Three new papers lined up

The UUCJC is picking up slowly, trying to find the exact format. We already had to slip discussion of the first meeting because I had a nasty cold, and we did not manage to complete reviewing the SMSD paper yesterday.

The aims of the journal club include to:

• learn to critically read scientific papers
• learn about important cheminformatics algorithms
• formulate a review report

We keep a schedule of alternating discussion of three topics:

• data and knowledge representation,
• cheminformatics algorithms,
• data analysis,
• learn your way around in modern publishing.

Meeting format
Everyone is free to join in on one or more meetings, but if you do join in on a meeting, it is expected that you take part in the discussions. If you are not interested in some parts of the discussion, you are free to express this; the order in which we discuss things in the paper is flexible. The meeting itself has a fixed format:

• a round where every one in two minutes:
  1. summarizes the paper,
  2. indicate what he found interesting and what not (affecting the order in which things will be discussed during the meeting),
  3. an overall (preliminary) verdict on the paper.
• walkthrough of the paper, paragraph by paragraph (affected by people's interest)
• formulation of the UUCJC opinion of the paper.

During the meeting, notes will be made, and after the meeting one or two participants will write up the formulated opinion of the paper for inclusion in this blog.

Social Web
The review for the first paper we discussed is now online, and I added a box down the end as expected by ResearchBlogging.org (see also this blogs entry). Because this blob also contains the DOI, it will also be picked up by Chemical blogspace, Nature.com Blogs, and possibly other social website. It will also be used by PLoS ONE to calculate article level metrics to reflect a paper's impact. Here is such the PLoS One metrics summary for a paper we will discuss later.

Updated Schedule

Next dates meeting dates are March 25 (we'll finish the SMSD paper), April 8 and 22, May 6 and 20. The papers we have lined up:

• Virtual screening of bioassay data, doi:10.1186/1758-2946-1-21
• ChemAxiom – An Ontological Framework for Chemistry in Science. doi:10.1038/npre.2009.3714.1
• How Large Is the Metabolome? A Critical Analysis of Data Exchange Practices in Chemistry. doi:10.1371/journal.pone.0005440
• pKa Prediction of Monoprotic Small Molecules the SMARTS Way, doi:10.1021/ci8001815