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 […]
Continue readingMartin visits the group of Carole Goble in Manchester
Martin Scharm is currently in Manchester to visit the group of Carole Goble. His stay is funded by the HERMES research funding program at the University of Rostock. Martins goals for the coming 8 weeks are to establish a closer collaboration with Manchester and to develop a grant proposal together with Mrs. Goble’s group. Martin […]
Continue readingBiVeS in PMR2
One of our main goals at HARMONY 2015 was to improve the version control of PMR2, as we described earlier. During HARMONY, Tommy Yu, main developer of PMR2, and Martin Scharm already achieved preliminary results. Today Tommy sent us the first version of BiVeS integrated into the CellML model repository: go here: http://staging.physiomeproject.org/workspace/beeler_reuter_1977/file/cb090c96a2ce627457b14def4910ac39219b8340/beeler_reuter_1977.cellml Then click […]
Continue readingNow 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 […]
Continue readingBachelor 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 […]
Continue readingCombineArchive Library version 1.0 released
We are happy to announce that version 1.0 of the CombineArchive Library, part of the CombineArchive Toolkit, was just released! Using JUnit tests we achieved a code coverage of about 91.3%, and as it is already integrated in a couple of other tools we assume it to be fairly stable. That said, do not hesitate […]
Continue readingSEMS@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 […]
Continue readingde.NBI:SYS-Bio kick-off in Bielefeld
The German Infrastructure for Bioinformatics, denbi, will kick-off tomorrow during the 10th CeBiTec Symposium: Bioinformatics for Biotechnology and Biomedicine. HITS and SEMS present their first poster on the goals of the de.NBI:SYS-Bio node.
Continue readingSEMS is hiring
We are seeking help with the implementation of data management for systems biology in Germany. This post is for a 3 years position to further develop, promote, and integrate existing model management solutions developed in our group. We look for an enthusiastic scientist who wants to spend the coming years with COMBINE standards, databases, bio-ontologies, and XML.
Continue readingBudHat user management closed
Those of you who have not been notified in advance might have recognized that it is currently not possible to log on to our demo web tool BudHat. Thanks to our faithful BudHat users, we were able to identify some space for improvements in our systems. Thus, we decided to freeze the database while we […]
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