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finally, cpath currently supports fetching and storing both psi-mi and biopax data from within the cytoscape software. we have a psi-mi extension and a cytoscape plugin available, and plan to extend cpath to support the export of the additional biopax types available in the psi-mi standard. on the client side, cpath currently supports fetching and storing biopax data in cytoscape 3.0 compatible format, and psi-mi and biopax data in cytoscape 2.5 compatible format.
the strength of cpath lies in its simplicity. cpath is easy to install on a local computer, and uses the cytoscape software as a front end. most people will already have cytoscape on their computer, and will need little training to use it. the psi-mi api makes it easy to fetch and store pathway data from an external data source.
cpath is powered by the cytoscape software, which is widely used for visualizing and analyzing biological data. the plugin for cpath is written in javascript, which makes it easy to create a plugin for different cytoscape software versions.
to get started with cpath, simply unzip the cpath zip file, and double click on cpath.exe. the cpath software displays an installer window, and the installation will be completed in a few simple steps. the software will also help you to install new data source types, as well as convert your existing data sets to the new format. once installed, cpath can be run from its start menu.
to facilitate its operation, cpath includes a set of configuration files containing information about the data sources, data format conversions, and other configuration parameters. these files are kept up-to-date with the released cpath version. check for these files in the cpath folder. you can find complete documentation in the documentation folder.
pathway data querying is the first iteration of cpath, but new queries will include other types of interactions, including go terms, small molecules and genomic loci, that collectively provide an increasingly integrated view of the genome. links to a few other examples of cpath-powered resources are provided on the cancer cell map and the cancer database web sites. a connection to a pathway editor, such as kegg [ 50 ], to view and manipulate pathway data is provided from the query results page. features of the pathway editor, such as the ability to graphically edit and alter pathways, would be the natural extension of cpath. several features are planned to streamline the cpath client, server and database. the database is currently updated asynchronously with a nightly post-commit database update, and the update and backup routines run only when the database is in use. although this database update scheme prevents cpath from being used during a batch upload, it limits the probability of a crash and provides a very low latency when users access cpath for first time. in addition to synchronizing the database nightly, cpath includes a feature to detect if the database is in use or not, and only perform a pre-commit database update in the case where the database is not in use. an additional feature will be added that will cause a pre-commit database update even if the database is not in use. this feature will cause the database to be updated on clients that recently uploaded data, but not on clients that are not currently actively downloading data. users who wish to avoid the nightly database update can explicitly call the update routine to upgrade their database. lastly, a feature will be added that will ensure that the database is backed up once a week. users can call this feature to schedule a backup once a week. however, the update, backup and schema versioning features will not protect cpath against a hard drive crash or server failure, thus users are strongly encouraged to back up their databases in the off-hours. 5ec8ef588b
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