rBioNet¶
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BalancePrep
(meta_meta)[source]¶ Balances the reactions, used in ReactionChecks
Usage
output = BalancePrep(meta_meta)Input
- meta_meta – matrix from ReconstructionTool
Output
- output – leftside, rightside, charge_l and charge_r in varargout
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CreateGPR
(varargin)[source]¶ m-file for CreateGPR.fig CreateGPR, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = addmetabolites(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = CreateGPR() %returns the handle to a new CreateGPR or the handle to the existing singleton*. CreateGPR('CALLBACK',hObject,eventData,handles,...) %calls the local %function named `CALLBACK` in CreateGPR.M with the given input arguments. CreateGPR('Property','Value',...) %creates a new CreateGPR or raises the %existing singleton*. Starting from the left, property value pairs are %applied to the GUI before `CreateGPR_OpeningFcn` gets called. An %unrecognized property name or invalid value makes property application %stop. All inputs are passed to `CreateGPR_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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GPR2Genes
(GPR)[source]¶ Input is a list of GPRs and output is a unique list of genes.
Usage
Genes = GPR2Genes(GPR)Input
- GPR – list of GPRs
Output
- Genes – unique list of genes
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GenesAndReactions
(varargin)[source]¶ m-file for GenesAndReactions.fig GenesAndReactions, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = GenesAndReactions(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = GenesAndReactions() %returns the handle to a new GenesAndReactions or the handle to the existing singleton*. GenesAndReactions('CALLBACK',hObject,eventData,handles,...) %calls the local %function named `CALLBACK` in GenesAndReactions.M with the given input arguments. GenesAndReactions('Property','Value',...) %creates a new GEN or raises the %existing singleton*. Starting from the left, property value pairs are %applied to the GUI before `GenesAndReactions_OpeningFcn` gets called. An %unrecognized property name or invalid value makes property application %stop. All inputs are passed to `GenesAndReactions_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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GenesReactions
(genelist, rxns)[source]¶ Returns genes in model and the associative reactions.
Usage
list = GenesReactions(genelist, rxns)Inputs
- genelist – list of genes
- rxns – reactions
Output
- list – genes in model and the associative reactions
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Keep_reactions
(varargin)[source]¶ m-file for Keep_reactions.fig Keep_reactions, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = Keep_reactions(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = Keep_reactions() returns the handle to a new Keep_reactions or the handle to the existing singleton*.% Keep_reactions('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in Keep_reactions.M with the given input arguments. Keep_reactions('Property','Value',...) creates a new Keep_reactions or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `Keep_reactions_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `Keep_reactions_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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LegalRxnFormula
(formula, abbreviation)[source]¶ Checks if all reactions are legal
Usage
result = LegalRxnFormula(formula, abbreviation)Inputs
- formula – cell vector with reactions formulas
- abbreviation – cell vector with reaction abbreviation (optional)
Output
- result – true if all reactions are legal, else false. msgbox lets user know which reaction is incorrect
Note
This script is just a start and only contains a few checks. Add more tests in near future.
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LoadReaction
(rxnline, metab, meta_compartment, rxn_line)[source]¶ Provides input argument for ReconstructionTool and ReactionChecks and other functions
Usage
output = LoadReaction(rxnline, metab, meta_compartment, rxn_line)Inputs
- rxnline – data of the reaction
- metab – from ReconstructionTool
- meta_compartment – from ReconstructionTool
- rxn_line – not used
Output
- output – input argument for ReconstructionTool and ReactionChecks and other functions
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ReactionChecks
(rxn, metab, meta_compartment, newrxns, data)[source]¶ This is an start to simplefying the balancing and similarity checking of reactions process.
Usage
data_output = ReactionChecks(rxn, metab, meta_compartment, newrxns, data)Inputs
- rxn – reactions
- metab – from ReconstructionTool
- meta_compartment – from ReconstructionTool
- newrxns – reactions to be added to model
- data – data of reactions process
Output
- data_output –
if everything is okay
- newrxns - (reactions can be removed) set table
- handles.data - all similarity info including dispdata.
