editing of chemical and biological files, to resolve conflicts, and rollback any undesired changes.

The current solution requires some editing in the Subclipse source due to unresolved dependencies, but I will contact the Subclipse team and try to resolve this.

Links: Bioclipse wiki page

Bioclipse 1.2.0 released

2007-12-21T18:33:00.000+01:00

The Bioclipse Team is happy to announce the release of Bioclipse 1.2.0. This release means that the 1.x branch will no longer be supported. Version 1.2.0 contains (apart from numerous bug fixes) several exciting new features:

An interactive console view for writing scripts in Javascript
QSAR plugin with an extension point for descriptor calculations from chemical structures - mix different descriptor providers Read more...
Create CDK descriptors and JoeLib descriptors using a wizard (select 1-N molecules and right-click -> Calculate descriptors). Sets up Descriptor Dataset (matrix). Read more...
Matrix editor for editing spreadsheet-like files with custom matrix implementations (Jama is default implementation)
Chart view for displaying charts from e.g. Matrix editor (select cells and right-click to try) Read more...
Select cells in Matrix and visualize in Chart
Select in chart highlight cells in MatrixEditor (only scatterplot so far)
Spectrum feature is available again
SpecMol allow for visual inspection and peak assignment to atoms in spectra by clicking on molecular structure
Ability to easily add scripting commands via an extension point. Read more...
Jmol now supports switching between models of e.g. a PDB-file (animation)
Experimental support for BioMoby Read more...

Please note that it is not possible to upgrade to Bioclipse 1.2.0 via the online update version; it requires a new download from sourceforge.

Thanks to all developers and contributors that made this release possible!

The Bioclipse Team

Links

Towards standards for QSAR data setup

2007-12-21T11:31:00.000+01:00

I have started to explore the possibilities of Bioclipse2 when it comes to projects with natures and autobuilds. This gave me the idea of automatic QSAR descriptor calculations, based on mine and Egon Willighagens work with QSAR in Bioclipse 1.x. The idea is to have a file (qsar.xml) that defines molecules and descriptors and might look something like below (note: demonstrational example, info and URL's are made up):


<qsar>
 <molecules>
  <molecule id="http://www.mol.repo.org/molecule?abc123" ns="myNS">
  <molecule id="http://www.mol.repo.org/molecule?abc234" ns="myNS">
 </molecules>
 <descriptors>
  <descriptor id="http://www.cdk.sf.net/descriptors/xlogp:implementation1" name="XlogP">
   <parameter key="cutoff" value="10">
  </descriptor>
  <descriptor id="http://www.cdk.sf.net/descriptors/ZagrebIndex:02"/ name="Zagreb Index">
 </descriptors>
</qsar>

The implementation would be an automatic build that calculates all descriptors for each molecules when the qsar.xml changes, but only for deltas (i.e. partial build, do not build already built). This means, add a new descriptor to the qsar.xml and on save it will be calculated for all molecules. This would be done on the background and produce a descriptor matrix (dataset.csv). Any plots of this matrix would also be updated.

I have started to implement this in Bioclipse2 and intend to also create a public repository for storing these QSAR setups.

So, what is missing? Having unique ID's following the REST architecture for descriptors and molecules would make it a standards candidate for QSAR data matrices setup. I shall explore this with the CDK people. Comments on the project's design and implementation are very welcome.

R, matey

2007-12-14T13:18:00.000+01:00

Try this: launch Bioclipse 2 (after the usual updating of all plugins you can think of), open up the Javascript Console, and type this:


js> R
R> x <- matrix( c(9, 9, 0, 1, 3, 2, 0, 7, 6), 3 )
R> y <- matrix( c(4, 7, 2, 1, 1, 0, 1, 6, 5), 3 )
R> x * y
     [,1] [,2] [,3]
[1,]   36    1    0
[2,]   63    3   42
[3,]    0    0   30

R> q()
js>

Shiver me timbers! That's R, matey! Big kudos to kaskelot++ for making it work this far.

