All posts by Teddy Gray

Catching up on computational biology resources

With the arrival of summer, now is great time to catch up on these resources in computation biology and bioinformatics:

BioStar: Have a question on bioinformatics, computational genomics and biological data analysis but not sure who to ask? Try BioStar, which is an online open community of biologists ready to answer questions, even from “newbies”. You are also welcome to answer and comment on the questions. The more you do, the more reputation points you can earn toward your BioStar badge.

OpenHelix: The site provides a searchable collection of tutorials,  training materials, and exercises on the most popular genomic resources. The folks at OpenHelix also contract with resource providers to offer onsite, hands-on workshops at institutions. While most of their tutorials and training materials require a subscription, they do provide a suite of free tutorials, including ones on the UCSC Genome Browser and the RCSB Protein Data Bank.

Database: The Journal of Biological Databases and Data Curation: While maybe not beach reading, Database is a nice complement to the Nucleic Acids Research annual database issue. This open-access journal, launched in 2009, aims to provide a “platform for the presentation of novel ideas in database research and biocuration, and aims to help strengthen the bridge between database developers, curators, and users.”

Have a computation biology resource you would like to recommend? Please leave a comment.

Surveying Our Researchers

Understanding library users’ research goals remains a key element of the Perkins Library’s Strategic Plan.  As part of the Library’s User Studies Initiative, Teddy Gray surveyed the Biology Department in the Fall of 2010 to discover what tools and resources departmental members use in their research, researchers’ data management needs, and the impact of the BES Library closing in 2009.

From the 18 interviews of faculty, graduate students, postdocs, and lab managers, we learned–not surprisingly–that nearly all the interviewees use data in their research, most of which they generate themselves. Half incorporate data from others into their work with nearly a third using sequence data from GenBank. Out of the 12 interviewees who generate data in their labs, two-thirds archive their data in existing repositories.

In addition to the interviews, this survey also examined research articles produced by Duke Biologists from 2009 in which we paid special attention to their methods sections and citation patterns. From analyzing departmental research articles, we found out the nearly 40% of the authors deposited their research data into either GenBank or a journal archive. Only one author deposited data into another existing scientific repository. Again nearly 40% of the authors used a general statistical package in their work (SAS and R being the most popular), while nearly half used a biology-specific statistical tool.

Almost everyone interviewed uses statistical tools in their research with over half now using R. Many also use biology-specific statistical programs.

All but one of the interviewees prefer the online versions of library material over the print. A third use image databases–primarily Google Images–in their teaching and presentations; however, only one interviewee knew of subject specific image databases such as the Biology Image Library. And while some interviewees missed the convenience of easy shelf browsing with the BES Library so close by, all are happy with the daily document delivery to the building.

We are grateful to the Biology Department for their support (and time) in conducting this survey and plan to use the results as the basis for library services.  Data and GIS Services is always interested in hearing more from Duke researchers about the nature of your research! Please let us know if you would like to discuss your research interest and/or library needs.

What’s hot in molecular biology databases

The journal Nucleic Acids Research has just published its 18th annual database issue. The current issue summarizes 96 new and 83 previously reviewed molecular biology databases, including GenBank, ENA, DDBJ, and GEO. Also included in the issue is an editorial advocating the creation of a “community-defined, uniform, generic description of the core attributes of biological databases,” which would be known as the BioDBCore checklist. Such a checklist would benefit both database users and provides: users would have a much easier time finding the appropriate resource and providers would be able to highlight specialized resources and the lesser known functionality of established databases.

Besides the databases reviewed in the current issue, Nucleic Acids Research maintains a select list of 1330 molecular biology databases that have been profiled in various database issues over the past 18 years.