News

SABIO-RK in de.NBI course

01-31-2018

de.NBI course "Tools for systems biology modeling and data management"

April 24th-26th, 2018 in Magdeburg, Germany



Website: Tools for systems biology modeling and data management

Registration: https://goo.gl/forms/8iUxUnNZrpkoaDKE2

Contents:
Key concepts of stoichiometric and kinetic modeling of biochemical networks:
- stoichiometric matrix and stoichiometric networks
- steady state flux distributions
- principles of constraint-based modeling
- metabolic flux analysis and flux optimization (flux balance analysis)
- metabolic pathway analysis with elementary flux modes
- metabolic network design via minimal cut sets
- simulation of dynamic (kinetic) models
- sensitivity analysis
- carrying out parameter estimation tasks
- model exchange using SBML

Data and model management:
- manual/programmatic access to reaction kinetics data from SABIO-RK
- storage and exchange of data and models using FAIRDOM Hub/SEEK
- modeling specific functionalities in FAIRDOM Hub/SEEK

Learning goals:
During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The second day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOM Hub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists.
The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks.

Prerequisites:
Some knowledge of mathematical modeling will be advantageous.
The participants should bring their own laptop with MATLAB installed (if you do not have MATLAB please let us know during registration).
Download and preinstallation of COPASI and CellNetAnalyzer is recommended but not mandatory.


New SABIO-RK paper

11-06-2017

SABIO-RK update paper published in Database issue of Nucleic Acid Research:
https://doi.org/10.1093/nar/gkx1065


More export formats supported

10-12-2017

Besides SBML, SBBioPax and spreadsheet export, SABIO-RK supports now the export of kinetics data in a variety of additional formats including e.g. Matlab, BioPAX level 2 and level 3, DOT, Octave, XPP and SBGNML.


SABIO-RK in MetaNetX

09-26-2017

MetaNetX integrated SABIO-RK and implemented cross-references to compounds and reactions in SABIO-RK.
MetaNetX is an online platform for accessing, analyzing and manipulating genome-scale metabolic networks as well as biochemical pathways.


SABIO-RK at ICSB2017

05-29-2017

COMBINE - de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology


Dates: Sunday, August 6th, 2017
(9:00 - 18:00)

Location: BLacksburg, Virginia (USA)

Website: http://co.mbine.org/events/tutorial2017

This tutorial workshop is a satellite of the 18th 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 experime ntal 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 dem onstrated along with the basic principles of the underlying standard formats.


SABIO-RK Training Event

04-06-2017

cancelled
SABIO-RK Introduction and Hands-on Training
Wednesday, May 31st, 2017 in Heidelberg

Target audience:
People interested in systems biology or biochemistry

Learning goals:
- Introduction to the biochemical reaction kinetics database SABIO-RK
- Learning and working with the tools of the database

Hands-on training:
- SABIO-RK web interface
- Export functionalities
- SABIO-RK web services

Prerequisites:
- Basic knowledge and interest in biochemistry or enzymology
- It is recommended to bring your own laptop


The participation is free of charge but registration is required until May 24th.
Please send an email to: maja.rey@h-its.org
Certificate of attendance can be issued.