Package: compath
An integrative and extensible web application for exploring, analyzing, and curating pathway databases. ComPath is publicly available athttps://compath.scai.fraunhofer.de/.This package exposes the Bio2BEL pathway packages into a web application containing multiple built-in visualization and
analytics tools allowing for their analysis and comparison. By default, this packages wraps the following default
packages:Bio2BEL KEGGBio2BEL ReactomeBio2BEL WikiPathwaysBio2BEL MSigNew pathway/gene signatures resources can be added by forking theComPath Template Repository.CitationIf you use ComPath in your work, please consider citing:[1]Domingo-Fernández, D.,et al.(2018).ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases.npj Syst Biol Appl., 4(1):43.Installationcompathcan be installed easily fromPyPIwith the
following code in your favorite terminal:python3-mpipinstallcompathor from the latest code onGitHubwith:python3-mpipinstallgit+https://github.com/bio2bel/compath.git@masterSetupEasiestAfter installingcompath, run from the command line:python3-mcompathpopulateThis command populates all of the relevant Bio2BEL repositories for the default list, and if any optional ComPath
repositories have been registered with entry points, will also populated.For DevelopersIf you just cloned the repo and installed it from the source code, you can run the sh scriptload_compath.shby
typingsh load_compath.shin your terminal. This script will first install all packages and later populate the
database.If you have already installed the packages, but not loaded the data. First, loadBio2BEL HGNC(see ‘Mapping across gene/protein identifiers’ section). Next, load all individual pathway database
packages KEGG, Reactome, WikiPathways, and MSigDB  withpython3 -m compath populate. This command assumes that
these packages are already installed in your Python environment. You can check the packages installed by runningpython3 -m compath lsin your terminal. Alternatively, you can populate each package independently by running:python3 -m bio2bel_kegg populate,python3 -m bio2bel_reactome populate,python3 -m bio2bel_wikipathways populate, orpython3 -m bio2bel_msig populate.Mapping across gene/protein identifiersIn order to load the gene sets from default packages, ComPath assumes thatBio2BEL HGNChas been already installed and populated. This package is required to perform the mapping from multiple Protein/Gene identifiers to HGNC symbols. The following steps are needed to install Bio2BEL HGNC:python3 -m pip install bio2bel_hgncpython3 -m bio2bel_hgnc populateRunning the Web ApplicationThe application can be run simply withpython3-mcompathwebThis command the Flask development server locally, by default on port 5000 (http://localhost:5000).Curation InterfaceLoad mappings between pathways directly from theComPath Curationpackage.python3-mcompathload_mappings--connection="sqlite:////data/bio2bel.db"Load hierarchical mappings from a pathway database already containing that information (e.g., Reactome).python3-mcompathload_hierarchies--connection="sqlite:////data/bio2bel.db"Create a user.python3-mcompathmanage--connection="sqlite:////data/bio2bel.db"usersmake_user'email''password'Make user admin.python3-mcompathmanage--connection="sqlite:////data/bio2bel.db"usersmake_admin'email'Docker InstructionsDeployment of ComPath with DockerBuild the container with compath as a name.dockerbuild-tcompath:0.0.1.Create the data container in which the data will be located.docker create -v /data --name compath-data compath:0.0.1Run docker container and connect it with the data containerdocker run --name=compath --volumes-from compath-data --restart=always -d compath:0.0.1For admin purposes and deploying ComPath inside Fraunhofer you can also run the following commandshcreate_and_build_container.shLoad DataLoads the KEGG, Reactome, and WikiPathways modules into ComPath.dockerexec-t-itcompath/opt/compath/src/bin/load_data.shRestart ContainerRestarts the compath containerdockerrestartcompathDisclaimerComPath is a scientific software that has been developed in an academic capacity, and thus comes with no warranty or guarantee of maintenance, support, or back-up of data.