

Applying hclasp to Metabolic Network Expansion in ASP
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Files and folders:
 heuristics/: heuristic files used with hclasp
 network-expansion/: encoding ans instances from http://www.cs.uni-potsdam.de/bioasp/expansion.html

We recommend to read ReadMe.txt in network-expansion/ for information on the basic usage of gringo and clasp
 for the experiments.


USAGE:

To compute the minimal number of reactions (from metacyc-7000_0) that need to be added with the draft network 0444 to produce all target metabolites,
 using sign=-1 for the abducibles, type:

  gringo -c mode=sign -c value=-1 heuristic-template-1.lp card_min_extensions_all_targets.lp ecoli-networks/ecoliDraft_0444.lp ecoli-seeds-and-targets/ecoli_seeds.lp ecoli-seeds-and-targets/ecoli_targets_all.lp metacyc-networks/metacyc_7000_0.lp draftnetwork_id.lp | \
   hclasp --heu=domain

For other hclasp configurations, give other values to constants mode and value (f.e., "-c mode=factor -c value=2").

To combine two heuristic modifiers, use file heuristic-template-2.lp and give the corresponding values to constants mode, value, mode2 and value2.
For example, to use sign=1 and factor=2 for abducibles, type:

  gringo -c mode=sign -c value=-1 -c mode2=factor -c value2=2 heuristic-template-2.lp card_min_extensions_all_targets.lp ecoli-networks/ecoliDraft_0444.lp ecoli-seeds-and-targets/ecoli_seeds.lp ecoli-seeds-and-targets/ecoli_targets_all.lp metacyc-networks/metacyc_7000_0.lp draftnetwork_id.lp | \
   hclasp --heu=domain

