We are assuming the directory structure is as follow:

/-> root directory where this file lies.
/datasets/classical/          (6 sub-directories, for Alzheimers, Carcinogenesis, DSSTox, Pyrimidines and Proteins)
/datasets/phase_transition/   (8 sub-directories)
/GILPS/
/Aleph/

There are several scripts in the command line. They are assumed to be executed in Linux.
To execute under Windows try using Cygwin.

ProGolem
********

To run ProGolem on the Phase Transition dataset please use the script run_gilps_pt.sh

To run ProGolem on the classical ILP datasets please use:

yap -l run_classical -g dataset

E.g.
  yap -l run_classical -g pyrimidines

(have a look at the file run_classical.pl to adjust the datasets paths)

To run ProGolem on the phase transition datasets please use:


Aleph
*****

To run Aleph on the phase_transition dataset use, e.g. :

yap -L datasets/phase_transition/p.m6.l12/run_aleph
(replace p.m6.l12 for the possible datasets, e.g. p.m7.l12,..., p.m17,l12)

To run Aleph on the classical non-determinate datasets use, e.g. :
run_aleph.sh datasets/classical/alzheimers/ log_amine.txt
(replace alzheimers by the other possible directories, e.g: carcinogenesis, dsstox).

Then collect these results and paste them to the aleph_results.xls spreadsheet

To run Aleph on the classical determinate datasets (i.e. Proteins and Pyrimidines) use:

yap -L datasets/classical/pyrimidines/run_aleph
yap -L datasets/classical/proteins/run_aleph



Jose Santos <jcas81@gmail.com>, January 2010
