The ChEMBL-og

The results of the  Teach-Discover-Treat (TDT) 2014 challenge were out earlier this week. TDT is an initiative to provide high quality computational chemistry tutorials that impact education and drug discovery for neglected diseases with a special focus on freely available software tools and reproducibility.  We are very happy to announce that Rodrigo Ochoa , former summer intern in the group two years ago, won the second place (KNIME award) at the TDT challenge . Rodrigo’s entry was based on myChEMBL ( Open Innovation track) and contains several KNIME and IPython Notebook tutorials within an NTD computational research setting.   More details  here . PS: Watch this space for an update on myChEMBL very soon.  Team myChEMBL

Here's a free to enter competition for a brand new, fully working raspberry pi running the brand new chempi implementation . It includes everything you need to get started at home with ChEMBL - a sort of in silico Breaking Bad maybe (hopefully not, thinking about it). It includes everything you need, with the exception of a power supply and ethernet cable. We have run out of our creative juices, and cannot think of a suitable poem to mark the release of chempi - so the competition is for you to finish a limerick for us, starting with the line. There once was a hacker with chempi.... Entries must be posted in the comments section. Obscene or defamatory entries will be removed (all comments are moderated, so it may take a few hours for you entry to appear, so do not repost twenty times!). We haven't really decided how to pronounce chempi (with a hard 'k' start or a soft 'sh' start, just as with ChEMBL, both are used in the wild; and also does it rhyme...

This week, our ChEMBL NAR Database paper made the milestone of over a hundred citations (in less than a year too). This made us all very, very happy, and for a few moments, we rested our fingers from our keyboards, and used our them instead to grasp a mug of coffee/tea; but only for a few seconds, before we got back to mixing and baking and cooking ChEMBL 15 for you all. Here's a list to the current citations of Gaulton et al., NAR Database, 40 , D1100-D1107, 2012 . Remember this is an Open Access paper. Please keep, keeping us happy by using our work, it's probably the biggest satisfaction we can get :)

So, congratulations are in the air again - this time to Janet Thornton  (although the wikipedia page is now out of date), Director of the EMBL-EBI . Janet has just been awarded the British honour of Dame Commander of the Most Excellent Order of the British Empire (DBE) in the 2012 Queen's Birthday Honours list . This is absolutely fantastic news, and well done from all in the ChEMBL group. Many of you will already know Janet's fantastic track record of innovation in the study of protein structure, enzyme function, and more recently in some of the molecular processes of ageing - but Janet has also done great things in championing the sharing of biological data, and in encouraging sharing and collaboration on a global and international scale, for example via the establishment of the ELIXIR infrastructure. It's great to see her achievements and service recognised more broadly in society through this titular honour. Update : someone has updated the wikipedia page. C...

Congratulations to one of our collaborators, Paul Workman  FMedSci of the Institute of Cancer Research on being awarded the RSC Chemistry World Entrepreneuur of the Year award for 2012 . This award recognizes individuals that have made significant contributions to the commercialisation of science. Paul has of course got a fantastic record of significant scientific discovery in the area of molecularly targeted cancer research, but has consistently searched for ways of generating value and patient benefit from these by founding a number of companies to move these discoveries forward to potential therapies and products - spending time with Paul really makes clear the drive, belief and energy that's required to make a great scientific entrepreneur and innovator. Examples of his commercialisation of science include the founding of Piramed (acquired in a successful exit by Roche ) and Chroma Therapeutics . So well done Paul! And for readers of the blog interested in hearing some ...

This morning, there was a press release released, marking the official release of chembl_02. More details are in the press release, but for the blog audience, the data is available in the interface , and the databases available for download on the ftp site . Work is already underway on chembl_03, with some associated minor changes to parts of the schema and additional curation of data. There is also something exciting and special in chembl_03, but more of that later. There is approximately 20% more data in chembl_02 than chembl_01 and new content highlights include a significant expansion of Natural Product records, and unification of all compound identifiers across all EMBL-EBI records (we use ChEBI ids) all chembldb compounds should now seemlessly and quickly make their way into PubChem . Many, many thanks to those who have told us of the errors and ambiguities you have found. We will incorporate all of these back into the database for the entire community. For newer read...

It is snowing here in the south-east corner of the United Kingdom, and the traditional winter holidays are almost here, so here is our card, from us, to you, with all our best wishes and thoughts.

The ChEMBL caravan will always have a place in our hearts, but now we have an office, and we must move on from the pain. It has some walls and a door, with a nice hook for jackets and coats. It is nice, bijou even, and has bought a smile to all our faces. Most importantly it gives us a place to entertain guests and visitors, so if anyone is in the area, please pop by and have a cup 'o tea and a slice 'o cake. As a sideline, to fund the tea and cakes, we have a nice T-shirt - XXXL only, minimum order 10 pieces if you are interested.

I have provisionally planned the ChEMBL group retreat for 2009. It will be in Crieff, Scotland , and will be in late September. The format will allow detailed discussion and brainstorming of ideas for the ChEMBL project, and will be themed around the following areas. Open-Source Drug Discovery and Open Science. Patent data-mining and indexing. Auto-curation and in-line predictive model generation. An Ontology for drug discovery screening cascades. A web-services primer. The mornings and evenings will be informal discussions of science, while the afternoons will be fun, fungi, flora and photography (who said alliteration is dead!) oriented walks in the wooded areas around Crieff. The picture above is of a reasonably rare parasite of truffles (a Cordyceps sp. ) found in Crieff around the same time of year in 2008. This is the fruiting stage of the fungus (the teleomorph), the non-fruiting body stage (the anamorph) of a closely related fungus is the source of the powerful immunosupp...