Bioclipse 2.0 Release Candidate 5

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

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

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

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

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

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

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

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 website
• Bioclipse wiki
• Installation instructions

Bioclipse 2.0-beta2 released

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 website
• Bioclipse wiki
• Installation instructions
  

Bioclipse 2.0beta released

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

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

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

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:

• Bioclipse website
• Bioclipse wiki
• Installation steps
  

/The Bioclipse Team

Threading and Javascript

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.