Support is still a bit spotty. If you happen to aggravate R in any way, it walks the plank and does not come back, and you're going to have to relaunch Bioclipse. But things can only get better from here. Expect some Bioclipse/R integration soon, for example.

Update: Thanks to some impressive C hackery from kaskelot++, R no longer crashes and goes away forever when input is less than syntactical.

A first stab at echoing

2007-12-13T15:22:00.000+01:00

Update: After a suggestion from olas++, this feature is now called "echoing", to distinguish it from actual logging. Please revise your subjective histories.

Last week, after pondering how to structure the consoles around echoing, and receiving a fair bit of help with listeners from jonalv++, I got my reward: a big fat SWTException (Invalid thread access).

Now all this is fixed, and you can experience the joys of echoing in Bioclipse 2 at home if you want:

Update all your checked-out Bioclipse plugins, or at least net.bioclipse.core (where the console echoer is), net.bioclipse.scripting (where we've put scripting nowadays) and net.bioclipse.ui (where you'll find the scripting console).

Open net.bioclipse.core.Activator in the Eclipse Java editor.

Find the method start and add the following code:


public void start(BundleContext context) throws Exception {
    super.start(context);
    plugin = this;

    new Thread() {
        public void run() {
            for (int i=0; ; i++) {
                try {
                    Thread.sleep(5000L);
                } catch (InterruptedException e) {
                }

                CONSOLE.echo("Now is the time");
                CONSOLE.echo("for all good men");
                CONSOLE.echo("to come to the aid");
                CONSOLE.echo("of their country");
            }
        }
    }.start();
}

Start Bioclipse.

Make sure the Javascript Console is opened.

The famous phrase, used in the early 20th century when demoing typewriters, should now appear on the Javascript Console every five seconds. In the above example, we've put the echoing code into net.bioclipse.core.Activator, but generally it would of course go in Your Favorite Module in need of echoing something to the consoles.

I'd be happy to hear about bugs or oddities related to the consoles or echoing that you may find.

Bioclipse awarded at Trophees du Libre

2007-11-30T22:39:00.000+01:00

I just arrived home from the international contest for free software, Trophees du Libre 2007, which was held in Soissons, France. Bioclipse was awarded the Special Prize of the jury, and the prize was handed over by the president of the Free Software Foundation Europe (FSFE), Georg Greeve, who also was the chairman of the jury. It was a great event; great to meet other open source developers and people representing organizations and companies who actively support free software. Apparently we received the Special Prize because we were too famous already :-).

Scripting in Bioclipse 2

2007-11-22T16:05:00.000+01:00

Go to Window → Show View → Other... in the application menu in Bioclipse 2. Under the heading Scripting, we find Groovy Console and Javascript Console. Pick Groovy Console.

groovy> "CCCTCGCCACCTATACCCAG".replace("T","U")
CCCUCGCCACCUAUACCCAG
groovy> ["Alanine", "Glutamic Acid", "Methionine", "Tryptophan"].findAll { it.endsWith("ine") }
[Alanine, Methionine]

Performing more integrated Bioclipse actions depends on getting more of the data model done, but the above should give a sense of why command-line scripting is something we want.

Our dream is something along the lines of being able to turn many of the common actions in Bioclipse into pieces of scripts, so that actions can be recorded and saved, much like macros in some applications.

The fact that we now have two scripting engines in net.bioclipse.core spurred some discussion on the channel, which has given me food for thought. I do think the scripting capability in Bioclipse 2 should be built-in to the point of being hard to avoid... but there's nothing that says that this capability needs to be a language engine like Rhino or Groovy. Instead, one could imagine it being an API of some sort.

If that turns out to be the way we do it, neither Rhino nor Groovy need be core. My hope is that we can make things decoupled enough to be able to move them out into separate plugins. But it's too early to tell; still too many unknowns.

Coming up: Ruby!

Bioclipse2 and Spring

2007-11-21T11:27:00.000+01:00

Yesterday wasn't a great day for me. I was trying something called Spring-osgi and nothing worked. But I should take it from the beginning or at least a bit earlier.

