Help:Supported Software Tools
If you know of a tool or resource that makes use of our curated pathway content, announce them on our mailing list and add them to the list below.
List of bioinformatics software tools using WikiPathways
- PathVisio is a tool for displaying and editing biological pathways. In a sense PathVisio lets you draw pathways as you would in any drawing program, like PowerPoint or Photoshop. But the difference is that PathVisio can understand the biological context of a pathway, because you can link biological entities (genes or proteins) in your pathways to biological data using database identifiers. This will let you map experimental data (e.g. microarray data) and visualize it on top of the pathway drawing.
- Cytoscape is an open source software platform for visualizing complex-networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web. WikiPathways can be easily imported via web services using the WikiPathways app. Pathways in gpml format created in PathVisio or WikiPathways can be loaded as either their native diagram format or as simplified network graphs, supporting either data visualization or network analysis and augmentation use cases. A brief tutorial is available on OpenTutorials and a detailed description of the app and its usage was published in the Cytoscape App Collection in F1000Research.
- Eu.Gene Analyzer is an easy-to-use, stand-alone application that allows rapid and powerful microarray data analysis in the context of biological pathways. Its intuitive graphical user interface makes it an easy and flexible tool, even for the first-time user. Pathways can be downloaded from WikiPathways in EuGene's .pwf format.
- GO-Elite is a software tool designed to identify a minimal non-redundant set of Gene Ontology (GO) biological terms or pathways to describe a particular set of genes. GO-Elite uses WikiPathways as its official pathway source. GO-Elite is also available as a Cytoscape plugin.
- The purpose of SNPLogic is to provide comprehensive interactive SNP annotation, selection and prioritization system for focused genotyping projects and/or analysis and interpretation of SNP data. The user can create one or more SNP lists and populate them by adding SNPs either directly or by picking genes, pathways, chromosomal locations or by uploading own SNP lists.
- WebGestalt is a "WEB-based GEne SeT AnaLysis Toolkit". It is designed for functional genomic, proteomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources, including WikiPathways, and provides an easy way for biologists to make sense out of gene lists.
- BioServices is a Python package that provides access to many Bioinformatics Web Services (including WikiPathways) and a framework to easily implement Web Service wrappers (based on WSDL/SOAP or REST protocols).
List of databases and resources that include WikiPathways content
- Use BioPortal to access and share ontologies that are actively used in biomedical communities. WikiPathways uses BioPortal to power its ontology tagging system and BioPortal lists all ontology-tagged pathways as resources.
- ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions, as well as interactions that we have curated from literature, including WikiPathways.
- The free encyclopedia that anyone can edit. In collaboration with MCB and GeneWiki, we have added interactive pathway maps using WikiPathways (example).
- NCBI Biosystems
- The NCBI BioSystems Database is a centralized repository containing biological pathways from several resources and connects those with associated literature, molecular and chemical data throughout the Entrez system. This makes it possible to link to WikiPathways directly from NCBI pages. Whether you are browsing Gene, Pubchem or Structure entities at NCBI, you will find relevant summaries, images and links to WikiPathways. They are listed as "Pathways from BioSystems" under the "General gene information" section (example). You can also view information about a single pathway on the summary pages and browse our pathway content by gene, pubchem or structure frequency.
- IMPaLA is a new web tool, developed for integrated pathway analysis of metabolomics data alongside gene expression or protein abundance data. It works through extending over-representation and enrichment analyses to multiple data types. It uses pathway data from several different online pathway databases, eg. KEGG, Reactome, BioCyc, NetPath, WikiPathways,...
- The NIF (Neuroscience Information Framework) is a dynamic inventory of Web-based neuroscience resources. WikiPathways is included as one of the resources.
- Pathway Commons
- coming soon...
- Therapeutic Targets Database
- TTD is a database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets.
- Lynx: an Integrated Systems Biology Platform
- Lynx is a database and knowledge extraction engine for integrative medicine.
- miRNA Pathway Dictionary Database (miRPathDB)
- miRPathDB aims to augment available target pathway web-servers by providing researches easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific the regulations are.