- handles.check
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ReactionEq
(react, rxns)[source]¶ Compares reactions for equality
Usage
matched = ReactionEq(react, rxns)Inputs
- react – new reaction
- rxns – similar reactions
Output
- matched – abbreviation name for exact reaction match
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ReconstructionCreator
(varargin)[source]¶ m-file for ReconstructionCreator.fig ReconstructionCreator, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = ReconstructionCreator(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = ReconstructionCreator returns the handle to a new ReconstructionCreator or the handle to the existing singleton*. ReconstructionCreator('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in ReconstructionCreator.M with the given input arguments. ReconstructionCreator('Property','Value',...) creates a new ReconstructionCreator or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `ReconstructionCreator_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `ReconstructionCreator_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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ReconstructionTool
(varargin)[source]¶ m-file for ReconstructionTool.fig ReconstructionTool by itself, creates a new object or raises the existing singleton*.
Usage
varargout = ReconstructionTool(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = ReconstructionTool() returns the handle to a new ReconstructionTool or the handle to the existing singleton*. ReconstructionTool('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in ReconstructionTool.M with the given input arguments. ReconstructionTool('Property','Value',...) creates a new ReconstructionTool or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `ReconstructionTool_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `ReconstructionTool_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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addmetabolites
(varargin)[source]¶ m-file for addmetabolites.fig addmetabolites, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = addmetabolites(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = addmetabolites() %returns the handle to a new addmetabolites or the handle to the existing singleton*. addmetabolites('CALLBACK',hObject,eventData,handles,...) %calls the local %function named `CALLBACK` in addmetabolites.M with the given input arguments. addmetabolites('Property','Value',...) %creates a new addmetabolites or raises the %existing singleton*. Starting from the left, property value pairs are %applied to the GUI before `addmetabolites_OpeningFcn` gets called. An %unrecognized property name or invalid value makes property application %stop. All inputs are passed to `addmetabolites_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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addmissing
(varargin)[source]¶ MATLAB code for addmissing.fig addmissing, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = addmissing(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = addmissing() %returns the handle to a new addmissing or the handle to %the existing singleton*. addmissing('CALLBACK',hObject,eventData,handles,...) %calls the local %function named `CALLBACK` in addmissing.M with the given input arguments. addmissing('Property','Value',...) creates a new addmissing or raises the %existing singleton*. Starting from the left, property value pairs are %applied to the GUI before `addmissing_OpeningFcn` gets called. An %unrecognized property name or invalid value makes property application %stop. All inputs are passed to `addmissing_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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addreactions
(varargin)[source]¶ m-file for addreactions.fig addreactions, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = addreactions(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = addreactions() %returns the handle to a new addreactions or the handle to %the existing singleton*. addreactions('CALLBACK',hObject,eventData,handles,...) %calls the local %function named `CALLBACK` in addreactions.M with the given input arguments. addreactions('Property','Value',...) %creates a new addreactions or raises the %existing singleton*. Starting from the left, property value pairs are %applied to the GUI before `addreactions_OpeningFcn` gets called. An %unrecognized property name or invalid value makes property application %stop. All inputs are passed to `addreactions_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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balancecheck
(meta_meta, output)[source]¶ Returns balance - if empty it means that balance checks out, otherwise the output is a cell matrix
Usage
balance = balancecheck(meta_meta, output)Inputs
- meta_meta – is cell matrix meta_meta type, with one metabolite in each line, rows are [Abbreviation, Description, Coefficient, Compartment, Side, Charge formula].
