# cellDesigner¶

addAnnotation(fname, fname_out, infix, model, infix_type)[source]

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)[source]

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.

Outputs

• ref – An updated parsed CellDesigner model structure
• listRxnColour
addFlux(model, FBA_result, parsed, listRxn)[source]

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)[source]

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 inputs

• 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 outputs

• 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)[source]

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)[source]

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.

Output

• 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)[source]

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 outputs

• 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
colourNode(parsed, fname_out, list_Rxn, list_Met, list_Colour_Met)[source]

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 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] = 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)[source]

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 input

• 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)[source]

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)[source]

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)[source]

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

Example

parsePD_1 = parseCD('PD_140620_1.xml')

position(str_long, str_ID)[source]

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)[source]

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

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)[source]

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.

Output

• 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)[source]

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)[source]

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)[source]

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)[source]

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

Usage

[text] = writeTXT(para, fname_out)

Inputs

Optional output

• text – The lines of the text file
writeText2XML(text, fname_out)[source]

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)[source]

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.

Output

• annotedText – A matlab variable storing the all the XML lines

Example

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