Category: News

This release includes contributions from Diego Martinez Salvanha of the Vêncio lab at the University of Sao Paulo, Ribeirão Preto, Brazil and Kai Chen of Genomatica. Thanks to them!

gaggle.systemsbiology.net/docs/geese/genomebrowser

Experimental analysis of TFB family proteins in a halophilic archaeon reveals complex environment-dependent fitness contributions. Gene conversion events among these proteins can generate novel niche adaptation capabilities, a process that may have contributed to archaeal adaptation to extreme environments.

Florian Battke, Stephan Symons, Alexander Herbig and Kay Nieselt at the University of Tuebingen published a paper on their GaggleBridge software. GaggleBridge transparently extends Gaggle to allow data exchange between users at different geographic locations using network communication. GaggleBridge can automatically set up SSH tunnels to traverse firewalls while adding security features.

GaggleBridge is available as open-source software at http://it.inf.uni-tuebingen.de/gb.

The Institute for Systems Biology hosted a workshop focusing on interoperability between bioinformatics software tools, bringing together over 40 software developers and scientists for discussion and collaboration. The format was one day of talks, followed on the second day, by a hackathon, a forum for coding, discussion, informal presentations and collaboration.

Thanks to all who participated!

Visit the workshop site for more information.

A prototype implementation of Gaggle data types encoded in JSON is available at gaggle-json.systemsbiology.net. Additional prototyping of support for HTTP and JSON transport in the Gaggle Boss is available in Wei-ju Wu’s Github repo.

miRvestigator is a web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling.

miRvestigator was published in the Webserver issue of Nucleic Acid Research.

Talk to any biofuels entrepreneur, and you are likely to hear a passionate riff on why their technology trumps all the up-and-comers.

Some, like San Diego-based Sapphire Energy, say you’ve got to harness free sunlight and the magic of photosynthesis, to grow oil-rich algae in open ponds at the scale of modern agriculture.

Ballard High School Students have partnered with Baliga Lab to send an experiment aboard the last space shuttle mission.  Ballard’s experiment will launch a population of E. coli into space to test for changes, such as mutations, plasmid uptake ability and growth rate, while it grows for two weeks in microgravity.

The OpenHelix blog features a screencast on the Gaggle Genome Browser:

Tip of the Week: Gaggle Genome Browser

The Introduction to Systems Biology course was held at ISB in Seattle the week of August 2, 2010. Topics covered included proteomics, DNA microarrays, and network inference integrating bench work with computational biology.

Data analysis was performed using Gaggle software tools.

The Gaggle Genome Browser joins heterogeneous data by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation.