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

- This file
  * README

- Repair encoding
  * repair.lp

- Specialized repair encoding implementing inclusion-minimality
  * repair_direct.lp

- Subfolder "data" including
  * data/tf_sig_bnum.lp : transcriptional network of Escherichia coli
  * data/instances/*.lp : 100 (samples of) experimental observations

- Subfolder "opti" including repair-enabling facts
  * opti/mode_1.lp : allow for flipping vertex labels
  * opti/mode_2.lp : allow for turning vertices into inputs
  * opti/mode_3.lp : allow for flipping edge labels

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/.
The meta-programs meta.lp, metaD.lp, and metaO.lp must be available too (e.g., in a folder "../encodings").

COMMAND-LINE CALLS
==================

- subset minimization via meta-programming (repair.lp)
  * SCHEME
    $ gringo --reify repair.lp opti/<some_mode> data/tf_sig_bnum.lp data/instances/<some_instance> | \
      gringo - ../encodings/{meta.lp,metaD.lp,metaO.lp} - <(echo "optimize(J,W,incl) :- minimize(J,S), wlist(S,_,_,W).") | \
      claspD
  * EXAMPLE
    $ gringo --reify repair.lp opti/mode_1.lp data/tf_sig_bnum.lp data/instances/Stat_vs_Exp_6_06.lp | \
      gringo - ../encodings/{meta.lp,metaD.lp,metaO.lp} - <(echo "optimize(J,W,incl) :- minimize(J,S), wlist(S,_,_,W).") | \
      claspD

- subset minimization via direct encoding (repair_direct.lp)
  * SCHEME
    $ gringo repair_direct.lp opti/<some_mode> data/tf_sig_bnum.lp data/instances/<some_instance> | \
      claspD
  * EXAMPLE
    $ gringo repair_direct.lp opti/mode_1.lp data/tf_sig_bnum.lp data/instances/Stat_vs_Exp_6_06.lp | \
      claspD