Spring is a java framework that delivers great features (like Aspect oriented programming) for building java applications. The problem is that Eclipse's plugin structure makes things a little bit more complicated. This is where the Spring-OSGI project enters the scene. The OSGi framework specification forms the basis of the Eclipse Runtime and Spring-osgi is a project for using Spring in an osgi framework. So far so good (in theory). Spring-osgi seems to be a relatively new project and I am not sure that it is mature enough to be a part of Bioclipse 2.

What I tried to get working yesterday was a little mini example Spring service supplied by the Spring osgi project. I failed horribly when it came to running the osgi integration tests.

It would be great to have this in Bioclipse 2 but as things are right now I am not sure it is worth it. We will see what will happend.

First screenshot of Bioclipse2

2007-11-21T09:53:00.000+01:00

Yesterday I added the first editor to Bioclipse2, based on Jmol. The major thing now is to adapt everything to Eclipse, and port e.g. ChemTree to Outline View. I will dig into this while Jonathan works on the Spring core functionality, and Carl works on the scripting language and -console.

Adding scripting commands to Bioclipse

2007-11-05T13:02:00.000+01:00

Following up on my recent post on Scripting BioMoby in Bioclipse, I have created a new extension point to be able to hook in additions to the Rhino scripting language in Bioclipse with a namespace. Add an example extension like below to the plugin.xml of your plugin (example is from net.bioclipse.biomoby.ui):

<extension
     point="net.bioclipse.rhino.scripting">
  <ScriptContribution
        class="net.bioclipse.biomoby.ui.scripts.MobyServiceScripting"
        id="net.bioclipse.biomoby.ui.scripts.MobyServiceScripting"
        namespace="moby">
  </ScriptContribution>
</extension>

The class must implement IScriptProvider and namespace is the desired namespace you like to have (see examples below). An example is the class net.bioclipse.biomoby.ui.scripts.MobyServiceScripting:

public class MobyServiceScripting implements IScriptProvider{

    public void showMessage(String title, String message) {
       MessageDialog.openInformation(
          getShell(),
          title,
          message);
    }

 }

Now it's possible to issue commands in Bioclipse like the following:

  moby.showMessage("wee", "how");

Very convenient in my opinion. This will be extensively used in the upcoming Bioclipse2, which currently is in design phase.

Scripting BioMoby in Bioclipse

2007-11-02T14:19:00.000+01:00

I have been working hard on a BioMoby plugin to get BioMoby into Bioclipse. The ultimate goal is to mix and match between local functionality and remote services, and I have created some sample scripts to assist with this. It is not much for the moment but demonstrates how Bioclipse can take advantage of the many services in BioMoby, both in the GUI and in the scripting language (currently based on Rhino).

A sample script that retrieves a sequence from GenBank via a Moby service, and translates it into FASTA-format using the local library BioJava, is provided below.

console = Packages.net.bioclipse.util.BioclipseConsole;
moby = Packages.net.bioclipse.biomoby.ui.scripts.MobyServiceScripting;
biojava = Packages.net.bioclipse.biojava.scripts.BioJavaScripting;

prot=moby.downloadGenbank("NCBI_GI","111076");
seq=biojava.parseString(prot);
fasta=biojava.toFasta(seq);

console.writeToConsole(fasta);

The ouput of the script is:

Calling service...
Done.
Read: 1 sequences. Returning first.
>gi|111076|lcl|D31461.0|D31461 T-cell receptor delta chain BDN7, thymus - mouse
ATYFCALMERVSRRGAPDKLVFGQGTQVTVEP
Rhino script done.

More information and other sample scripts are available on the net.bioclipse.rhino (formerly bc_rhino) plugin page on the Bioclipse wiki.

Bioclipse 1.1.5 pre-release

2007-10-03T17:15:00.000+02:00

Bioclipse 1.1.5 pre-release is a development release available only from the links below, and will be moved to Sourceforge once more testing is performed. Note that you have to point the update site (available in Preferences... -> Update Site) to http://update.bioclipse.net/dev in order to get the latest available plugins.

Among the new features are worth mentioning: CDK descriptor calculations, a GridEditor for matrices, and a new charting plugin. See the Bioclipse wiki for more information regarding the latest plugins.

