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Gaggle News

April 06, 2012 Mapping transcription factor binding sites

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.

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February 29, 2012 Systems Bioinformatics Workshop 2012

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

  • network inference and analysis
  • scientific computing in the cloud
  • biological data visualization
  • software architecture for biological research
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January 07, 2012 Genome Browser 1.0 Build 186 released

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!

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July 15, 2011 GaggleBridge: collaborative data analysis

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

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June 13, 2011 The Gaggle Systems Bioinformatics Workshop 2011

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.

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May 28, 2011 Gaggle-JSON prototype

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

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October 26, 2010 The Gaggle Systems Bioinformatics Workshop 2011

Building on the success of the previous Gaggle workshops, the 2011 workshop will bring together software developers and scientists to promote interoperability among bioinformatics software and databases and to explore opportunities for collaboration between developers and users of computing tools in the systems biology domain.

Visit the workshop site for more information.

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August 11, 2010 Gaggle Genome Browser featured on OpenHelix blog

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

Tip of the Week: Gaggle Genome Browser

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August 05, 2010 Introduction to Systems Biology Course 2010

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.

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July 22, 2010 Gaggle Genome Browser paper published


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.

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