Ok guys, $Stuff is now distributed around different servers, domains, services, people… Here are some links for external users to find the resources: SEMS web page The wordpress site has been serialised to static web content and is now available through sems.bio.informatik.uni-rostock.de. All sems.uni-rostock.de/.* links should send proper HTTP redirects, so your browser will automatically […]
Continue readingThe SEMS project came to an end
As you may have guessed from this website’s quiet news section: The SEMS project came to an end. Tom was bravely holding the fort, spending the last few cents of our budget in July 2017. But do not worry, not all is lost! SEMS peeps will continue their fights for improved management of computational models […]
Continue readingSEMS extended until July 2017
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.
Continue readingEnd 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 exploration of SBGN maps using graph databases
Vasundra Touré et al. published a paper on the STON framework in BMC Bioinformatics! STON is meant to explore biological networks in SBGN using a graph database called Neo4j. The framework enables the query of SBGN maps. Paper abstract: Background When modeling in Systems Biology and Systems Medicine, the data is often extensive, […]
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 readingA container for the CombineArchive Web interface
Following the BiVeS-WebApp example, the CombineArchive Web interface jumps onto the Docker hype as well! It is now also available as a container from the Docker hub and we will automatically create new versions of the image with every release of the application. To run the application just call the following command: 1docker run -it […]
Continue readingBiVeS-WebApp as a Docker image
Today we compiled the BiVeS web application into a Docker image. Using Docker it is very simple to run the application on your desktop, your server, your cloud… The Docker image is available from the Docker Hub as binfalse/bives-webapp. To pull the latest version of the BiVeS web application just call 1docker pull binfalse/bives-webapp Running […]
Continue readingNew paper on Functional Curation
Martin Scharm’s paper about the Cardiac Electrophysiology Web Lab, work done during his research stay at the University of Oxford, is published in the current issue of the Biophysical Journal!
Continue readingMartin Peters visits the JJJ lab in Stellenbosch
Martin Peters is at the Stellenbosch University, South Africa to visit the research group of Jacky Snoep and work on SED-ML.
Continue reading