Here we report that during continuous culture of Methanococcus maripaludis under defined nutrient conditions, growth yields relative to methane production decreased markedly with either H(2) excess or formate excess.

This model accurately recapitulates known dynamical properties of the Cu circuit and predicts that intracellular Cu-buffering emerges as a consequence of the interplay of paralogous metallochaperones that traffic and allocate Cu to distinct targets.

The Marc Facciotti lab at UC Davis published A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq. This paper demonstrates a novel ChIP-seq workflow for mapping genome-wide binding sites of natively expressed transcription factors in archaea. Gaggle software features prominently.

The Systems Bioinformatics Workshop 2012 will be held at ISB on September 10th and 11th. Presentations and tutorials will cover the following topics:

Seattle Local Health Guide Blog published an interview about our recent paper “Niche adaptation by expansion and reprogramming of general transcription factors”.

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.