We are going to speak in the Data Integration and Knowledge Management track at the Bio-IT World (Europe) meeting to be held in the beautiful city of Hannover, Germany, October 5th to 7th 2009. Should be a good meeting...
Tuesday, 31 March 2009
Thursday, 26 March 2009
Although the majority of effective therapeutics are small molecules, there is relatively little readily accessible public domain data mapping drugs to their molecular targets. When one considers clinical trial stage, or discovery stage data, the situation deteriorates further. However, this type of data is essential for Chemical Biology experiments, and is crucial for informed target selection in drug discovery. To address this issue, we have built a series of large scale databases, known as ChEMBL, that map small molecule structures to their target genes and also their functional effects. This data also captures a large ammount of human and model organism pharmacological data, systems often used in pre-clinical validation and safety pharmacology testing. A variety of applications of these databases in the area of target prioritisation, lead discovery, lead optimisation and drug repurposing will be described.
Wednesday, 25 March 2009
%A Toby Segaran %T Programming Collective Intelligence %I O'Reilly %D 2007 %O ISBN 978-0596529321
Monday, 23 March 2009
No, this isn't a hotel review, despite the picture above; however since finding this image, I now feel compelled to visit Carlsbad, NM to pose under the sign. Now for the post itself; find below some screenshots for an internal interface for StARlite data developed by our close collaborators at the Institute of Cancer Research in Sutton. This interface for StARlite shows some basic workflow themes that give some ideas as to the potential uses of StARlite 'straight out of the tin'. Several of the views will be incorporated into the EMBL-EBI public web interface ;) Bissan's group is developing an integrated system for cancer chemogenomics, called canSAR.
Compound Browsing: A "Top Trumps" view on compounds is quite a useful paradigm for browsing and selecting compounds for further analysis. As an aside, for an example of sensory overload on a web page, try out the current Top Trumps company website.
This page uses the Google Chart API to do some of the heavy lifting. In which the chart itself is made using a URL of the form...
Which produces the following (and you thought Google could do no Evil).
I thank Mark Halling-Brown, and Bissan Al-Lazikani of the ICR for the images. However, I do not thank them for the geek joke in the use of the StarWarsTM font for StARlite (Ha, ha, ha, ha, ha.....).
Friday, 20 March 2009
Books and Papers - 7 - Population Genetics, Molecular Evolution, and The Neutral Theory by Motoo Kimura
The theme of the book is around The Neutral Theory, quite a contentious issue in evolution (essentially, this states that the vast majority of observed mutations at a molecular level are not adaptive; now flame me!) This book changed the way I thought about mutation, protein sequence and structure and function. Forever.
%T Population Genetics, Molecular Evolution, and The Neutral Theory %A Motoo Kimura %E J.F. Crow %D 1994 %I Chicago %O ISBN: 0-226-43562-8
Tuesday, 17 March 2009
|Name||Target Class Focus||Approx size|
The comparable number from StARlite (31) are 507,645 (of which 186,370 are better than 100nM) for affinity class end-points. Oh, and we have started a new load.....
Friday, 6 March 2009
The next web-meeting for a walkthrough of the StARlite schema, data model assumptions and sample queries will be at 11am to noon local UK time (so at this time of year GMT/UT) on Friday 20th March. If you wish to take part in this meeting please use this link (do not modify the header of the email in any way!).
The last time we tried a web meeting, my domestic broadband connection could not cope with audio and the slides at the same time, so you will need to dial into a UK land line number; unfortunately, this will not be a freephone number.
Finally, if you can't make this time, we will set up a similar meeting in another few weeks or so.
Tuesday, 3 March 2009
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 immunosuppresive drug cyclosporin, wow!
I will try and get some really special VIP guests as surprise speakers and participants! ;)