opencor/NuML

Numerical Markup Language

NuML - Numerical Markup Language

Project Information

The Numerical Markup Language (NuML) aims to standardize the exchange and archiving of numerical results. NuML originates from the numerical aspects of the Systems Biology Results Markup Language (SBRML) with the aim of re-using it in multiple other standardization efforts.

This project hosts the schema, the specification of NuML, as well as the library for reading and writing NuML (libNUML).

Get involved:

Join our mailing list at: http://groups.google.com/group/numl-discuss/

NuML is being / planned to be used by:

• SBRML
• SED-ML

Software supporting NuML:

• SBRML.NET

Example of a NuML Document

<?xml version="1.0" encoding="UTF-8"?>
<numl version="1" level="1" xmlns="http://www.numl.org/numl/level1/version1">   
  <ontologyTerms>
      <ontologyTerm id="term1" term="time" sourceTermId="SBO:0000345" ontologyURI="http://www.ebi.ac.uk/sbo/" />         
      <ontologyTerm id="term2" term="concentration" sourceTermId="SBO:0000196" ontologyURI="http://www.ebi.ac.uk/sbo/" />
  </ontologyTerms>
  <resultComponent id="component1">
      <dimensionDescription>
        <compositeDescription name="Time" ontologyTerm="term1" indexType="double">
            <compositeDescription name="Species" indexType="xpath">
              <atomicDescription name="Concentration" ontologyTerm="term2" valueType="double" />
            </compositeDescription>
        </compositeDescription>
      </dimensionDescription>
      <dimension>
        <compositeValue indexValue="0">
            <compositeValue indexValue="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='x_CO2']">
              <atomicValue>1</atomicValue>
            </compositeValue>
            <compositeValue indexValue="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='RuBP_ch']">
              <atomicValue>0.33644</atomicValue>
            </compositeValue>
            <compositeValue indexValue="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PGA_ch']">
              <atomicValue>3.35479</atomicValue>
            </compositeValue>
        </compositeValue>
        <compositeValue indexValue="1">
            <compositeValue indexValue="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='x_CO2']">
              <atomicValue>0.66356</atomicValue>
            </compositeValue>
            <compositeValue indexValue="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='RuBP_ch']">
              <atomicValue>8.90632e-31</atomicValue>
            </compositeValue>
            <compositeValue indexValue="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PGA_ch']">
              <atomicValue>3.35479</atomicValue>
            </compositeValue>
        </compositeValue>
        <resultComponent id="recomponet2"> ... </resultComponent>
      </dimension>
  </resultComponent>
</numl>