Editing File format specifications

'''Flat files specifications'''

A model to be loaded into OptFlux 2 from flat files must specify the following:


== Reactions file (mandatory) ==

In this file, each row specifies a reaction in the model.

Each row specifies a number of fields separated by a symbol (separator) that can be chosen by the used (by default a comma).

The number of fields has to be 2 or 3 in each row:

the first field is always the ID of the reaction; 

if the user specifies the bounds of the fluxes for the reaction, 3 fields will be used - the second and third fields will be the lower and upper bound, respectively;
example: PGI,-10000.0,10000.0
(specifies reaction PGI with flux bounds -10000 and 10000) 

if the user only specifies the reversibility of the reaction, only 2 fields will be used, and the second field will either be the letter R (reversible) or I (irreversible). In this case, the bound are 0 and 10000 (irreversible) and -10000 and 10000 (reversible).
example: PGI,R
(specifies reaction PGI to be reversible) 

''Note: different rows within the same file can use 2 or 3 fields.''


== Metabolites file (optional) ==


In this file each row specifies a metabolite in the model.

Each row specifies a number of fields separated by a symbol (separator) that can be chosen by the used (by default a tab).

Each row can have 1 or 2 fields.

the first field is always the ID of the metabolite; 
if a second field is used, it specifies if the metabolite is internal (letter I) or external (letter E); if the field is not used the metabolite is, by default, internal.
example: NADHcyt
		(specifies the metabolite NADHcyt, internal by default)
		example: SUC,E
		(specifies the metabolite SUC as external)

''Note 1: different rows within the same file can use 1 or 2 fields.

Note 2: for all external metabolites identified, a drain reaction will be created with the ID “EX_” followed by the metabolite ID.

Note 3: if the metabolites file is not given, it is assumed that metabolites will have predefined IDs (“m1”, “m2”, …). 

Note 4: if no external metabolites are identified in this file, it is assumed that external metabolites will be identified by gathering all drain reactions in the matrix file.''


Stoichiometric matrix file (mandatory)

This file specifies the stoichiometric matrix as a sparse matrix file. Thus, each row of the file specifies an element of the matrix different from zero. Each row has 3 fields separated by a symbol (separator) that can be chosen by the used (by default a tab). The first field states the index of the matrix row, the second the index of the matrix column and the third the coefficient value. The first index to be used (normally zero or one) can be defined by the user.
Note 1: the set of genes for the model is determined by gathering the different symbols in the right hand sides.
The index of the rows (metabolites) is given by the order of the metabolites in the file, and the same is true for the index of the columns regarding the reaction file.

<nowiki>	Example: 6	29	1.0
	(sets the element on row 6 and column 29 of the stoichiometric matrix to 1)</nowiki>

''Note: If the external metabolites were not given in the previous file, a process is run to identify all drain reactions from the matrix, after this file is loaded. All columns identified as drains (only one coefficient different from zero) will allow to identify the corresponding external metabolites.''



== Gene- reaction rules (optional) ==


This file specifies gene-reaction associations. It is composed of rows with the following format:

	ReactionID = geneID and/or geneID and/or … 

- the left hand side is a reaction ID of the model (as specified in the first file). This should be unique, i.e. there should only be one row for each reaction ID.

- the right hand side is a Boolean expression including a number of gene IDs; the Boolean expression can include the symbols and, or and not meaning the respective logical operations. Parentheses can also be included to define the order of the operations.


''Note 1: the set of genes for the model is determined by gathering the different symbols in the right hand sides.''