Bioinformatics Open Source Conference 2011 — Day 2 afternoon talks

Ben Vandervalk — SADI for GMOD: Bringing Model Organism Data onto the Semantic Web

SADI is a Semantic Web framework developed to get RDF documents, described with OWL. Ben wrote several SADI services to access sequence feature data from GMOD. Takes in input RDF, does a query, and returns back feature descriptions in RDF. SADI service works off GFF files and is a CGI script. Can get from SADI GMOD google website.

Stian Soiland-Reyes — Scufl2: because a workflow is more than its definition

Scufl2 is a workflow format for Taverna. Wanted to handle workflows and be compatible with Semantic Web technologies. Capture information to re-run and re-use any part of workflow. Idea is to get fully reproducible workflow from a paper.

Workflow distributed as a bundled zip file. It contains a workflow bundle RDF file along with workflow RDF, profile RDF, annotation RDF, input and output RDFs. Main development page is at workflow4ever and code on Github. Currently in alpha stage, aiming for releases later in the year.

Tomasz Adamusiak — OntoCAT – an integrated programming toolkit for common ontology application tasks

Tomasz starts off by calling everyone wolves. Then mentions that the problem with the 3 little pigs is that they did not provide a consistent API. Relevance of RDF is that we have multiple ontology repositories: EBI, BioPortal, plus local ontologies. OntoCAT is a database and browser, REST service and GoogleApp. It provides an extraction layer over the different resources so provides a set of common methods to access ontologies. Has a web tool and R package.

Steffen Moeller — Debian Med: individuals’ expertize and their sharing of package build instructions

Bioinformatics has an enormous number of bioinformatics tools that are specialized and can be challenging to install. Debian Med is a community package repository: publication of packages, collaboration and public engagement. Packaging is all volunteer work and shared with Bio-Linux and other communities. Current work is incorporating additional Java packages, establishing complete workflows, data management with BioMaj.

Andreas Hildebrandt — The Biochemical Algorithms Library for Rapid Application Development in Structural Bioinformatics

Motivation: difficult to design new drugs, despite improvements in data generation, knowledge and techniques. Want to improve drug design. Approach is to generate structures: start with PDB, parse them, add missing atoms, infer bonds and optimize atom positions. Biochemical Algorithims Library helps handle these steps. It has Python language bindings so you can work with it directly from scripting languages. The viewer has some beautiful pictures of 3D structures.

Simon Mercer — A Framework for Bioinformatics on the Microsoft Platform

Simon talks about the work Microsoft is doing to build a reusable Bioinformatics toolkit built on the .NET framework. The Microsoft Bioinformatics Framework is at version 2.0; cross platform and works on Mono. The name of the project is going to change as they are moving to the OuterCurve foundation and will not be guided or owned by Microsoft.

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