Download Bioclipse 1.1.5 pre-release for macosx(carbon, x86), windows(win32, x86), linux (gtk, x86).

Design of Bioclipse2 has started

2007-09-04T16:55:00.000+02:00

Bioclipse has outgrown its original design. We have therefore decided to start the design of Bioclipse2, which will be a complete rewrite of the core API and extension points to overcome the many deficiencies of the current design/implementation. I have established a wiki page for this. If you'd like to participate in the redesign, please add your name in the members section. The discussion will be carried out in IRC (irc.freenode.net, #bioclipse) and on the mailing list bioclipse-devel.

Getting started guide for Bioclipse

2007-09-04T16:53:00.000+02:00

There's an updated Getting Started guide available in PDF-format from the Bioclipse homepage, documentation section:

BioMoby in Bioclipse

2007-08-14T16:28:00.000+02:00

For the last week or so I've been working on a Bioclipse-plugin for BioMoby.

From the BioMoby homepage: "BioMoby defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next."

In short, BioMoby structures inputs and outputs in an extendable ontology which allows services to accept and produce data in well structured ways. By adding a repository, BioMoby also allows for service lookup. The current services are focused on Bioinformatics, but there is nothing preventing us from extending with new data types for e.g. pharmacology and chemistry, and setting up new BioMoby servers with services utilizing these data types.

Using the semantic service discovery and -invokation of BioMoby from within Bioclipse will add a lot of online functionality and also possibilities. I have created a beta-version of the plugin and screenshots are available from the Bioclipse wiki. The plugin utilizes the data type ontology and autogenerates a GUI for each service on the fly, and places them in a Wizard. The plugin is currently not functional but requires some more testing. I will continue that work and the setup up a BioMoby server with some local services in pharmacology when I get back from vacation in 2 weeks.

Bioclipse 1.1.3 released

2007-06-21T17:44:00.000+02:00

Bioclipse 1.1.3 was released today with bug fixes and new features to download from the update site. It is now possible to construct your own update site and add it to Bioclipse. I will set up a wiki page about this when I get back from a week among the Croatian islands.

See www.bioclipse.net for download info.

Proceedings of the Bioclipse Workshop 2007

2007-06-01T15:04:00.000+02:00

The Bioclipse Workshop 2007 was held May 23-25 in Uppsala, Sweden, in
collaboration with Embrace and was a great success. The 45
participants were faced with a mix of Bioclipse-presentations
ranging from visions to practical software development issues. The
hands-on tutorials were mostly given as integrated CheatSheets in
Bioclipse, and although several bugs were found it was overall
considered as a good way of exploring the many features of Bioclipse.

I have put most presentations and tutorials on this Bioclipse wiki page.

Thanks to all who made the workshop possible!

Bioclipse 1.1.1 released

2007-05-18T17:50:00.000+02:00

The Bioclipse team is proud to announce the release of Bioclipse beta release 1.1.1. The release constitutes a major step forward for Bioclipse as we have moved to Features. This means the Bioclipse Workbench's download is now 25 Mb, and all functionality must be added using the menu alternative "Add extensions...". It contacts the Bioclipse Update Site (http://update.bioclipse.net) and the user can select any features he'd like to install. It is also possible to perform online updates when a new version of Bioclipse is released.

* Download Bioclipse 1.1.1
* License statement
* Frequently asked questions

2007-02-22T11:37:00.000+01:00

The Bioclipse project team is proud to announce that the Bioclipse article was published today in BMC Bioinformatics.

Bioclipse: An open source workbench for chemo- and bioinformatics
Ola Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E.S. Wikberg
BMC Bioinformatics 2007, 8:59 (22 February 2007)
[Abstract] [Provisional PDF]

Embrace Workshop on Bioclipse 2007

2007-02-12T23:09:00.000+01:00

Announcement

===========================================
Embrace Workshop on Bioclipse 2007 (EWB '07)
May 23 -25 2007
Uppsala Biomedical Centre (BMC), Uppsala, Sweden
===========================================

Contents:
Bioclipse is an open source workbench for chemo- and bioinformatics with rich functionality for molecules, sequences, proteins, spectra, and scripts. Bioclipse has advanced plugin architecture which facilitates integration of new functionality, such as algorithms, editors, visualizations, Web services, and third party applications. The Embrace Workshop on Bioclipse 2007 (EWB '07) will consist of lectures and hands-on labs to demonstrate the features of Bioclipse, the power of the plugin architecture, and how to integrate new features into the framework.

