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Numerical Markup Language
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libnuml
.gitattributes - ensure libnuml can be used with libsbml compiled using c++ namespaces Apr 22, 2016
.gitignore - Issue #10: add support for notes / annotations Aug 8, 2017
NUMLDocument.xml Initial Example File Oct 9, 2011
NUMLSchema.xsd Corrected the use of NML instead of NuML in schama, thanks to Nicolas. Mar 5, 2012
README.md - added link to spec Mar 26, 2015
_config.yml Set theme jekyll-theme-minimal Sep 26, 2017
numl-spec-l1v1.doc Draft of numl specification in pdf and word (.doc) format Oct 21, 2011
numl-spec-l1v1.docx - updated formatting fixed a couple of typos Jan 15, 2012
numl-spec-l1v1.pdf

README.md

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:

Software supporting NuML:

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>
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