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Pack gbn -- Readme.md

gBN: BNs for large cohort genomic studies.

gBN runs the BN learning algorithm Gobnilp and implements many post-processing visualisation functions for analysing large scale patient studies from genomic information. Specially so for cancer patient data.

Currently only tested on *nix like systems. Developed on Linux Mint 2020.\ It should also work on MacOS with one of the linux-like platforms installed.

Executable dependencies

The following executables should be installed on your local machine.

  • SWI-Prolog (swipl in $PATH)
  • R (compiled with --enable-R-shlib, the resulting libR.so should be in $LD_LIBRARY_PATH)
  • GOBNILP (C language version with SCIP-solver; gobnilp should be in $PATH)
  • SCIP SCIP ILP solver (needed by Gobnilp at installation time)
  • graphviz (for displaying, dot executable should be in $PATH)

R dependencies

The following R packages will be asked for installation at loading time, if not already present in local R installation.

  • RColorBrewer
  • cowplot
  • ggplot2
  • ggpubr
  • gridExtra

SWI pack dependencies

Pack lib (pack(lib)), developed by us is central to loading all the Prolog dependencies.

% swipl
?- pack_install(lib).

The following will be installed, interactively, by pack(lib), at loading time if they are not already present in the local SWI installation.

  • mtx
  • real
  • os\_lib
  • by\_unix
  • disp\_bn
  • options
  • debug\_call
  • stoics\_lib
  • pack\_errors
  • svg You can install each pack above independently/separately from within SWI-Prolog, for example: 
    % swipl
?- pack_install(mtx).

    All packs installable this way can be found on the SWI-Prolog pack list.

Installation, Loading & Testing

% swipl

?- pack_install(gbn).

?- use_module(library(gbn)).
% Loading installed R library: RColorBrewer
% Loading installed R library: cowplot
% Loading installed R library: ggplot2
% Loading installed R library: ggpubr
% Loading installed R library: gridExtra

?- gbn([debug(true)]).
% Turning debugging on for predicate handle: gbn(gbn)
% Options: [$restore(gbn,debug,false),copy(false),data(pack(gbn/data/asia.dat)),display_dot(svg),odir(_33202),std_output(std_file)]
% Output directory: 'asia-20.09.27'
% Settings on: asia.set

A more complex example:

% swipl

?- use_module(library(gbn)).

?- [cancer(aml)].

?- aml.
% Starting: aml
% Starting: fisher_nets
% Starting: fam_hmaps
% Starting: gates_nets
% Starting: svg_legend
% Finished: aml
true.

The above would create an output directory: aml_min60-21.01.19 where the date stamp will reflect the current date.

Cancer datasets from our paper (each can be run as per example above):

  • aml (Acute myeloid leukaemia)
  • coa (Colon Adenocarcinoma, from TCGA)
  • gbm (Glioblastoma)
  • mpn (Myeloproliferative neoplasms)
  • mye (Multiple myeloma)

Data

Datasets are in the source directory: data/ (with cancer datasets in data/gbns_in_cancer/).

Pack info

Publications

  • Classification and Personalized Prognosis in Myeloproliferative Neoplasms, 10.1056/NEJMoa1716614
  • Genomic Landscape and Chronological Reconstruction of Driver Events in Multiple Myeloma, 10.1038/s41467-019-11680-1
  • Molecular Evolution of IDH Wild-Type Glioblastomas Treated With Standard of Care Affects Survival and Design of Precision Medicine Trials: A Report From the EORTC 1542 Study, 10.1200/JCO.19.00367

Author

Nicos Angelopoulos,\ London, 2021