Signalarium is a system for programmatically exploring empirical information about signaling pathways in biology. The system encodes guidelines and heuristics for semi-mechanically translating pathway models (such as those from KEGG) into Kappa models, augmented by information acquired from across the bioinformatica. The system generates local databases for protein sets of interest on the fly from authoritative public data services, and analyzes this data programmatically to create instances of model families consistent with published empirical consensus.
The software is distributed as an OCaml library, and the primary user interface is the OCaml REPL as:
bin/ocrun src/test.ml # compile using ocrun
rlwrap ocaml -I src/_build/ -I src/_build/ocrun_libs/lib/
with a ~/.ocamlinit such as
#use "topfind" ;;
#require "batteries" ;;
#require "netclient" ;;
#require "pxp" ;;
#install_printer Pxp_document.print_node;;
#install_printer Pxp_document.print_doc;;
#require "parmap" ;;
#require "sqlite3" ;;
#load "util.cmo" ;;
#load "xml.cmo" ;;
#load "protein.cmo" ;;
#load "db.cmo" ;;
#load "db_sql.cmo" ;;
#load "pdb.cmo" ;;
#load "interval.cmo" ;;
#load "http.cmo" ;;
#load "query.cmo" ;;
Most immediately-useful functions are to be found in the Query module. The
Db_sql module is required to instantiate a local database to query. In most
cases, there is no need to populate the database. You may readily query for
entries that are not in the database, such as
open Query ;;
let db = Db_sql.dbopen "temp.sqlite3" ;;
uniprot db "AXIN1_HUMAN" ;;
and all the required information will be retrieved from relevant web services.