- output – default = 0, other option = 1
Output
- balance – is empty if balance checks out, if unbalanced it returns cell matrix with Elements, prod and sub;
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compartment
(varargin)[source]¶ m-file for compartment.fig compartment, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = compartment(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = compartment() %returns the handle to a new compartment or the handle to %the existing singleton*. compartment('CALLBACK',hObject,eventData,handles,...) %calls the local %function named CALLBACK in compartment.M with the given input arguments. compartment('Property','Value',...) %creates a new compartment or raises the %existing singleton*. Starting from the left, property value pairs are %applied to the GUI before `compartment_OpeningFcn` gets called. An %unrecognized property name or invalid value makes property application %stop. All inputs are passed to `compartment_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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data2model
(data, description, database)[source]¶ Takes in data from rbionet to create a complete reconstruction
Usage
model_out = data2model(data, description,database)Inputs
- data – data from rbionet
- description – model description
Optional input
- database – file with reaction and metabolite database in format: database.reactions=reaction database database.metabolites=metabolite database
Output
- model_out – creates a complete reconstruction
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formula2mets
(formula)[source]¶ Takes a rxn formula and produces a list of metabolites
Usage
metabolites = formula2mets(formula)Input
- formula – rxn formula
Output
- metabolites – list of metabolites
Note
uses parseRxnFormula.m (Cobra Toolbox)
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getgenelist
(input_dir)[source]¶ Reads gene-list text file and returns data. Default SIZE for GENELIST.txt is 7 columns! Each column is separated with a tab.
Usage
out = getgenelist(input_dir)Input
- input_dir – gene-list text file
Output
- out – data
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load_reaction
(varargin)[source]¶ m-file for load_reaction.fig load_reaction, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = load_reaction(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = load_reaction returns the handle to a new load_reaction or the handle to the existing singleton*. load_reaction('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in load_reaction.M with the given input arguments. load_reaction('Property','Value',...) creates a new load_reaction or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `load_reaction_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `load_reaction_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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met_charge_formula
(varargin)[source]¶ MATLAB code for met_charge_formula.fig met_charge_formula, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = met_charge_formula(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = met_charge_formula() returns the handle to a new met_charge_formula or the handle to the existing singleton*. met_charge_formula('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in met_charge_formula.M with the given input arguments. met_charge_formula('Property','Value',...) creates a new met_charge_formula or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `met_charge_formula_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `met_charge_formula_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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metabolites_in_database
(varargin)[source]¶ m-file for metabolites_in_database.fig metabolites_in_database, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = metabolites_in_database(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = metabolites_in_database() returns the handle to a new metabolites_in_database or the handle to the existing singleton*. metabolites_in_database('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in metabolites_in_database.M with the given input arguments. metabolites_in_database('Property','Value',...) creates a new metabolites_in_database or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `metabolites_in_database_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `metabolites_in_database_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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mets2str
(str)[source]¶ Creates strings for message boxes
Usage
outstr = mets2str(str)Input
- str – struct of names
Output
- outstr – ‘act’, ‘acon-C’, ‘pep’
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model2data
(model, fordb)[source]¶ Load complete reconstructions and output format for rBioNets ReconstructionCreator.
Usage
data_out = model2data(model, fordb)Inputs
- model – model
- fordb – 1 if metabolite table is wanted, default 0 if not
Output
- data_out
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model2text
(data, model)[source]¶ This script takes in a reconstruction model and prints it out into a text file. It can be used standalone from the rBioNet.
Usage
model2text(data, model)Inputs
- data – model or .mat datafile table as in ReconstructionCreator (RC)
- model – true if data is a model, false if RC table.
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model_description
(varargin)[source]¶ m-file for model_description.fig model_description, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = model_description(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = model_description() returns the handle to a new model_description or the handle to the existing singleton*. model_description('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in model_description.M with the given input arguments. model_description('Property','Value',...) creates a new model_description or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `model_description_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `model_description_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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model_stats
(varargin)[source]¶ MATLAB code for model_stats.fig model_stats, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = model_stats(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = model_stats() returns the handle to a new model_stats or the handle to the existing singleton*. model_stats('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in model_stats.M with the given input arguments. model_stats('Property','Value',...) creates a new model_stats or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `model_stats_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `model_stats_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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neighborRxn2data
(model, rxn_numb)[source]¶ Program used to get neigbor reactions and set up correct format for the Reconstruction analyzer.
