• 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...