cellDesigner

ColorMet

reaction

addAnnotation(fname, fname_out, infix, model, infix_type)

Retrieves omics data from a COBRA model structure and add them to a CellDesginer XML file; The omics data will be shown as texts in CellDesigner or ReconMap online.

USAGE:

[var] = addAnnotation(fname, fname_out, infix, model, infix_type)

INPUTS:

fname: an XML file to be modified to include annotations fanme_out: the name of the output XML file infix: The metabolite/reaction IDs to be used to retrieve omics data

in the COBRA model structure.

model: a COBRA model structure that contains the annotations which

can be retrieved by using the infix as the index value.

OPTIONAL INPUT:

infix_type: ‘name’ or ‘id’

  1. ‘name’ indicates that ‘infix’ contains a list of reaction names, which are normally used in a COBRA model structure.

  2. ‘id’ indicates that ‘infix’ contains a list of IDs used in CellDesigner such as ‘re32’.

OPTIONAL OUTPUT:

var: the content of the moidfied XML file with annotations

addColour(parsed, listRxn_Color, colorScheme)

Changes colour attributes of the reaction links in a parsed CellDesigner model structure given a list of reaction IDs

USAGE:

[ref, listRxnColour] = addColour(parsed, listRxn_Color, colorScheme)

INPUTS:

parsed: A parsed model structure generated by parseCD function listRxn_Color: A list of reaction IDs that need to be highilighted by

changing the colour attributes of the reaciton links in the CellDesigner model. The first column stores a list of reaction IDs whose reaction links need to be highlighted, whereas the second column saves a list of html Colours.

OUTPUT:

ref: An updated parsed CellDesigner model structure listRxnColour:

addFlux(model, FBA_result, parsed, listRxn)

Changes the thickness attributes of the reaction links in a CellDesigner model structure and make them propotional to the flux values obtained from COBRA functions

USAGE:

[ref, normalizedFlux, newListRxn] = addFlux(model, FBA_result, parsed, listRxn)

INPUTS:

model: A COBRA model structure FBAresult: FBA results of a COBRA simulation by the

optimizeCbModel function

parsed: The CD model structure outputed by the parseCD

function

listRxn: A list of reaction IDs, after which the flux values

are modified or added. P.s., the reaction IDs must be present in both the parsed CD model and the COBRA model structures. the reactions can be examined by cmpR function.

OUTPUTS:
ref: An updated parsed CellDesigner model that include

information about the width of reaction links

normalizedFlux: A list of normalised flux values generated based on

FBAresult.

newListRxn: New list of reaction IDs

Example

[parsed_1] = addFlux(recon2, fba_results, parsePD, listRxn);

addMiriam(fname, fname_out, infix, model, infix_type, list, miriam_path)

Adds Miriam information to CellDesigner XML file. The Miriam information is retrieved from a COBRA model structure using Metabolite/Reaction IDs as the name of entry. The omics data will be shown as texts hyperlinking to external databases in CellDesigner or ReconMap online.

USAGE:

[fname_out, var] = addMiriam(fname, fname_out, infix, model, infix_type, list, miriam_path)

INPUTS:

fname: An XML file to be modified to include annotations. fname_out: The name of an output XML file. infix: A list of metabolite/reaction IDs to be used to retrieve omics data

in the COBRA model structure.

model: a COBRA model structure contains the annotations that can be

retrieved by using the infix as the index value.

list: Column 1 stores a list of the fieldnames of the COBRA model

strucutres that contains MIRIAM information; Column 2 stores a list of MIRIAM types corresponding to each field; column 3 stores a list of relations

OPTIONAL INPUT:

infix_type: ‘name’ or ‘id’;

  1. ‘name’indicates that ‘infix’ contains a list of reaction names, which are normally used in a COBRA model structure.

  2. ‘id’ indicates that ‘infix’ contains a list of IDs used in CellDesigner such as ‘re32’.

miriam_path: the file path of the miriam registry’s dataset (*.mat).

