News
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.
COMBINE Tutorial at ICSB
09-23-2015
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.
Topics
- 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
more details about the COMBINE Tutorial 2015
SABIO-RK links to MetaCrop
08-21-2014
Enzymes in SABIO-RK are now linked to corresponding plant data in the MetaCrop database.
MetaCrop is a database that contains diverse information about metabolic pathways in crop plants.
COMBINE & ERASysAPP Tutorial
06-18-2014
COMBINE & ERASysAPP Tutorial
Modelling and Simulation of Biological Models
http://co.mbine.org/events/tutorial2014
Date: Sunday, September 14th, 2014 (9:00 - 18:00)
Venue: To be advised (in the vicinity of the ICSB venue)
Focus
Participants will learn setting-up computer models of biological networks and simulating them in different systems biology platforms, as well as using databases and applying modelling standards. Hands-on sessions, lectures and software demonstrations will be included providing attendees with the necessary skills.
Topics
- 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
Standards (http://co.mbine.org/): CellML, SBGN, SBML, SED-ML
Databases: BioModels, JWS Online, Physiome Repository, SABIO-RK, SEEK
Modelling tools: CellDesigner, COPASI, OpenCOR, SBGN-ED, SYCAMORE, Virtual Cell
Target audience
Experimentalists and modellers with basic experience in modelling and simulation
Tutors (confirmed)
- Akira Funahashi and Noriko Hiroi: Keio University (Yokohama, Japan)
- Martin Golebiewski: Heidelberg Institute for Theoretical Studies (Germany)
- Mike Hucka: California Institute of Technology (Pasadena, CA, USA)
- Ursula Kummer and Jürgen Pahle: University of Heidelberg (Germany)
- Nicolas Le Novère: Babraham Institute (Cambridge, UK)
- Ion Moraru: University of Connecticut Health Center (Farmington, CT, USA)
- David Nickerson: Auckland Bioengineering Institute (New Zealand)
- Falk Schreiber: Monash University (Melbourne, Australia)
- Jacky Snoep: Stellenbosch University (South Africa)
- Natalie Stanford: University of Manchester (UK)
Tutorial coordinator
Martin Golebiewski
HITS gGmbH, Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
Email: martin.golebiewski@h-its.org
STRENDA Special Issue
06-16-2014
Special Issue: Reporting Enzymology Data – STRENDA Recommendations and Beyond – a highly educational, open access collection of 14 articles (published May 2014)
The STRENDA (Standards for Reporting Enzymology Data) Commission was set up almost ten years ago to address the improvement of the reporting quality of functional enzyme data in order to support the community with the efficient application of enzyme kinetics in the investigation of biological systems in vivo, in vitro and in silico. The Commission proposes guidelines as to how functional enzyme data should be described in the literature, with a detailed checklist of information, such as an unambiguous identification of the enzyme, a description of its preparation and of the conditions under which it was assayed. Experts from a wide range of specific research areas within enzymology were invited to add their views on, for example, thermodynamics, isotope effects, application of NMR, development and application of enzyme nomenclature, methods in designing enzyme assays in basic research and industrial biocatalysis as well as on the issues of data capturing, storage and mining in databases. This open access collection of 14 articles is addressed to all readers, including students, researchers and professors, who are interested in general aspects of data quality and in ways to interpret already published data.
Computational data in SABIO-RK
02-19-2014
In February 2014 SABIO-RK started to include in silico data from computational models. The search can be defined by selecting the filtering option "BioModel".
Data are uploaded via SBML format and linked to the original source e.g. BioModels Database.
