Software

The following programs are written in Prolog and R.

Most projects are hosted on github and distributed as SWI-Prolog libraries (see packs list).

Cancer

gBN: BNs for large cohort genomic studies.

gBN: A suite of analysis tools around learning of Bayesian networks, via GOBNILP, for large genomic, cancer cohorts.

Bayesian models of age-incidence for sporadic and inherited ccRCC.

Age related Bayesian models from our paper:
Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal
Github: ccRCC_incidence_models

Molecular timing of genomic aberrations.

R function for calculating the timing of DNA aberration events from NGS data.
Github: mol_time

Computational Biology

scRNA

Supervised the R code development for our paper: Porcine respiratory coronavirus as a model for acute respiratory disease: mechanisms of different infection outcomes
Github: prcv

Real

Real: integrative functional statistics with R and logic programming.
RealOS: a data analytics desktop OS for Raspberry 4.

bio_db

bio_db: Prolog access to high-quality biological databases.
Includes 4 back-ends: Prolog facts, proSQLite, RocksDB and Berkeley DB.
Supports: human, mouse, chicken and pig.

bio_analytics

bio_analytics Suit of libraries for biological data analytics.

Probabilistic Logic Programming

Bims: Bayesian inference of model structure

Bims: implementing Markov chain Monte Carlo over Model Structures (see publications).
(Earlier versions distributed as MCMCMS.)

Parameter estimation for SLPs

pepl: an implementation of the FAM algorithm for Stochastic Logic Programs.

probabilistic finite domains

pfds: a meta-interpreter for Pfds.

Logic Programming

proSQLite

proSQLite: a Prolog library for the SQLite database system.

pubmed

pubmed: pubmed interrogation tool for Prolog.

by_unix

by_unix: an elegance layer to calling unix commands.

r_session

r_session: a first attempt to Prolog<->R communication.

http server for ODBC databases

hdb is a generic http server for odbc databases. Currently this has limited documentation.

upsh

Upsh: run Prolog scripts from the operating system command prompt.

ex libris

ExLibris: a library-centric approach to developing and distributing Prolog, open-source.