OPTIONAL OUTPUT:

fname_out: the name of an output XML file. var: the content of the modified XML file with annotations

Example

%the following example command is intended to add all MIRIAM information %for the metabolites in the ReconMap [var] = addMiriam(‘ReconMap.xml’, ‘ReconMap_annotated.xml’, recon2.mets(:), recon2)

cmpMet(parsed, model)

Compares metabolites in a parsed CellDesigner model structure (imported by ‘parseCD’) and a COBRA model Matlab structure.

USAGE:

[results] = cmpMet(parsed, model)

INPUTS:

parsed: A parsed model structure generated by parseCD function. model: A COBRA model Matlab structure.

OUTPUT:

results: contains three fields:

  • listOfFound - A list of reactions in the test model that are present in the reference COBRA model.

  • listOfNotFound - A list of reactions in the test model that are NOT present in the reference COBRA model.

  • list_of_rxns_not_present_in_ReferenceModel - A list of reactions in the reference model that are NOT included in the test model.

Example

results_M = cmpM(parseRecon2_species, recon2)

cmpRxn(parsed, model)

Compare reactions in a parsed CellDesigner model structure (imported by parseCD) and a COBRA model Matlab structure.

USAGE:

[results] = cmpRxn(parsed, model)

INPUTS:

parsed: A parsed model structure generated by parseCD function. model: A COBRA model Matlab structure.

OUTPUTS

results: Consist of four fields

  • listOfFound - A list of reactions in the test model that are present in the reference COBRA model.

  • listOfNotFound - A list of reactions in the test model that are NOT present in the reference COBRA model.

  • found_rxns_and_mets - A list of matched reactions in both the test model and the COBRA model; The lists of substrates and products for each rections stored in the sub field of rxns_mets

  • list_of_rxns_not_present_in_ReferenceModel - A list of reactions in the reference model that are NOT included in the test model.

Example

cmp_PD_recon2_result = cmpRxn(parsePD, recon2)

colourAll(fname, parsed, fname_out, new_colour)

Change the colours of all metabolite nodes to a specific colour.

USAGE:

[mainText_new, keyText, numText] = colourAll(fname, parsed, fname_out, new_colour)

INPUTS:

fname: An XML file that needs to be modified to change the colour

of all metabolite nodes

fanme_out: The name of the output XML file parsed: A parsed model structure generated by parseCD function new_colour: a colour hex code such as ‘5bcdb8’ or ‘#5bcdb8’. A list of

reaction IDs that need to be highilighted by changing the colour attributes of the reaciton links in the CellDesigner model. The first column stores a list of reaction IDs whose reaction links need to be highlighted, whereas the second column saves a list of html Colours.

OPTIONAL OUTPUT:

mainText_new: Lines of the XML file keyText: Lists of retrieved alias and species IDs numText: Lists of the corresponding line numbers for each alias

and species ID

colourCode

Convert 7 digits to 9 digits for CellDesigner to recongnise. a=’a’

colourNode(parsed, fname_out, list_Rxn, list_Met, list_Colour_Met)

Changes the colours of metabolite nodes

USAGE:

[parsed_updated, mainText_new, final_list] = colourNode(parsed, fname_out, list_Rxn, list_Met, list_Colour_Met)

INPUTS:

fname_out: The name of the output XML file parsed: A parsed model structure generated by parseCD function list_Rxn: A list of reaction IDs that need to be highilighted by

changing the colour attributes of the reaciton links in the CellDesigner model. The first column stores a list of reaction IDs whose reaction links need to be highlighted, whereas the second column stores a list of html Colours.

OPTIONAL INPUTS:

list_Met: The list of metabolite IDs to be highlighed list_Colour_Met: Colour Hex Codes for Metabolite IDs in list_Met.

OPTIONAL OUTPUT:

parsed_updated: An updated parsed model structure. mainText_new: The lines of the new XML file. final_list: A list of the metabolite nodes whose colour attributes are modified.

Example

[var] = colourNode(‘fatty_acid_synthesis_Miriam__rxns_test.xml’, ‘fatty_acid_synthesis_Miriam__rxns_test_colour.xml’, parsed_fatty_acid, list_nodes)

colourNodeWhite(parsed, fname_out, list, list_Met)

Highlights the metabolite nodes using the same colour scheme as in addColour function while changing the colours of rest nodes to white

USAGE:

[parsed_update, mainText_new, final_list] = colourNodeWhite(parsed, fname_out, list, list_Met)

INPUTS:

fanme_out: The name of the output XML file parsed: A parsed model structure generated by parseCD function list: A list of reaction IDs that need to be highilighted by

changing the colour attributes of the reaciton links in the CellDesigner model. The first column stores a list of reaction IDs whose reaction links need to be highlighted, whereas the second column stores a list of Html Colours.

OPTIONAL INPUTS:

list_Met: The list of metabolite IDs to be highlighed

OPTIONAL OUTPUTS:

parsed_updated: An updated parsed model structure. mainText_new: The lines of the new XML file. final_list: A list of the metabolite nodes whose colour attributes

are modified.

Example

[var, final_list] = colourNodeWhite(‘fatty_acid_synthesis_Miriam__rxns_test_white.xml’, ‘fatty_acid_synthesis_Miriam__rxns_test_white_colour.xml’, parsed_fatty_acid_new, list_nodes)

correctMetName(parsed, cmpM_results, listR)

Correct the inconsistent species name in the test model (identified by the cmpM function) according to a reference list of species names.

USAGE:

[parsed_updated] = correctMetName(parsed, cmpM_results, listR)

INPUTS:

parsed: A parsed CD model structure generated by parseCD function. cmpM_results: the output of the cmpM function. A list of species names

that are present in the reference model (A COBRA model structure, but not in the test model (the parsed model structure of a CD XML file).

listR: A new list of species names that will be used to substitute

the incorrect names (as listed in listN)

OUTPUT:

parsed_updated: The corrected CD model structure

Example

ref_corrected = correctMetName(ref, cmp_recon2map_M.listOfNotFound(:, 6), listForCorrection(:, 2))

intergrate(fname, fname_out, model, FBAsolution, listRxn)

USAGE:

intergrate(fname, fname_out, model, FBAsolution, listRxn)

INPUTS:

fname: The name fo the file fname_out: The name of the output XML file name. model: A COBRA model structure FBAsolution: FBA results of a COBRA simulation by the

optimizeCbModel function

listRxn: A list of reaction IDs, after which the flux values are modified

or added. P.s., the reaction IDs must be present in both the parsed CD model and the COBRA model structures. the reactions can be examined by cmpR function.

OUTPUT:
fname_out: A new XML file with the width of reaction links

changed according to flux values calculated by COBRA

Example

intergrate(‘anno_test.xml’, ‘anno_test_2_ecoli.xml’, model_ecoli,solution, model_ecoli.rxns(:))

parseCD(fname)

Parse an XML file into two types of CellDesigner model structures. The first type organises data by reaction; the second type organises data by property (namely, ID, width, colour, etc.)

USAGE:

[annotation] = parseCD(fname)

INPUT:

fanme: A CellDesigner XML file

OUTPUT:

annotation: The first type of the parsed model structure

  • annotation.r_info - The second type of the parsed model structure

Examples

parsePD_1 = parseCD(‘PD_140620_1.xml’)

position(str_long, str_ID)

Retrieve the value of an attribute (str_ID) in the line (str_long) of the XML file and identify the starting and ending indices of the value in the attribute line of the XML file.

USAGE:

[string, p_st, p_ed] = position(str_long, str_ID)

INPUTS:

str_long: A string of the line of the XML file str_ID: The name of the attribute

OUTPUTS:

string: The value of the attribute p_st: The starting index of the value p_ed: The ending index of the value

readCD(parsed)

Convert the a type of the parsed model structure (orgnised by reaction) into the other type of the parsed model structure (organised by property (namely, ID, width, colour, etc.)

