-
DNA
- Referenced in 8 articles
[sw26923]
- provide valuable information about the underlying biochemical pathways. Differential network analysis with appropriate connectivity scores...
-
Path2Models
- Referenced in 4 articles
[sw29332]
- scale generation of computational models from biochemical pathway maps. Background: Systems biology projects and omics ... growing number of biochemical pathway models and reconstructions. However, the majority of these models...
-
BioMiner
- Referenced in 3 articles
[sw23101]
- BioMiner - modeling, analyzing, and visualizing biochemical pathways and networks. MOTIVATION: Understanding the biochemistry ... system--BioMiner--for analyzing and visualizing biochemical pathways and networks. BioMiner is based ... which can be used to model biochemical pathways and networks. As a first application ... present PathFinder, a new tool predicting biochemical pathways by comparing groups of related organisms based...
-
Pathway Commons
- Referenced in 9 articles
[sw23072]
- pathway data via a common repository. Pathways include biochemical reactions, complex assembly, transport and catalysis ... proteins, DNA, RNA, small molecules and complexes. Pathway Commons aims to collect and integrate...
-
MetaCyc
- Referenced in 29 articles
[sw08243]
- pathways of organisms from their sequenced genomes, supporting metabolic engineering, helping to compare biochemical networks...
-
BioPath
- Referenced in 4 articles
[sw07462]
- well-known Boehringer poster and the Biochemical Pathways atlas. These networks are very complex...
-
E-CELL
- Referenced in 23 articles
[sw07917]
- Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis ... CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed...
-
libSRES
- Referenced in 2 articles
[sw12828]
- Estimation of kinetic parameters in a biochemical pathway or network represents a common problem ... software for study of non-linear biochemical pathways. This library implements...
-
iPath
- Referenced in 3 articles
[sw16937]
- iPath: interactive exploration of biochemical pathways and networks. iPath is an open-access online tool...
-
MISA
- Referenced in 3 articles
[sw13359]
- those involved in a specific biochemical pathway. Given this data, we are interested in addressing...
-
MoVisPP
- Referenced in 3 articles
[sw35665]
- based tool to model and visualise biochemical pathways using Petri Nets. Petri net models...
-
expa
- Referenced in 3 articles
[sw35555]
- expa: a program for calculating extreme pathways in biochemical reaction networks. Summary ... pathways, a generating set for all possible steady-state flux maps in a biochemical reaction ... well-known algorithm to compute these pathways and give a summary of the features...
-
Cell++
- Referenced in 2 articles
[sw35406]
- Cell++ - simulating biochemical pathways. Motivation: With the generation of a wealth of information, detailing cellular ... capacity to study a wide variety of biochemical processes within a spatial context. Results: Focusing ... evolution and engineering of signaling and metabolic pathways. In addition to altering signaling and metabolic...
-
HGV
- Referenced in 2 articles
[sw00406]
- call graphs in software engineering or biochemical pathways, with a particular need to manipulate...
-
COVAIN
- Referenced in 1 article
[sw10556]
- multivariate statistics, network topology and biochemical pathway mapping analysis is in all cases recommended. Therefore ... pathways this approach allows for a systematic investigation of perturbation sites in the biochemical network...
-
TFGD
- Referenced in 1 article
[sw18850]
- genes, significantly affected biological processes and biochemical pathways from gene expression data sets and miRNA...
-
WinBEST-KIT
- Referenced in 5 articles
[sw35398]
- Windows) for analyzing complicated biochemical reaction systems such as metabolic pathways. WinBEST-KIT provides ... will become one of the most efficient biochemical reaction simulators for experimental researchers...
-
Onto-Tools
- Referenced in 10 articles
[sw10974]
- pathways. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function ... genes present on the array represent specific pathways. Onto-Compare is a tool that allows...
-
CRNreals
- Referenced in 5 articles
[sw13616]
- analyzing complex biochemical systems such as metabolic networks and cell signalling pathways. Being able...
-
HMDB
- Referenced in 9 articles
[sw28995]
- other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other ... GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive...