Software

Analysis

Collection of tools (Linklist of the Systems Biology Institute Japan)
http://www.systems-biology.org/002/006.html

Bio Modells Database

Bio Modells Database is an effort to develop a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
http://www.ebi.ac.uk/biomodels/

BioPax

Data exchange format for biological pathway data.
http://www.biopax.org/

Cell Designer

Diagram editor for drawing gene-regulatory and biochemical networks.
http://www.celldesigner.org/

GelInspector

for detecting correlated blotting errors and applying suitable error reduction strategies.
http://www.fdm.uni-freiburg.de/~maiwald/GelInspector/

In silico Organisms

SBML versions of the in silico reconstructions on several organisms.
http://systemsbiology.ucsd.edu/organisms/index.html

JWS Online

Systems Biology tool for simulation of kinetic models from a curated model database.
http://jjj.biochem.sun.ac.za/

Modell editors

Collection of tools (Linklist of the Systems Biology Institute Japan).
http://www.systems-biology.org/002/008.html

Online Course

Overview of modeling techniques (MIT Open Courseware).
http://ocw.mit.edu/OcwWeb/Physics/8-591JFall2004/CourseHome/index.htm

Sabio-RK

SABIO-Reaction Kinetics Database.
http://sabio.villa-bosch.de/SABIORK/

SBGN

Systems Biolgy Graphical Notation.
http://sbgn.org/

SBML

Systems Biology Markup Language.
http://sbml.org/index.psp

Simulation

Collection of tools (Linklist of the Systems Biology Institute Japan).
http://www.systems-biology.org/002/005.html

Utility

Collection of tools (Linklist of the Systems Biology Institute Japan).
http://www.systems-biology.org/002/007.html