Usage
data = neighborRxn2data(model, rxn_numb)Inputs
- model – model
- rxn_numb – number of reactions
Output
- data
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rBioNetAbout
(varargin)[source]¶ MATLAB code for rBioNetAbout.fig rBioNetAbout, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = rBioNetAbout(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = rBioNetAbout returns the handle to a new rBioNetAbout or the handle to the existing singleton*. rBioNetAbout('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in rBioNetAbout.M with the given input arguments. rBioNetAbout('Property','Value',...) creates a new rBioNetAbout or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `rBioNetAbout_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `rBioNetAbout_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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rBioNetSaveLoad
(mode, type, data)[source]¶ Through here the metabolite and reaction databases are loaded and saved. This script makes it possible to store databases in any path set in matlab. Missing for compartments, thats for later.
Usage
output = rBioNetSaveLoad(mode,type,data)Inputs
- mode – ‘save’ or ‘load’
- type – ‘met’, ‘rxn’ or ‘comp’
- data – data to save
Output
- output – if ‘load’ then data else 1 if succes by save, 0 if empty or failed
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rBioNetSettings
(varargin)[source]¶ MATLAB code for rBioNetSettings.fig rBioNetSettings, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = rBioNetSettings(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = rBioNetSettings() returns the handle to a new rBioNetSettings or the handle to the existing singleton*. rBioNetSettings('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in rBioNetSettings.M with the given input arguments. rBioNetSettings('Property','Value',...) creates a new rBioNetSettings or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `rBioNetSettings_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `rBioNetSettings_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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rBioNet_search
(table, column, str, exact)[source]¶ Performs simple searches in rBioNet tables.
Usage
output = rBioNet_search(table, column, str, exact)Inputs
- table – Table or model
- Column – number
- String – search phrase
- Exact match – true or false
Output
- output – Array containing results.
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sim_general
(varargin)[source]¶ MATLAB code for sim_general.fig sim_general, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = sim_general(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = sim_general returns the handle to a new sim_general or the handle to the existing singleton*. sim_general('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in sim_general.M with the given input arguments. sim_general('Property','Value',...) creates a new sim_general or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `sim_general_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `sim_general_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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similarities
(varargin)[source]¶ m-file for similarities.fig similarities, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = similarities(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = similarities() returns the handle to a new similarities or the handle to the existing singleton*. similarities('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in similarities.M with the given input arguments. similarities('Property','Value',...) creates a new similarities or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `similarities_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `similarities_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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similarity
(formula, data, bar)[source]¶ Returns the reaction lines with similarities
Usage
reactions = similarity(formula,data,bar)Inputs
- formula – reaction formula
- data – reaction list
- bar – waitbar exists then 1, else 0, default 1
Output
- reactions – numbers of rxn lines that share similarity
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unbalanced
(varargin)[source]¶ m-file for unbalanced.fig unbalanced, by itself, creates a new object or raises the existing singleton*.
Usage
varargout = unbalanced(varargin)Input
- varargin – various input arguments
Output
- varargout – various output arguments
Example
H = unbalanced returns the handle to a new unbalanced or the handle to the existing singleton*. unbalanced('CALLBACK',hObject,eventData,handles,...) calls the local function named CALLBACK in unbalanced.M with the given input arguments. unbalanced('Property','Value',...) creates a new unbalanced or raises the existing singleton*. Starting from the left, property value pairs are applied to the GUI before `unbalanced_OpeningFcn` gets called. An unrecognized property name or invalid value makes property application stop. All inputs are passed to `unbalanced_OpeningFcn` via `varargin`.
Note
See GUI Options on GUIDE’s Tools menu. Choose “GUI allows only one instance to run (singleton)”. See also: GUIDE, GUIDATA, GUIHANDLES
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webDatabases
(db, str, type)[source]¶ Small script that links to major databases.
Usage
webDatabases(db, str, type)Inputs
- db – database = {‘kegg’, ‘ec’, ‘pubchem’, ‘chebi’, ‘hmdb’}
- str – ID of metabolite / reaction
Optional input
- type – 1 if reaction, 0 for metabolite (only used for the KEGG database.