For registration and more information, please see the workshop homepage and http://www.bioclipse.net.

Bioclipse 1.0.1 released

2007-02-02T16:00:00.000+01:00

Bioclipse 1.0.1 was relesed 2007-02-01. It contains numerous bug fixes and the new plugin bc_rhino which provides Bioclipse with a powerful scripting language.

Links:

Download Bioclipse 1.0.1 from Sourceforge
Release notes for version 1.0.1
The Installation guide is updated
A License statement has been created
Documentation for release 1.0.1 is now available on bioclipse.net in addition to from within the Bioclipse application.
Frequently asked questions have been updated

Outcome of the Bioclipse Autumn Worskop 2006

2006-11-03T14:22:00.000+01:00

The Bioclipse Autumn Workshop 2006 in Cologne has just ended; 3 full days of presentations, demos, discussions, and hacking sessions. Check out the outcome and highlights on the wiki, but I feel that I must mention the new Bioclipse plugin bc_rhino which brings scripting capability (Javascript) into the Bioclipse workbench! Johannes Wagener (edrin) will be working on a general Web service feature using scripts, which in my opinion could be extremely powerful.

I’d like to thank Christoph Steinbeck and the CUBIC crew for a very nice and productive workshop and hope to be able to welcome you all in Uppsala for the Bioclipse Spring Workshop 2007!

Bioclipse 1.0 released

2006-08-11T17:00:00.000+02:00

The Bioclipse team is proud to announce the release
of Bioclipse 1.0.

Bioclipse is a free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc. The major features of version 1.0 are:

* Import and export in various file formats
* Visual editing of molecular 2D-structures
* 3D-visualization of molecules and proteins
* Editing and visualization of sequences and features (DNA, RNA, proteins etc)
* Graphing and editing of various types of spectra, e. g. NMR, MS
* Retrieval of resources (sequences, proteins, etc) from public data repositories
* Scripting of 3D-visualizations with syntax highlighting and content assistance
* PDB-editor with syntax highlighting for working with PDB files
* CMLRSS-viewer for downloading chemical content published on the web using RSS-feeds
* Integrated, searchable help-system
* Hierarchical view of molecular and macromolecular substructures and calculation of chemical properties* Connection with external programs, e. g. PyMol

Bioclipse is a rich client, which means it is run on your local computer but also gives the possibility to communicate with servers for data retrieval and computational services. The powerful plugin architecture is based on Eclipse, and results in a responsive, integrated user interface designed for simple and intuitive operations that at the same time is easy to extend with custom functionality.

There is much ongoing work with Bioclipse and new features are constantly added. Please visit the Bioclipse Wiki in order to get the latest information regarding the development.

Bioclipse is available for download from Sourceforge.

Thanks to all developers who have made this release possible!

Bioclipse 0.9.10 released

2006-08-06T01:14:00.000+02:00

After a major cleanup of jars and testdata, as well as some bug fixes we decided to release Bioclipse 0.9.10, which has a dramatically smaller archive size of ~40 Mb. Available from Sourceforge.

Bioclipse 0.9.9 released

2006-07-31T12:58:00.000+02:00

Bioclipse 0.9.9 has been released as the last pre-1.0 version. The download is available from Sourceforge [1]. We would appreciate everyone to test this version and report bugs to the sourceforge project site [2]. Version 1.0 is scheduled for release on August 11th.

