implementation
Bio-Calculus
Moirai
BioPSI
AlChemy
KEGG
CSNDB
TRANSPATH
INTERACT
TAMBIS
GIMS
TaO
GRAIL
UM-BDD
CORE
aMAZE
EcoCyc
GeneOntology
Cutenet
Rhaphsody
CellML
Kinetikit
GENESIS
SCAMP
DBSolve
GeNet
NetWork
GeneGraph
Virtual Cell
Virtual Laboratory
BioSim
DMSS
QSim
SPICE
DDLAB
Gepasi
Electronic Biochemical Pathways
MARG
IMIS
MetabSim
MetaNet
PED
PEDVisor
INA
METATOOL
BioQUEST
BIND
SBML
Electronic Arc
AIGNET
UltraSAN
BioNLP
ToPLign
BioJAKE
Highlight
EMPathIE
Graphviz
PIES
E-cell
Jarnac
BioSpice
SBW
ERATO
PIMRider
DIP
Boehringer
MetabVis
PathDB
HinCyc
MetaCyc
MPW
EMP
WIT
PUMA
CKSD
A-Cell
MEG
GENESYS
Pathway Explorer
GENIES
StochSim
PubGene
FlyNets
PROMOT
logic
prolog
semantics
declarative
graph
graphical
calculus
linear logic
lambda calculus
proof nets
Petri net
pi-calculus
grammar
object-oriented
UML
description logic
graph reaction networks
Statecharts
markup
circuit
interaction map
Model Description Language
hybrid
kinetic
delay differential equations
algebraic
power law formalism
Bayesian network
S-system
activation-inhibition network
Boolean network
Boolean logic
hierarchical
neural network
PDP network
kinetic logic
combinatorial
ASN.1
program tree
conceptual graph
frames
molecular
biochemistry
signaling
DNA regulatory element
metabolism
regulatory
protein-protein
nucleic acids
complex
transport
metadata
structure
compartment
immune
whole genome
physicochemical constraints
mutation
multicellular
image
conformation
domain
qualitative
quantitative
semi-quantitative
executable
continous
stochastic
discrete
feedback
modular
temporal
spatial
steady state
stoichiometry
diffusion
asynchronous
synchronous
linear
non-linear
knowledge representation
database
ontology
simulation
analysis
molecular control
metabolic control
flux balancing
flux route
phenotype phase plane
phenotype phase diagram
robustness
extreme pathways
topology
self dependent subset
numerical
statistical
logical constraints
connectivity
optimization
formal verification
deadlock
small world
comparative
pathway alignment
pathway discovery
pathway classification
score
mathematically controlled comparison
structural class
behavioral class
equivalence
phylogenetic profile
Rosetta stone
reconstruction
literature
inference
information extraction
correlation metric construction
multidimensional scaling
Expansion
Exchange
visualization
Engineering
systemic
abstraction
type hierarchy
NLP
UMLS
genetic programming
java
interactive