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: