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Software platform, allows organizations to integrate, analyze, and share complex biomedical data Linux, macOS, Windows: Apache: LabKey Software Foundation LAMMPS: Molecular dynamics program written in C++: Linux, macOS, Windows: Apache: Sandia National Laboratories. mothur: Software for analysis of 16S rRNA gene amplicon sequence data Linux ...
Systems Biology Pathway Exchange (SBPAX) is an extension for Level 3 and proposal for Level 4 to add quantitative data and systems biology terms (such as Systems Biology Ontology). SBPAX export has been implemented by the pathway databases Signaling Gateway Molecule Pages, [1] and the SABIO-Reaction Kinetics Database.
curated resource of human signal transduction pathways MEGA: free, online, open-source, phylogenetic analysis, drawing dendrograms etc. REACTOME free, online, open-source, curated pathway database encompassing many areas of human biology WikiPathways: curate biological pathways MetaboMAPS: visualize omics data on shared metabolic pathways [1]
Reactome is a free online database of biological pathways. [ 1 ] [ 2 ] [ 3 ] It is manually curated and authored by PhD-level biologists, in collaboration with Reactome editorial staff. The content is cross-referenced to many bioinformatics databases.
NCI-Nature Pathway Interaction Database; Netpath: curated resource of signal transduction pathways in humans; Reactome: navigable map of human biological pathways, ranging from metabolic processes to hormonal signalling (Ontario Institute for Cancer Research, European Bioinformatics Institute, NYU Langone Medical Center, Cold Spring Harbor ...
PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible. [1] [2] [3]
The SuperPred web server compares the structural fingerprint of an input molecule to a database of drugs connected to their drug targets and affected pathways. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find ...
Based on the manual curation done, BioCyc database family is divided into 3 tiers: Tier 1: Databases which have received at least one year of literature based manual curation. Currently there are seven databases in Tier 1. Out of the seven, MetaCyc is a major database that contains almost 2500 metabolic pathways from many organisms.