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.

Download PDBs with Bioclipse

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

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

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

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:

	//==============================================================
	//Filter a StructureDB instance using the VScreen feature
	//Author: Ola Spjuth
	//==============================================================
	var DB = "Drugbank"; //Refer to an existing StructureDB database
	//Add some filters
	filters=java.util.ArrayList();
	//Xlogp should be between -2 and 4
	filters.add(vscreen.createFilter("XlogP" , "<" , 4));
	filters.add(vscreen.createFilter("XlogP" , ">" , -2));
	filters.add(vscreen.createFilter("MW" , "<" , 450));
	filters.add(vscreen.createFilter("MW" , ">" , 150));
	filters.add(vscreen.createFilter("restrictElement", "C,N,O,Cl,S,F"));
	filters.add(vscreen.createFilter("RingCount" , ">=" , 1));
	filters.add(vscreen.createFilter("RuleOfFive" , "<=" , 1));
	filters.add(vscreen.createFilter("TPSA" , "<" , 200));
	filters.add(vscreen.createFilter("TPSA" , ">" , 80));
	filters.add(vscreen.createFilter("SMARTS" , "a[N;X2]=O CO[N;X2]=O"));
	//Do screening of DB, results in a subset in same database
	//vscreen.filter(DB,filters,"filtered");
	//Do screening of DB, results in a subset in new databse
	vscreen.filter(DB,filters,"DBF1","filtered");

view raw vscreen.js hosted with ❤ by GitHub

A screenshot from Bioclipse is shown below:

Bioclipse 2.1.0 development release

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

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

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

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.