Trendspotting in the Protein Data Bank

Our most recent article has become publicly available. It describes some of the trends that we can observe in the Protein Data Bank:

Trendspotting in the Protein Data Bank. FEBS Letters, (0). Berman, H. M., Coimbatore Narayanan, B., Costanzo, L. D., Dutta, S., Ghosh, S., Hudson, B. P., Lawson, C. L., et al. (n.d.). doi:http://dx.doi.org/10.1016/j.febslet.2012.12.029

http://www.sciencedirect.com/science/article/pii/S0014579313000240

RCSB PDB's NAR paper

The manuscript describing recent developments at the RCSB PDB has been released as part of the latest Nucleic Acid Research database issue.

View the manuscript at NAR

The Author Profile provides a graphical timeline on when a particular structure was released in the PDB.

Some of the highlights of this year are improvements in the following areas:

• Searching
• Better simple searches
• Auto suggest provides quick access to relevant results
• More advanced search options
• More and better tools
• Structure alignments now domain based
• Visualization
• Better ligand reporting and visualisation
• Visualisation of molecular surfaces
• Web services
• many new services
• customization of reports
• Mobile phone app
• New iPhone app
• PDB101 educational section
• Structural view of biology - browse through molecule of the month articles
• Author profiles

Our continuous efforts to provide a structural view of biology are also reflected by an increase in our user base.  The RCSB PDB web site currently hosts ∼240 000 unique visitors per month (based on the number of unique IP addresses), an increase from the 180 000 visitors last reported in 2011. 

Ten Simple Rules For The Open Development of Scientific Software

Jim Procter and I drafted a new manuscript for PLOS Computational Biology describing ten simple rules for the open development of scientific software. Our motivation for writing this was to make the development of open scientific software more rewarding and the experience of using software more positive.  The ten rules are intended to serve as a guide for any computational scientist:


Ten Simple Rules For the Open Development of Scientific Software (article)

Google Scholar Citations Open To All

This week Google Scholar citations opened up to the public. After the initial release which was providing limited access only, the latest versions is now open for all scientists. What is interesting is that they seem to have created profiles for many scientists in an automated way. While the transparency of this is amazing, I can also imagine that there will be a push-back about privacy issues.

You can check out e.g who are the most cited scientists in Computational Biology or scientists at UCSD or check out Author profiles (e.g. yours truly). At the moment those lists are sorted by number of citations. Would be nice to have a few more sort fields like the already calculated h-index. Another missing feature is an API. Would be nice to be able to script their database and create custom reports.

I believe Google Scholar is setting a new standard for tracking success of scientists and is a serious threat to the ISI web of knowledge.

Google Scholar Citations - Google Scholar Blog

Google is preparing the release of a new feature at Google Scholar - personalized user profiles. They can be used to track your citations and as a reporting tool for calculating the h-index. The access can be kept private or made public. I believe this can be a serious threat to the ISI Web of Science. Can't wait until I can get access to "My Citations" and play around with this new feature!

Read more at: Google Scholar Citations - Google Scholar Blog

UPDATE: In the meanwhile I got access to the new profile feature. The secret is to click on the "MyCitations" tab in Scholar every now and then, until it works. At the moment it found most, but not all of my papers, with some highly cited ones missing.  I will make my profile publicly available, as soon as I have figured out how to add the missing articles.

UPDATE 2: In the meanwhile I figured out how to find the missing articles. Scholar is using groups of citations. In my case my family name with the special character ć lead to two groups of citations, one for an author with and without the accent on the name. Using the import functionality those groups could get merged and my profile is now available from http://scholar.google.com/citations?user=LnXh0T8AAAAJ