Facebook Applications for Biologists

If you love spending time on Facebook, but want to keep on working while “Facebooking” (or whatever the correct verb is) don’t fear. Here are 4 (5) biology-related Facebook applications, most of which you can claim to be working while using.

F@H Protein Researcher Folding@Home (F@H) is a distributed computing project where individuals allow their free CPU time to create a world-wide super-computer that is used for the study of protein folding. The Protein Researcher Facebook application tracks user statistics for the F&H and includes team pages/walls, a profile box with your individual statistics, and ranked standings.

SciBook - Science Social Network SciBook is a Life science social network for scientists. It’s a way for scientists to add the publications they are reading or have successfully published to their profile and discover others on Facebook interested in the same papers.

Latest PHD Comics This application puts PHD comics on your profile. It updates automatically, so you don’t have to keep checking the website for new comics

Pubface. This application allows you to search pubmed directly from Facebook. It also has a tell-a-friend feature, where you can forward interesting papers onto your friends, and a library feature that allows you to store up to 300 articles. I’m not really sure why you’d want to search Pubmed from a social networking site but who am I to judge? Another application - PubMed Search - does a similar job


Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service, that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user with the ability to create his own database for a set of Key terms. Also the user could change the Keywords of preference from time to time, with changing research needs. The categorized sentences could then be tagged and shared across multiple users. Thus XTractor proves to be a platform for getting real-time highly accurate data along with the ability to Share and collaborate.

Sign up it's free, and takes less than a minute. Just click here:www.xtractor.in.

EBI-Led Consortium to Study How to Turn EU Bio-Databases Into Bioinformatic Network

The European Commission has awarded €4.5 million ($7 million) to a consortium of 32 research organizations, universities, and companies from 13 countries to determine how to transform Europe’s biomedical data resources into a transnational “sustainable integrative bioinformatics network” for the life sciences.

The consortium is led by the European Bioinformatics Institute. The first year and a half of this project, called ELIXIR, for European Life-science Infrastructure for Biological Information, is aimed at gathering input, performing technical-feasibility studies, and doing user surveys among researchers who generate and use data, and develop tools.

Much like the Oxford English Dictionary, which will remain useful as long as people speak English, so, too, will “the infrastructure for biological information … continue as long as people are interested in biology, health, and medicine,” she said.

But provisions must be made to allow that to happen, including upgrading the infrastructure itself, promoting database interoperability, and using distributed annotation technologies.

ELIXIR will not unfold with “a big bang” but rather evolve in stages. And it does not solely concern the lions of the European database world such as EBI and the Swiss Institute of Bioinformatics, said Thornton. There are internationally collaboratively maintained databases such as InterPro and IntAct, and also many small ones.

According to Thornton, of the world’s approximately 900 biomedical databases, 40 percent are in Europe, many of which are specialist databases. “They are often in an individual’s laboratory; a research group may have developed a data resource that other people begin to use, and we really need to find a way to incorporate those data resources into the larger network in a way that people can access them easily and without necessarily knowing that they were there in the first place,” she said.

ELIXIR will help link the core and the specialist resources more closely while remaining as “seamless and transparent as possible to our users,” said Thornton. Clicking through databases from link to link is possible for researchers, she said, but clickthrough gymnastics becomes an impossible exercise when a microarray delivers a list of hundreds of genes that must be analyzed with a systems perspective, requiring data to be plowed and mined that is stored in different ways with differing vocabularies.

VisANT: an integrative framework for networks in systems biology

Integrative Visual Analysis Tool for Biological Networks and Pathways

Already blogging on the topic Structured Digital Abstracts - Easier Literature Searching dicussing the inportance of networks in the form of interactions, and further in several others about visualization tools, here is one more.

The essence of a living cell is adaptation to a changing environment, and a central goal of modern cell biology is to understand adaptive change under normal and pathological conditions. Because the number of components is large, and processes and conditions are many, visual tools are useful in providing an overview of relations that would otherwise be far more difficult to assimilate. Historically, representations were static pictures, with genes and proteins represented as nodes, and known or inferred correlations between them (links) represented by various kinds of lines. The modern challenge is to capture functional hierarchies and adaptation to environmental change, and to discover pathways and processes embedded in known data, but not currently recognizable. Among the tools being developed to meet this challenge is VisANT (freely available at http://visant.bu.edu) which integrates, mines and displays hierarchical information. Challenges to integrating modeling (discrete or continuous) and simulation capabilities into such visual mining software are briefly discussed.

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