I'm just back from the EBI where I participated in a Wellcome Trust workshop "Molecular Informatics Open Source Software", organised by Mark Forster of Syngenta. I gave a talk on Cinfony (slides to follow), while fellow Open Babel developers Tim Vandermeersch and Chris Morley spoke about Open Babel.
What a great meeting.
It was 50% Open Source Software developers, and 50% pharma industry. Or so I thought at the start. It quickly became apparent that the scientists from pharma were also developing or supporting open source software through a variety of methods. Rajarshi's excellent overview gives a list of some of the talks from industry in this space. I will be following up some of these over the next while.
Of the projects from academia, some which were new to me were Bio-Linux (bio-focused Linux distro available on request as bootable USB sticks from NERC [one of the UK research agencies] - especially useful for teaching), ChemT (GUI for chemical library generation), MOLA (use USB sticks to turn a typical computer lab into a cluster for running AutoDock jobs), and OpenStructure (somewhat similar to PyMol).
The workflow softwares Taverna and KNIME are both doing well. Taverna is widely adopted in the bioinformatics community, while KNIME has considerable mindshare in pharma. An interesting aspect of Taverna is that workflows can be stored at http://myexperiment.org, and users can combine other workflows with full attribution. KNIME now has nodes for RDKit and Indigo (as well as most commercial vendors), toolkits which should be familiar to regular readers here.
Silicos now has several open source offerings for library design and general computer-aided drug design: Sieve (filtering on properties), Pharao (pharmacophore alignment), Piramid (shape-based alignment), Stripper (extract molecular scaffolds according to a variety of schemes), Spectrophores (3D fingerprint for QSAR). An interesting development is the ProfiLib web application which returns a PDF that characterises an uploaded molecular library (in SDF form).
There may be some outcomes from this meeting over the next while, so stay tuned...