• DNA

• Referenced in 7 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 28 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...

• 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...

• Cellnoptr

• Referenced in 5 articles [sw15114]
• pathways encoded as a Prior Knowledge Network, and trains it against high-throughput biochemical data...