%---------------------------------
%
% How to run MC-TopLog
%
%---------------------------------
To run MC-TopLog, please download YAP-6 at: http://www.dcc.fc.up.pt/~vsc/Yap/downloads.html


To generate the hypotheses for the dataset of 'Day1', please run the following command, 

yap -L 'mcTopLog_toxicology/run.pl' -- 'Day1' 

The output (hypotheses) will be stored in the following two files. 

1) Hypotheses in the format of logic program (mcTopLog_toxicology/logicFormatted_Day1_hypo.pl)
2) Hypotheses in a biologically readable format (mcTopLog_toxicology/bioFormatted_Day1_hypo.pl)

For other time points, replace 'Day1' with the corresponding time points. 

%---------------------------------
%
% Details about Input to MC-TopLog
%
%---------------------------------
A. Background knowledge
(1) Metabolic network
KEGG database is parsed by Ondex and output as ground clauses. This file is at: 
/dataset/toxicology/networkData/2012_2/keggmap_rn_rno.pl 

To get metabolite network in Prolog format for other systems, user is advised to use Ondex and use the appropriate KEGG parser followed by exporting the network in the Prolog format. 
Please see the information relevant to using Ondex at: 

http://www.ondex.org/

(2) Regulation rules - These rules are applicable universally irrespective to the system to be modelled. There regulation rules are encoded in the Prolog format 
and are given in the following files:

mcTopLog_toxicology/dataset/toxicology/regulationRules/2011_05_24/regulationRules.pl

(3) Gene expression
mcTopLog_toxicology/dataset/toxicology/observations/ge/allDoeseGE.pl

The above file contains gene expression level for enzymes in Prolog format as used by MC-TopLog. User may want to change it depending on the system to be model. 
The state for the enzyme (represented by the EC) that is, up/down/noChange could be defined either using the method as refered to in the manuscript or user could 
use the states defined using any other approach and provide them to MC-TopLog in the Prolog format as is the above file. 

(B) Examples - Metabolite abundances reflected by the three states (up/down or noChange)
mcTopLog_toxicology/dataset/toxicology/observations/metabolites/allTimepointMet.pl

The observed metabolite abundances are encoded in the Prolog format as follows:

ex(28,abundance('35945: cpd:C00183',down,'Day1'),1)

Where,
ex -> Example
28, index for the example
abundance(a set of arguments) -> A predicate with arguments.
('35945: cpd:C00183',down,'Day1') -> arguments of the 'abundance' predicate. 
	'35945' -> Ondex parser id for the corresponding metabolite. 
	'cpd:C00183' -> cpd:KEGG id for the metabolite
	'down' -> The observed metabolite abundance obtained from the published studies (see the manuscript for the citations to these studies).
	'Day1' -> The time point the observed metabolite abundance was reported.
,1) -> Boolean flag,  '1' denotes the positive example, and '0' a negative example. 



All the above files and their locations are loaded into MC-TopLog through the following file:
mcTopLog_toxicology/dataset/toxicology/top_commands.pl
