Blue Obelisk

We’re taking MALARIA as our lead project in @ccess. If you haven’t read about @ccess, read the previous post. Many peple are incredibly frustrated by lack of access to the scholarly literature. I call them the “Scholarly Poor”. If you...

Yesterday I blogged about our new project in Opening scholarship: @ccess. Several people retweeted it, and one asked “What’s @ccess for?” a good prompt for some more information. @ccess is to discover OPEN scholarly information, to label it,...

I am not a photoshop expert. Well, neither I have used it! But just using and knowing photoshop is not good enough to fool around. You must know what you are actually mocking. So this image on spotify website caught my attention: http://www.spotify.com/int......

We have started a really new exciting venture in making scholarship available to everyone. We’re starting from scratch. We’re still working out details. And “we” means “you”. About 3 weeks ago things came to a head. Many...

   ATC code R07AX02 Wikipedia Ivacaftor On January 31st, FDA approved Ivacaftor (previously known as VX-770, trade name Kalydeco) as a first-in-class oral drug for the treatment of a rare form of Cystic Fibrosis in patients aged 6 or older, caused...

Came across a link to a post to a Forbes article (via Greg Landrum) and thought I would post a link here. It's a simple economic analysis of the costs of Large Pharma drug discovery. Very simple, money in vs. drugs out. There is however a lot of complexity...

I have just discovered Elsevier’s content mining document. For those who don’t know I have been trying to get permission to text-mine Elsevier content for two years and have been treated as a second-class citizen and ultimately come away with nothing....

This course aims to give researchers of any discipline a broad introduction to the theoretical, practical and organisational aspects of small molecule drug discovery. Each topic will include a lecture together with discussion sessions or case histories to develop...

As mentioned by John Overington, the Joint EMBL-EBI/Wellcome Trust Course: Resources for Computational Drug Discovery on 2-5 July (see links here and here) is now open for registration. I'll be there as one of the trainers. From previous experience of similar...

With a little bit of data wrangling I was able to convert the kinase clinical data we have to a form which shows the highest phase achieved for a particular target class - major distinct known activities were clustered together, and not surprisingly, the largest...

I have just discovered Elsevier’s content mining document. For those who don’t know I have been trying to get permission to text-mine Elsevier content for two years and have been treated as a second-class citizen and ultimately come away with nothing....

We have set up a server for some of the ligand efficiency mapping work of Cele Abad-Zapatero and colleagues. The AtlasCBS server is at https://wwwdev.ebi.ac.uk/chembl... note this is on our dev server, so if some of the links out...

Creating this video was fun, and theres an obvious business model behind the company making it possible. Guess what? I just published it for free to a worldwide audience.Why doesnt science work this way?...

It is great to be able to perform confederated queries across data sources, really great. The greatness of this leads to the development of common representational and access standards (things like MIABE, InChI, and PSIQUIC, as examples that we are involved...

The previous post explored why E2 elimination reactions occur with an antiperiplanar geometry for the transition state. Here I have tweaked the initial reactant to make the overall reaction exothermic rather than endothermic as it was before. The change is...

Just a quick note to say that we have joined the Open PHACTS Project, and as our local contribution (there are multiple strands to the EBI's involvement) we will be enhancing rdf/SPARQL access to ChEMBL, and also developing some improved semantic indexing of...

Change is scary. Submitting your application paper to a new journal certainly. When that journal requires your have a strategy for code testing and maintenance even more. Hence, the Open Research Computation dillema. We you may or may not know, I'm on the editorial...

This blog has been tackling the problem of Open Access, what it’s vision is and how to get a coherent movement. I’ve been excited to get a comment from Eric Raymond (http://en.wikipedia.org/wiki... ). Eric (whom I shared a platform...

I’ve been off air for a bit as my hard disk crashed it emitted messages (“Your disk is about to crash”, then “Ctrl-Alt-Del to access dying disk”, then – the “rest is silence”). Since I live my life in the open...

I just enjoy writing stuff in TouchDevelop using my Nokia Lumia. So this time I wanted to write an app that generates on-device anaglyphs using two images (left and right channel photos). To use this script (3DCAM) head straight to : https://www.touchdevelop.com/gxtp...

Since we are getting more and more in trouble with SourceForge :( I started looking into the more standard git code review environment, called Gerrit, so that we can use that for the CDK. With some huge learning curve, lurking, googling, and seeing what Avagadro...

The so-called E2 elimination mechanism is another one of those mainstays of organic chemistry. It is important because it introduces the principle that anti-periplanarity of the reacting atoms is favoured over other orientations such as the syn-periplanar form;...

Wikipedia: Vismodegib On Jan 31st 2012 the FDA approved Vismodegib (tradename: ErivedgeTM), previously known as GDC-0449 and HhAntag691, a hedgehog signalling pathway inhibitor for the treatment metastatic basal cell carcinoma. This is a novel first-in-class...

I've written here before about how Kevin Lawson (of Syngenta) has developed a way to incorporate chemistry into Excel using only freely-available software, namely the CDK and JChemPaint (and also now OPSIN it seems). This system is called LICSS, and the corresponding...

It has been difficult to avoid the news of the continuous downsizing of Pharma, and to those in the UK this has been especially painful recently. There is an excellent opinion piece here, written by Simon Campbell, ex-head of R&D at Pfizer, and also ex-President...

If you are using Mendeley for handling citations in your research papers, you might have run into the issue that by default it cannot generate journal abbreviations. Hence you always get the full journal name which is a bit problematic when trying to adhere...

ATC Code: L01XE17Wikipedia: Axitinib On Jan 27th 2012, the FDA approved Axitinib (also known as AG-13736, trade name: Inlyta), a kinase inhibitor, for the treatment of advanced renal cell carcinoma after failure of a first line systemic treatment. Renal Cell...

A maintenance release of MeTA Studio is avilable via online update (Help -> Check for updates). The current version number is 2.0.31012012 If you are not able to use the online update, manually download and extract: http://metastudio.googlecode.com/files......

In the previous post, I went over how a reaction can be stripped down to basic components. That exercise was essentially a flat one in two dimensions, establishing only what connections between atoms are made or broken. Here we look at the three dimensional...