General Tools

Sycamore - A systems biology computational analysis and modeling research environment, at Univ. of Heidelberg
BNFinder - Find Bayesian networks from expression data, at Univ. Warsaw
SimCT - Visualize relationships between biological objects, at TAGC

State Transition

Multi-Protein States Query - functional modules and gene states, at Shanghai Institutes for Biological Sciences
KEA - Kinase Enrichment Analysis, at Mount Sinai School of Medicine

Disease States

dbNEI - correlates transcription factors, diseases, microRNA and drugs with neuro-endocrine-immune systems, at Tsinghua Univ.

Pathways and Metabolics

Reactome - a curated knowledgebase of biological pathways
KEGG - Kyoto Encyclopedia of Genes and Genomes
PID - Pathway Interaction Database, at NCI
BioCyc - Large collection of pathway/genome databases
MetaCyc - Non-redundant, experimentally elucidated metabolic pathways
PathCase - a system to store, query, visualize and analyze metabolic pathways, at Case Western Univ.
E-matrix - mathematical model of good old E. coli, at UC San Diego

Transcriptional Regulation and Systems Biology

BIOBASE Suite - TransFac, TransPath, TransCompel, and ExPlain (NIH only)
KEGGanim - visualize and animate KEGG pathways, at Univ. of Tartu
COTRASIF - genome-wide detection of putative TFBS in the promoters of the eukaryotic genes, at NAS of Ukraine
W-ChIPMotifs - de novo motif discovery from ChIP-based HT data, at The Ohio State Univ.