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 readingAuthor Archives: SEMS
de.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 readingKeynote talk at whole cell summer school
Jonathan Karr will give the keynote talk at our upcoming whole cell summer school. On March 9, 2015 he will speak about the path toward whole cell models for engineering. Announcement_keynote
Continue readingPresentation at the Joint Workshop on Data Management for Science (BTW)
We were accepted for a presentation at the Joint Workshop on Data Management for Science. The workshop is part of the BTW 2015. We will talk about Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit.
Continue readingERASYS-workshop moved
The planned workshop on “Standards for reproducible modeling results” will not take place in February, but has been moved to September 14-16 2015. More information on workshop & registration here.
Continue readingBest paper @ DILS 2014
Our paper on Annotation-based feature extraction from sets of SBML models has been selected as one of the best papers of the DILS 2014 conference.
Continue readingOff to DILS 2014
The SEMS team is about to leave for DILS 2014 in Lisbon. It is the third time we will present our work on model management at this conference (after joining in 2009, Manchester, and 2013, Montreal). This year, Rebekka Alm will present the results of her Master’s Thesis on feature extraction from arbitrary sets of […]
Continue readingAnnotation-based feature extraction from SBML models
Our paper evaluating different methods for annotation-based feature extraction from arbitrary sets of SBML models has been accepted for publication in the Proceedings of the 2014 DILS Conference. The paper summarises the results of Rebekka Alm‘s Masters Thesis. The results will be presented by Dagmar Waltemath at the 2014 DILS conference in Lisbon in July.
Continue readingReview on IR in the Life Sciences published
Our review on the use of Information Retrieval techniques in the life sciences has been published last week at Springer.
Continue reading