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  2. BioPAX - Wikipedia

    en.wikipedia.org/wiki/BioPAX

    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.

  3. List of biological databases - Wikipedia

    en.wikipedia.org/wiki/List_of_biological_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 ...

  4. Reactome - Wikipedia

    en.wikipedia.org/wiki/Reactome

    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.

  5. PathVisio - Wikipedia

    en.wikipedia.org/wiki/PathVisio

    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]

  6. List of open-source bioinformatics software - Wikipedia

    en.wikipedia.org/wiki/List_of_open-source...

    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, macOS, Windows: GPL: University of Michigan: PathVisio: Desktop software for drawing, analyzing, and visualizing biological ...

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  9. BioCyc database collection - Wikipedia

    en.wikipedia.org/wiki/BioCyc_Database_Collection

    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.