cy3sabiork - new Cytoscape app
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
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
SABIO-RK Curation Service
To improve the SABIO-RK database content and to better match user requirements, we encourage you to send us curation requests.
These requests can be either e.g. PubMed identifiers or a more general request for kinetic data associated e.g. with a particular biochemical pathway, organism or tissue. Currently, this service is still provided without any fee. In case of questions don't hesitate to send us an email.
On the Services page you can find our public curation list.
Please send us your request for SABIO-RK curation service.
COMBINE Tutorial at ICSB
COMBINE Tutorial at ICSB 2015
Modelling and Simulation Tools in Systems Biology
Date: Wednesday, November 25th, 2015 (9:00 - 18:00)
Venue: Yong Loo Lin School of Medicine, National University of Singapore
Participants of this one‐day tutorial 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.
- Model setup using different software tools and systems biology platforms
- Using experimental data for setting up kinetic models
- Parameter estimation, optimization and model fitting
- Simulation, analysis and visualization of biochemical models
- Database supported modelling: Data management and model databases
- Community standards and formats for systems biology models