Tuesday 18 December 2012

My year in review - Reviewing reviewing

Like most scientists, from time to time I get asked to review papers, and a few years ago I decided to keep track of the reviews I did for various journals. In 2010, 2011, and 2012 I was asked to review 7, 6 and 7 times respectively.

I've been trying to figure out is this a reasonable level of reviewing? I guess the question is, am I doing more reviewing for the chemistry community than they are doing for me? Not that I mind those freeloading slackers dumping it all on me - I'm just curious.

So what's the other side of the equation? In the same three years I've had my name attached to 8 peer-reviewed publications. If each was reviewed 2.5 times (a reasonable guesstimate), that's also 20 reviews.

And so the balance is maintained.

Note: I know what you're thinking...(eerie isn't it!)...you want to adjust the figures for multiple authors. But both of the values would have to be adjusted in the same way and so it just cancels out. (I think.)

Update (02/01/2013): The previous note is a load of rubbish. As Felix points out in the comments, I should be correcting for multiple authors. Oh well...

Image credit: After the Edit by Laura Ritchie (LMRitchie on Flickr)

Tuesday 11 December 2012

Cinfony 1.2 released

Cinfony presents a common API to several cheminformatics toolkits. It uses the Python programming language, and builds on top of Open Babel, the RDKit, the CDK, Indigo, OPSIN, JChem and cheminformatics webservices.

Cinfony 1.2 is now available for download.

The two major additions in this release are support for the JChem commercial cheminformatics toolkit, and the ability to specify options (via an 'opt' dictionary) for format conversion and some other operations. There were also some under-the-hood changes to consolidate source files for ease of maintenance.

These additions were principally contributed by AdriƠ Cereto MassaguƩ (of Universitat Rovira i Virgili and DecoyFinder) who joined the Cinfony team (i.e. me) earlier this year.

As usual, Cinfony has been updated to use the latest stable releases of each toolkit: Open Babel 2.3.2, CDK 1.4.15, RDKit 2012.09, Indigo 1.1, JChem 5.11 and OPSIN 1.3.

The Cinfony website has a somewhat condensed example showing the use of many of these resources in a dozen lines of Python. Here's a smaller example showing part of the new functionality:
>>> from cinfony import pybel, jchem
>>> mol = pybel.readstring("smi", "CC(=O)Cl")
>>> print mol.write("smi", opt={"f": 2, "l": 1}) # Make atom 2 the first and atom 1 the last
>>> fp = jchem.Molecule(mol).calcfp("ECFP")
>>> fp.bits
[39, 47, 55, 246, 397, 429, 700, 908]

To support Cinfony, please cite:
N.M. O'Boyle, G.R. Hutchison, Chem. Cent. J., 2008, 2, 24. [link]

Tuesday 4 December 2012

Intro to Open Babel

Recently I was asked (for the first time!) to provide introductory training for Open Babel. Here are the slides I put together:
If you're interested in this, you should follow up with the hands-on tutorial in the docs which I've mentioned previously. For further cheminformatics teaching material, see this post.