We are happy to announce that the SEMS project has been extended, and now runs until July 2017. During the remaining months, we will focus on improving our MOST tool for exploration of differences between versions of a model; and we will investigate how to measure differences between SED-ML files.
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End of 2016, end of SEMS?
It has been an exciting year for us, with good old and brand new collaborations, exciting projects, research stays close by and far away… We are right in the middle of the 5th year of SEMS funding, meaning that the project will come to an end soon – we’re closing down on the 28th of […]
Continue readingNew paper on standards and software for whole-cell modeling
After the successful Whole Cell Modeling Summer School in Rostock in March 2015, we ran a second meeting in Salt Lake City in 2015, co-located with COMBINE 2015. Both were practical meetings for young scientists aiming at recoding a Whole Cell model in standard formats and using open tools. We provide all code on github. […]
Continue readingSBGN symbol of the month relaunched
The SBGN symbol of the month project is relaunched on http://sbgn.org. SEMS memeber Vasundra Touré is currently responsible for the project. Symbol of the month for January is the SBGN compartment.
Continue readingde.NBI action at COMBINE 2015 tutorial
At this year’s COMBINE tutorial, a satellite to the ICSB 2015, we taught different tools and possibilities to prepare model-based results for publication in public repositories such as BioModels and PMR2. We also encouraged people to try out our own model management solutions, particularly BiVeS, MaSyMoS, M2CAT and CAT. The slides for the introductory talk […]
Continue readingCAT goes ICSB
We’ll be joining the COMBINE team at ICSB 2015 as tutors this year. During the COMBINE tutorial on modeling and simulation tools and standards, we’ll be giving a talk about the COMBINE Archive and the COMBINE Archive Web Tools. The talk will be followed by a hands-on session in the afternoon. Date: 25th November, 2015. […]
Continue readingWelcome to our new team member Vasundra
Vasundra Touré joined our team recently on the SBGN-ED+ project. She will work on SBGN, libSBGN and on the SBGN-ED software which is part of VANTED. The project runs until end of 2016. Vasundra is currently on a research stay at Monash University where she works with Prof. Falk Schreiber and Dr. Tobias Czauderna.
Continue readingSEMS group retreat 2015
We’re on a retreat in lovely Greifswald this week. Besides all the social and group building activities, we evaluate and discuss possibilities to provide metadata for computational models and COMBINE Archives. The idea is to harmonise current approaches to metadata annotation in SBML, CellML, COMBINE Archive, etc.
Continue readingVolkswagen Foundation funds second Whole Cell meeting in Salt Lake City
The Volkswagen Foundation supports a follow-up meeting of the Whole Cell Summer School we ran in Rostock earlier this year. The Whole Cell 2 will take place as a satellite meeting to the COMBINE 2015 meeting in Salt Lake City (US), October 10-11, 2015. We will be able to fully fund about 10 students from […]
Continue readingRegistration to DCite is open
We are co-organising a workshop on Citeable data and Reproducible models, DCite, in September this year in Rostock-Warnemünde. The workshop brings together scientists who wish to learn about open science, open data, and how to make their research results reproducible. In the mornings, invited key note speakers will talk about programs and initiatives such as […]
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