USAGE:

[r_info] = readCD(parsed)

INPUT:
parsed: the first type of the parsed model structure outputed by

parseCD function (more user-friendely to modify speicfic graphic properties for specific reactions)

OUTPUT:
r_info: the second type of the parsed model structure (similar to a

COBRA Matlab structure).

repairXML(parsed, fname_out)

Write the corrected CD model structure to an XML file

USAGE:

[annotedText] = repairXML(parsed, fname_out)

INPUTS:

parsed: A parsed model structure generated by ‘parseCD’function. fanme_out: The name of the output XML file.

OUTPUTS:

annotedText: A matlab variable storing the all the XML lines

Example

annotedText_fatty_acid = repairXML(parsed_fatty_acid_new_corrected, ‘fatty_acid_synthesis_species_corrected_2.xml’)

retrieveMet(parsed, lkup)

Retrieve all the identifiers for a metabolite in the parsed CD model structure; there could be multiple identifiers for a metabolite.

USAGE:

[identifier] = retrieveMet(parsed, lkup)

INPUTS:

parsed: A parsed model structure generated by parseCD function. lkup: A species name

OUTPUT:

identifier: The identifiers of a metabolite used the parsed CD model structure

updateCD(text, parsed, note)

Correct(Update) the species name according to a reference list of the names.

USAGE:

[results] = updateCD(text, parsed, note)

INPUTS:

text: A matlab variable that saves the lines of the XML file. parsed: A parsed CD model structure generated by parseCD function.

OPTIONAL INPUT:
note: The default value is ‘0’; It can be set as ‘true’;

Record the column number of the species that are to be replaced with a new name.

OUTPUTS:

text: The corrected lines of the XML file. number: The number of the line. changdStrLines: The changed line of text. col: Record the column number of the species that is to be

replaced with a new species name.

Example

[text, number, numberofchanges, col] = updateCD(annotedText, ref_corrected)

writeCD(parsed, fname_out)

Write the parsed CD model structure to a CD-compatible XML file.

USAGE:

[parsed_update, annotedText] = writeCD(fname, parsed, fname_out)

INPUTS:

fname: The original XML file parsed: A parsed model structure generated by parseCD function. fanme_out: The name of the output XML file.

OUTPUTS:

parsed_update: An updated version of the parsed annotedText: A matlab variable storing the all the XML lines

Example

aaa = writeXML(‘PD_140620_1.xml’, parsePD,’text.html’)

writeTXT(para, fname_out)

Write a txt file for online PD map to highlight specific reaction nodes.

USAGE:

[text] = writeTXT(para, fname_out)

INPUTS:
para: A variable that stores two columns: the first column

contains a list of reaction names,whereas the second column contains a corresponding list of the colours (Hex triplet, e.g., https://closedxml.codeplex.com/wikipage?title=Excel%20Indexed%20Colors)

fanme_out: The name of the output text file name.

OPTIONAL OUTPUT:

text: The lines of the text file

writeText2XML(text, fname_out)

An auxiliary function to write the lines of text generated by other CD package functions to a XML file.

USAGE:

writeText2XML(text, fname_out)

INPUTS:
text: A matlab variable contains the lines of the variable to be

written to a XML file.

fanme_out: The name of the output XML file name.

writeXML(fname, parsed, fname_out)

Write a parsed CD model strucutre to a CD-compatible XML file.

USAGE:

[annotedText] = writeXML(fname, parsed, fname_out)

INPUTS:

fname: The original XML file parsed: A parsed model structure generated by parseCD function. fanme_out: The name of the output XML file.

OUTPUTS:

annotedText: A matlab variable storing the all the XML lines

Example

aaa = writeXML(‘PD_140620_1.xml’, parsePD, ‘text.html’)