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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]
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 ...
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 ...
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.
The terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License apply to all software and code, e.g. relating to the functionality of the reactome.org, derived websites and webservices, the Curator Tool, the Functional Interaction application, SQL and Graph Database data dumps, and Pathway Illustrations (Enhanced High-Level ...
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]
Using the web-interface of the database, one can perform overrepresentation analysis, based on biochemical pathways or on neighbourhood-based entity sets (NESTs) that constitute sub-networks of the overall interaction network containing all physical entities around a central one within a "radius" (number of interactions from the center).