News
SABIO-RK mailing list
07-21-2016
Please join the SABIO-RK Google Groups mailing list for getting SABIO-RK news or contacting us, along with other users available at groups.google.com/d/forum/sabio-rk.
SABIO-RK at ICSB2016
07-13-2016
COMBINE - de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology
This tutorial workshop is a satellite of the 17th International Conference on Systems Biology (ICSB).
Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats. The topics will include:
Dates: Friday, September 16th, 2016
(8:30 - 13:30)
Location: Barcelona, Spain
Hosted by: HITS - Heidelberg Institute for Theoretical Studies
Website: http://co.mbine.org/events/tutorial2016
- Model setup using different software tools and systems biology platforms
- Using experimental data for setting up quantitative models
- Parameter estimation, optimization and model fitting
- Simulation, analysis and visualization of biochemical models
- Database supported modelling: integrated data management and model databases
- Community standards and formats for systems biology models
cy3sabiork - new Cytoscape app
06-29-2016
cy3sabiork - an app for querying and visualization of kinetic data from SABIO-RK in Cytoscape
cy3sabiork is a Cytoscape 3 app for accessing kinetic information from SABIO-RK via the RESTful web services.
cy3sabiork creates an intuitive visualization of kinetic entries as a species-reaction-kinetics graph, which reflects the reaction-centered approach of SABIO-RK. Kinetic entries can be imported in SBML format from either the SABIO-RK web interface or via web services queries.
A SABIO-RK web services client is now implemented in Cytoscape and available from the Cytoscape app store at http://apps.cytoscape.org/apps/cy3sabiork.
The source code is available at https://github.com/matthiaskoenig/cy3sabiork/.
cy3sabiork was developed by Matthias König.
Kinetics on the move
03-03-2016
Celebrating 10th Anniversary of SABIO-RK
Kinetics on the move: Workshop on Data for Computational Modeling
Date: May 30th-31st, 2016
Venue: Studio Villa Bosch, Heidelberg, Germany
Do you work in the lab and always wonder what these bioinformaticians do with the data you generate?
Would you like to use models to verify a hypothesis or test your experimental data?
Then this workshop may be right for you.
The workshop focuses on the publication, curation, retrieval, and usage of kinetic data from the reaction kinetics database SABIO-RK and on the use of data in modeling. There will be experience reports from scientists who successfully used experimental data to formulate or verify biological hypotheses with the computer, and you will experience how experimental data can be used with computational models.
Speakers:
Ursula Kummer, Sven Sahle, Melanie Stefan, Julio Vera, Dagmar Waltemath, Ulrike Wittig
Tools:
SABIO-RK , COPASI, SEEK, MaSyMoS, BiVeS
More Information:
Workshop website
