ARCHIVE CONTENTS
================

- This file
  * README

- Repair encoding
  * repair.lp

- Subfolder "data" including
  * data/tf_sig_bnum.lp        : transcriptional network of Escherichia coli
  * data/heatShock_WT/<%>/*.lp : (samples of) experimental observations
  * data/Stat_vs_Exp/<%>/*.lp  : (samples of) experimental observations

- Subfolder "opti" including optimization-related facts
  * opti/uniform_parall.lp : one priority level, same weight for repairs
  * opti/uniform_pareto.lp : one priority level, distinct weights for repairs
  * opti/layered_parall.lp : two priority levels, same weight for repairs
  * opti/layered_pareto.lp : two priority levels, distinct weights for repairs

REQUIRED/RECOMMENDED PROGRAMS
=============================

- gringo : version 3.0.3 (or later)
- claspD : version 1.1   (or later)

Sources (and binaries) are available at: http://potassco.sourceforge.net/.

USAGE
=====

For repairing w.r.t. custom minimality criteria, reification is applied to:
  * repair.lp
  * data/tf_sig_bnum.lp
  * some data file in data/heatShock_WT/<%>/ or data/Stat_vs_Exp/<%>/
  * some optimization configuration file in opti/
The reified program is then combined with meta-encodings and rules selecting
comparison relations. Finally, a disjunctive ASP solver is queried.

For instance, one can run repair inclusion minimization w.r.t. two priority
levels and distinct weights for repair operations as follows:

$ gringo --reify repair.lp opti/layered_pareto.lp data/tf_sig_bnum.lp data/heatShock_WT/15/heatShock_WT_1_15.lp | \
  gringo - ../encodings/{meta.lp,metaD.lp,metaO.lp} <(echo "optimize(J,W,incl) :- minimize(J,S), wlist(S,_,_,W).") | \
  claspD

FURTHER INFORMATION
===================

For further details, especially on the logical background of repairs, see KR'10
paper "Repair and Prediction (under Inconsistency) in Large Biological Networks
with Answer Set Programming" or consult: http://www.cs.uni-potsdam.de/bioasp/.
