Metabolic tasks¶

MATLAB functions in RAVEN/tasks of the RAVEN toolbox. Help text is collected from the source of the tracked branch.

Functions¶

Function	Summary
`checkTasks`	Perform a set of simulations as defined in a task file.
`parseTaskList`	Parse a task list file.

Reference¶

checkTasks¶

Perform a set of simulations as defined in a task file.

This function is used for defining a set of tasks for a model to perform. The tasks are defined by defining constraints on the model, and if the problem is feasible, then the task is considered successful. In general, each row can contain one constraint on uptakes, one constraint on outputs, one new equation, and one change of reaction bounds. If more bounds are needed to define the task, then several rows can be used for each task.

Input arguments:

Name	Type	Description	Default
`model`	`struct`	a model structure.	required
`inputFile`	`char`	a task list in Excel format. See the function parseTaskList for details (optional if taskStructure is supplied).	required

Name-value arguments:

Name	Type	Description
`printOutput`	`logical`	true if the results of the test should be displayed (default true).
`printOnlyFailed`	`logical`	true if only tasks that failed should be displayed (default false).
`getEssential`	`logical`	true if the essential reactions should be calculated for all the tasks. This option is used with runINIT (default false).
`taskStructure`	`struct`	structure with the tasks, as from parseTaskList. If this is supplied then inputFile is ignored.

Output arguments:

Name	Type	Description
`taskReport`	`struct`	structure with the results, with fields: id : cell array with the id of the task description : cell array with the description of the task ok : boolean array with true if the task was successful
`essentialRxns`	`logical`	MxN matrix with the essential reactions (M) for each task (N). An element is true if the corresponding reaction is essential in the corresponding task. Failed tasks and SHOULD FAIL tasks are ignored. This is used by the INIT algorithm (if tasks are supplied). If getEssential=false then essentialRxns=false(nRxns,nTasks).
`taskStructure`	`struct`	structure with the tasks, as from parseTaskList.
`essentialFluxes`	`double`	the fluxes of the essential rxns - same structure as essentialRxns.

Examples:

[taskReport, essentialRxns, taskStructure] = checkTasks(model, inputFile, ...
    printOutput, printOnlyFailed, getEssential, taskStructure);

parseTaskList¶

Parse a task list file.

Input arguments:

Name	Type	Description	Default
`inputFile`	`char`	a task list in either Excel (.xlsx, with a sheet named TASKS with all relevant content) or tab-delimited (.txt) format. The file may contain the following column headers (note, all rows starting with a non-empty cell are removed; the first row after that is considered the headers): ID : the only required header. Each task must have a unique id (string or numeric). Tasks can span multiple rows, only the first row in each task should have an id DESCRIPTION : description of the task IN : allowed input(s) for the task. Metabolite names should be on the form "model.metName[model.comps]". Several inputs can be delimited by ";". If so, then the same bounds are used for all inputs. If that is not wanted, then use several rows for the task IN LB : lower bound for the uptake of the metabolites in the row (optional, default 0 which corresponds to a minimal uptake of 0 units) IN UB : upper bound for the uptake of the metabolites in the row (optional, default 1000 which corresponds to a maximal uptake of 1000 units) OUT : allowed output(s) for the task (see IN) OUT LB : lower bound for the production of the metabolites in the row (optional, default 0 which corresponds to a minimal production of 0 units) OUT UB : upper bound for the production of the metabolites in the row (optional, default 1000 which corresponds to a maximal production of 1000 units) EQU : equation to add. The equation should be on the form "0.4 A + 2 B <=> (or =>) C" and the metabolites should be on the form "model.metName[model.comps]" (optional) EQU LB : lower bound for the equation (optional, default -1000 for reversible and 0 for irreversible) EQU UB : upper bound for the equation (optional, default 1000) CHANGED RXN : reaction ID for which to change the bounds for. Several IDs can be delimited by ";". If so, then the same bounds are used for all reactions. If that is not wanted, then use several rows for the task CHANGED LB : lower bound for the reaction CHANGED UB : upper bound for the reaction SHOULD FAIL : true if the correct behavior of the model is to not have a feasible solution given the constraints (optional, default false) PRINT FLUX : true if the function should print the corresponding flux distribution for a task. Can be useful for testing (optional, default false)	required

Output arguments:

Name	Type	Description
`taskStruct`	`struct`	array of structures with the following fields: id : the id of the task description : the description of the task shouldFail : true if the task should fail printFluxes : true if the fluxes should be printed comments : string with comments inputs : cell array with input metabolites (in the form metName[comps]) LBin : array with lower bounds on inputs (default, 0) UBin : array with upper bounds on inputs (default, 1000) outputs : cell array with output metabolites (in the form metName[comps]) LBout : array with lower bounds on outputs (default, 0) UBout : array with upper bounds on outputs (default, 1000) equations : cell array with equations (with mets in the form metName[comps]) LBequ : array with lower bounds on equations (default, -1000 for reversible and 0 for irreversible) UBequ : array with upper bounds on equations (default, 1000) changed : cell array with reactions to change bounds for LBrxn : array with lower bounds on changed reactions UBrxn : array with upper bounds on changed reactions

Examples:

taskStruct = parseTaskList(inputFile);

Notes

This function is used for defining a set of tasks for a model to perform. The tasks are defined by defining constraints on the model, and if the problem is feasible, then the task is considered successful. In general, each row can contain one constraint on uptakes, one constraint on outputs, one new equation, and one change of reaction bounds. If more bounds are needed to define the task, then several rows can be used for each task. To perform the task use checkTasks or fitTasks.

The general metabolites "ALLMETS" and "ALLMETSIN[comps]" can be used as inputs or outputs in the similar manner to normal metabolites. This is a convenient way to, for example, allow excretion of all metabolites to check whether it is the synthesis of some metabolite that is limiting or whether it is the degradation of some byproduct. One important difference is that only the upper bounds are used for these general metabolites. That is, you can only say that uptake or excretion is allowed, not that it is required. This is to avoid conflicts where the constraints for the general metabolites overwrite those of the real ones.