Courtesy of Andres Rueda, Flickr

There are still places available at the 2012 conference on Therapeutic Applications of Computational Biology and Chemistry (TACBAC), 12-14 March 2012, at the Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

This conference will bring together leading researchers investigating computational chemistry and biology techniques as applied to advancing our ability to predict, diagnose and modulate human disease. This broad and multidisciplinary meeting will explore the major challenges in drug discovery and development where innovation in computational approaches and tools can really make a significant and tangible contribution towards novel treatments.  You should attend this conference if you are a researcher interested in drug discovery, or developing or using computational approaches to the development of therapeutics, or if you are a key decision maker in a pharmaceutical or biotechnology company.

Each of the sessions, which progress from identifying disease mechanisms to implementing new therapeutic and diagnostic approaches in the clinic, will bring together experts in both the biomedical and the computational aspects of the topic under discussion. Sessions chairs will encourage discussion and contribution from the attendees.

Session topics
• Clinical implications of individual genomes
• Metabolism and biomarkers
• Computational systems biology
• Discovery of chemical probes
• Modelling xenobiotic metabolism

Registration and submission of abstracts is open now.

CDK-Taverna workflow

We are glad to announce that our article about CDK-Taverna, an open workflow solution for cheminformatics, is now online on BMC Bioinformatics. CDK-Taverna, which lives at http://www.cdk-taverna.de/, features more than 160 workers for various tasks in molecular informatics.

The workflow paradigm allows scientists to flexibly create generic workflows using different kinds of data sources, filters and algorithms, which can later be adapted to changing needs. In order to achieve this, library methods are encapsulated in Lego(TM)-like building blocks which can be manipulated with a mouse or any pointing device in a graphical environment, relieving the scientist from the need to learn a programming language. Building blocks, so-called workers, are connected by data pipelines to enable data flow between them, which is why pipelining is often used interchangeably for workflow.

non-chem doodle by Dan Paluska

Colleague Noel O’Boyle has already reported it: There is now an open collection of javascript-based chemistry components for the web, called ChemDoodle, released under GPL license by iChemLabs, inc. The stuff looks really neat.

The collection comprises viewers, an editor, a look-up component (try entering accession numbers such as “1″, “2″ or “3″ (you get the point?)) and more. The interesting part is that no java applet needs to be loaded and things are supported by the browser directly. This does not mean that they didn’t have to go through a hell of compatibility testing.

We now invite papers for our symposium on computational aspects of Metabolomics at the 239th National Meeting
of the American Chemical Society (ACS) in San Francisco next spring.

Metabolomics studies the occurrence and change of concentrations of small molecular weight chemical compounds (metabolites) in organisms, organs, tissues, cells and ultimately cell compartments in the context of environmental changes, disease or other boundary conditions. It does this by means of spectroscopic and chromatographic techniques and by observing at once not only a few but all compounds visible to the particular technique used. As such, it is a field at the boundary between chemistry and biology, helping to answer biological questions using analytical chemistry and cheminformatics techniques.

The metabolomics symposium at the 239th ACS national meeting in San Francisco invites submissions of talks about computing, informatics as well as chemical information aspects of metabolomics. Topics could include the analysis of metabolomics experiments, metabolomics databases, computer-assisted structure elucidation of metabolites and more. Abstracts may be submitted via http://abstracts.acs.org. You’ll find the metabolomics session as part of the CINF division symposiums. Deadline is October 19, 2009. In case of questions, please email Christoph Steinbeck at steinbeck@ebi.ac.uk.

Now, this does of course include the chemical structure editor mentioned above. As a pure coincidence , I had started a chemical structure editor in the late 1990s, called JChemPaint, which was later influenced a lot contribution from Egon Willighagen and others. JChemPaint experienced several rounds of re-architecture but for some reason it was never really considered to be production-ready.

We are now taking another go at it, at its applet version to be precise. And this time my charming profession team will give it a try and I’m confident that this time we’ll get it right. The fact that we are not alone in developing JChemPaint is both boon and bane. Everyone in an open source project is happy about harvesting the man-power of others but on the other hand you loose some control. While we, for example, are looking at the applet from a usability and GUI perspective, Egon and Arvid at Uppsala do a re-architecturing of the controler (the piece of software dealing with the user input) in order to make it maintainable through modularization.

So, in order to get an idea of what we actually need, we decided to do an analysis of a) existing structure editor applets and what they to well and not so well and b) how our curators do their work. For the latter, we did a screen recording of our curators’ work and looked at the type of functionality they used and how they did this (keyboard shortcuts, mouse, buttons, menus). The preliminary results are available on the JChemPaint wiki and we are more than happy to receive input from the community about this.

The European Bioinformatics Institute (EBI)

If the pompous title caught your attention, and you are ashamed of that: Don’t worry. It is all true. My cheminformatics and metabolism group at the European Bioinformatics Institute (EBI) is looking for a phd student this year and all you need to do is apply through the regular route.  The range of possible topics is wide open, going from metabolomics via automated structure elucidation of metabolites to mining chemical information from the printed literature, and more. Your own suggestions are of course welcome.

The EBI is the world’s largest open provider of biological and chemical information.We are located, together with the Sanger Institute for Genome Research, on the beautiful campus of Hinxton Hall, a few miles south of Cambridge.

One of the small lakes on the Wellcome Trust Campus in Hinxton

Our PhD students are enrolled with the University of Cambridge.

The important part for now: The application deadline for the Fall PhD selection is July 15, 2009. And: Please drop me a note if you applied.

We are pleased to announce release 56 of our database of Chemical Entities of Biological Interest (ChEBI).

SDF files are now available with ChEBI Release 56. They can be exported via the Downloads section or the search results page. We also have automatically generated links from IntEnz (www.ebi.ac.uk/intenz) and Rhea (www.ebi.ac.uk/rhea). This release contains 17842 annotated chemical entities (and not compounds, as I wrote earlier – we also have classes of compounds and abstract concepts) with 74 of them new submissions entered via the ChEBI submission tool. The next ChEBI Release will be on the 27 May 2009.

See our entity of the month, Ethyl formate.

All data are also available on the public FTP site:

ftp://ftp.ebi.ac.uk/pub/databases/chebi/

The workshop itself was phantastic – we had 40 participants with well balanced contributions from industry and academia. The first half day was dedicated to tutorials on various aspects of CDK, basic installation, our CDK and Oracle-based chemical search engine, scripting of CDK from within Bioclipse and CDK-based workflows in KNIME. The second day brought talks about science and applications based on CDK by John van Drie, Asad Rahman und Oliver Karch.  I reported earlier on those talks.

This official part was followed by a developers workshop in the format of an unconference.  Participants suggested topics on the fly and then voted with their feet. The topics that then made it where:

• Clojure
• Mining ChEMBL with CDK pharmacophore stuff
• Threading group
• Top 10 improvements (CDK WS 2009 unconference)
• JChemPaint/Rendering

all of which reported their results on the CDK wiki.

Another important outcome was a movement to join forces in creating and maintaining joint CDK-based plugins for KNIME and Bioclipse. There is a lot of synergy to be harvested. Licensing problems will need to be overcome but that seems doable.