News

Please evaluate SABIO-RK!

01-22-2017

SABIO-RK is part of the German Network for Bioinformatics Infrastructure de.NBI which provides comprehensive first-class bioinformatics services to users in life sciences research, industry and medicine.
In order to improve our SABIO-RK services as well as de.NBI services in general, we offer the possibility to provide user feedback.

Please go to the SABIO-RK evaluation page!

The submitted information will be stored and handled anonymously.


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


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

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:
- 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


SABIO-RK Curation Service

11-11-2015

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.