skm

A Python library for building, converting, and simulating Boolean and semi-quantitative Boolean network models. Wraps pyboolnet for prime-implicant-based Boolean algebra and adds network I/O (SBML-qual, GraphML, bnet, SIF, Cytoscape), ODE-based continuous/semi-quantitative relaxations of Boolean models, and simulation-result plotting.

Hand-curated knowledge base of mTOR biology, linking 360+ primary studies to genes, drugs, diseases, pathways and outcomes. Every study carries a code for the kind of study behind it - synthesis of human data, human, animal, molecular or review - which names the system a finding was established in rather than ranking it, alongside open research questions.

This tool estimates the completeness of KEGG pathway modules from the presence or absence of KEGG orthologues (KOs)

Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.

Web application and service for visualizing small- to medium-scale models of gene regulatory networks. It automatically lays out either an unweighted or weighted network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges and has general applicability.

PinPath enables flexible visualization of (omics) data onto pathways diagrams, allowing users to pinpoint where the relevant changes occur. It supports pathway diagrams from WikiPathways and KEGG, as well as custom GPML and KGML files. Data can be displayed on both native pathway layouts and network representations