Rbionet¶

Gui

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

CreateGPR(varargin)[source]¶

m-file for CreateGPR.fig CreateGPR, by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = addmetabolites (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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

GenesAndReactions(varargin)[source]¶

m-file for GenesAndReactions.fig GenesAndReactions, by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = GenesAndReactions (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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

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)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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.

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

OUTPUTS

output – input argument for ReconstructionTool and ReactionChecks and other functions

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

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

ReconstructionCreator(varargin)[source]¶

m-file for ReconstructionCreator.fig ReconstructionCreator, by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = ReconstructionCreator (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

ReconstructionTool(varargin)[source]¶

m-file for ReconstructionTool.fig ReconstructionTool by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = ReconstructionTool (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

addmetabolites(varargin)[source]¶

m-file for addmetabolites.fig addmetabolites, by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = addmetabolites (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

addmissing(varargin)[source]¶

MATLAB code for addmissing.fig addmissing, by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = addmissing (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

addreactions(varargin)[source]¶

m-file for addreactions.fig addreactions, by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = addreactions (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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;

closeGUI()[source]¶

USAGE: closeGUI()

compartment(varargin)[source]¶

m-file for compartment.fig compartment, by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = compartment (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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

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)

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

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)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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)
INPUTS: varargin – various input arguments
OUTPUTS: 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

mets2str(str)[source]¶

Creates strings for message boxes

USAGE: outstr = mets2str (str)
INPUT: str – struct of names
OUTPUT: outstr – ‘act’, ‘acon-C’, ‘pep’

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

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.

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)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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

rBioNetAbout(varargin)[source]¶

MATLAB code for rBioNetAbout.fig rBioNetAbout, by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = rBioNetAbout (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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

rBioNetSettings(varargin)[source]¶

MATLAB code for rBioNetSettings.fig rBioNetSettings, by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = rBioNetSettings (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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.

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)
INPUTS: varargin – various input arguments
OUTPUTS: 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

similarities(varargin)[source]¶

m-file for similarities.fig similarities, by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = similarities (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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

unbalanced(varargin)[source]¶

m-file for unbalanced.fig unbalanced, by itself, creates a new object or raises the existing singleton*.

USAGE: varargout = unbalanced (varargin)
INPUTS: varargin – various input arguments
OUTPUTS: 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

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.

webKeggMapper(id, str)[source]¶

Small script that links to kegg mapper.

USAGE

webKeggMapper (id,str)

INPUTS

id – Either ‘ec’ or ‘kegg’
str – ID of themetabolite / reaction