Category Archives: announcements

Welcome back @ SEMS, Ron!

In July 2015, Ron Henkel joined our team. He is now a member of the de.NBI project, the newly established German Bioinformatics Infrastructure. Within de.NBI, Ron is employed at the HITS where he works towards better model management for systems biology projects. His major tasks in the project are: to implement SED-ML support, version control and […]

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SEMS’ Gallery

Yeah! SEMS now has a gallery :) At gallery.sems.uni-rostock.de you’ll find images, logos, and figures that we created. If you click on an image you’ll get more information about it. The number of images is currently fairly small, but will hopefully be increasing in the future.

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Bachelor Thesis completed: Visualising sub-networks in SBML models

Last week, Tom Gebhart successfully defended his Bachelor’s Thesis on “Visual-interactive support for detecting submodules in SBML Models”. In his thesis, he developed a tool that displays SBML reaction networks using Anchored Maps. Users can define submodules of interest, or choose from a pre-defined set of motifs. His algorithm then detects all occurrences of these […]

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Now running Jessie

As the SEMS team is fighting for free and open software we obviously avoid using proprietary products. Thus, all our machines run GNU/Linux based operating systems, specifically Debian. The Debian project just released a new stable version: code name “Jessie”. We just updated all our machines to the latest Debian release and want to take […]

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Bachelor Thesis completed: Classifying reactions of computational models

Fabienne Lambush just defended her Bachelors thesis Classification of Reactions of Computational Models, which she wrote within the SEMS group. She applied graph algorithms to study the reactions of computational models stored in Masymos. As a result, Fabienne was able to identify patterns in reaction networks which will help us to develop a measure for […]

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SEMS@HARMONY 2015

The SEMS team is currently in Wittenberg to contribute to the this years HARMONY! :) Our goal is to further improve the development of standard, such as SBML or SED-ML. Moreover, we’re very interested in development of the CombineArchive. We proposed an update to the meta data standard and had a couple of discussions with […]

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