[x]omics

Systems biology combines the different kinds of *omics (proteomics, transcriptomics, etc.)

Databases
CellML repository (Auckland, NZ)
Human Metabolome Database
Panther Classification Systems - Panther Pathways
KDBI - Kinetic Data of Biomolecular Interactions
The Systems Biology Researcher Database

Standards and Ontologies
Systems Biology Markup Language
Systems Biology Graphical Notation
Systems Biology Ontology
Minimum Information Requested In the Annotation of Models
BioPAX
CellML

Bioinformatic Tools
ABC-SysBio - This package employs approximate Bayesian methods for inference in systems biology models.
BioCatalogue - a curated catalogue of Life Science Web Services.
Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
GATE: Grid Analysis of Time-series Expression is a computational software platform for integrated visualization and analysis of expression time-series.
Genes2Networks places lists of mammalian genes in the context of a background mammalian signalome and interactome networks.
Lists2Networks Integrated Analysis for Lists of Mammalian Genes. Lists2Networks is a web-based system that will allow users to upload and analyze lists of mammalian gene-sets in a client-server-based software application.
Downloadable Systems Biology Software(ISB)

Models
Cytoscape
Database of Quantitative Cellular Signalling (Bangalore, India)
E-Cell Project University Keio
The Harvey Project
C. elegans, DKFZ
Virtual Cell Portal
Molecular Simulation Virtual Lab
ModelDB
The yeast silicon cell
BioModels Database (Cambridge, UK)
GENESIS
Silicon Cell ready to use
Virtual Cell Plant
M-Cell

Modelling tools
JWS Online - Online Cellular Systems Modelling
Dizzy stochastic simulations tool
JSim - a Java based simulation system
PyBioS - web server for modeling and simulation of cellular systems
Pasadena Twain ODE solver of the SWB package
CADLIVE - network construction system
CaliBayes - Bayesian calibration of biological simulators
CellDesigner - a modeling tool for biochemical networks
CellWare - building computational chassis for systems and synthetic biology
COPASI - Complex Pathway Simulator
PLAS Power Law Analysis and Simulation tool
Dynetica - a simulator of dynamic networks
E-Cell project
Gepasi - Biochemical Kinetics Simulator
Modelling Tools
STOCKS - Stochastic kinetic simulations
Virtual Cell Internet simulation server at NRCAM