Bioclipse homepage: www.bioclipse.net

[1] Bioclipse downloads
[2] Bioclipse bug reports

Bioclipse 0.9.2 released

2006-06-08T07:49:00.000+02:00

Today, Bioclipse 0.9.2 was released. The new version includes (apart from numerous bugfixes) the following additions:

Updated PDB-parsing
A new PDBEditor for visualization of PDB-files with highlighting and code completion
New help topics

Download the release from SourceForge. Bioclipse is now ready for some serious testing and please report any errors using the SF bugtracker.

Links:
Bioclipse homepage
Bioclipse wiki
Getting Started Tutorial

Bioclipse 0.9.1 released

2006-05-18T16:31:00.000+02:00

Hi,

Bioclipse [1] version 0.9.1 was released today for Linux and Windows, containing bugfixing and updates according to the Wiki [2]. Files are available from Sourceforge [3].

Please report any errors using the SF bugtracker.

[1] Bioclipse homepage
[2] Bioclipse roadmap towards 1.0
[3] Bioclipse downloads

Bioclipse double slam at JAX 2006

2006-05-12T00:22:00.000+02:00

What a day! Bioclipse wins not only the 3'rd prize in JAX Innovation awards 2006 (http://www.jax-award.com/) but also the Audience Award!

I'd personally like to thank all developers and contributors of Bioclipse as well as all the included components (CDK, JChempaint, Jmol, CML, and Biojava) without whom this project would not have been possible.

The award money will be used to fund meetings, workshops, and other events supporting the development of Bioclipse.

Bioclipse nominated for the JAX Innovation Award 2006

2006-05-05T16:23:00.000+02:00

Bioclipse has been nominated as one of the ten candidates for the JAX Innovation ward 2006. The first prize will be awarded to the most innovative projects based on Java and Eclipse. The award ceremony takes place in Wiesbaden May 10th at the JAX 2006 conference, and me and Christoph Steinbeck will be there representing Bioclipse.

Link: http://jax-award.com/

/Ola

Bioclipse 0.9.0 released

2006-05-04T18:17:00.000+02:00

Bioclipse v. 0.9.0 (linux, windows) is now available from SourceForge. The new release features:

Molecular management using CDK
Molecular editing in 2D using JChemPaint
Molecular visualization in 3D using Jmol
Spectra visualization
Sequence management and visualization using BioJava
CMLRSS newsreader

+ and much more exciting features!

Note: This is a feature freeze for v. 1.0 and from now on only bugfixes will be contributed.

To get started, see the Getting Started Tutorial

Please see the Bioclipse wiki for more information on the development.

Bioclipse 0.8.1 released

2006-04-11T10:14:00.000+02:00

Finally I managed to create packages for Linux, Windows and Mac. Bioclipse 0.8.1 includes the new CMLRSS plugin, properties for ChemObjects (such as bonds, atoms in the ChemObjectTree) and fixes several bugs. Download from Sourceforge and simply unzip (creates a "bioclipse" directory). Needs Java 1.5 to run, and if you have multiple Java installed you need to add the following line to the file "bioclipse.ini":

-vm /path/to/java1.5/bin/java

The current version has not been tested on Mac (as we have no machines for testing), so please report to me if it runs (or not) and what VM you used.

See the Bioclipse website and Bioclipse Wiki for more information about the project.

.../Ola Spjuth

Bioclipse 0.8.0 linux released

2006-04-06T20:44:00.000+02:00

Today, Bioclipse v. 0.8.0 was released. Unfortunately it is only available for linux (gtk, x86) due to problems with the latest Eclipse version. We hope to have a Windows version out soon.

The new version is fully functional but is in no way to consider stable. Nevertheless it has all basic functionality such as molecular browsing, 2D-editing (using JchemPaint), 3D-visualization (using Jmol), spectrum analysis and visualization, CML-support and much more. See the Bioclipse Wiki for more information and tutorials.

The release is available from Sourceforge.

Ola Spjuth

Bioclipse listed on Eclipse.org

2006-03-04T13:39:00.000+01:00

Check out http://www.eclipse.org/community/rcpOS.php.
Looks good!

BioclipseBlog up and running

2005-11-29T16:23:00.000+01:00

This blog is intended for the development of Bioclipse.

/Ola Spjuth, core developer