Follow these steps to submit a job to NEOS via XML-RPC clients:
  1. Save the following template using your browser's copy and paste tools
  2. Using your favorite editor, plug your data files and parameters into the message in the indicated spots
  3. Descriptions of the input are written with the web interface in mind. If the description asks for the name of a file, then you will instead need to insert the contents of the file itself.
  4. The <![CDATA[ ... ]]> tag is an escape indicator. This will ensure that any special characters in your inputs (such as <, >, &, etc.) will be interpreted correctly.

For XML-RPC, you need to submit the contents of this file to NEOS with the submitJob() method, and retrieve the results with the getResults() method. Go here for more information on using the XML-RPC interface to NEOS.

<document>
<category>application</category>
<solver>ECM</solver>
<inputMethod>csv</inputMethod>

<stoich><![CDATA[...Insert Value Here...]]></stoich>

<keqs><![CDATA[...Insert Value Here...]]></keqs>

<kcats><![CDATA[...Insert Value Here...]]></kcats>

<kms><![CDATA[...Insert Value Here...]]></kms>

<metfixed><![CDATA[...Insert Value Here...]]></metfixed>

<rates><![CDATA[...Insert Value Here...]]></rates>

<boundse><![CDATA[...Insert Value Here...]]></boundse>

<boundsx><![CDATA[...Insert Value Here...]]></boundsx>

<moietymet><![CDATA[...Insert Value Here...]]></moietymet>

<moietyval><![CDATA[...Insert Value Here...]]></moietyval>

<weights><![CDATA[...Insert Value Here...]]></weights>

<activators><![CDATA[...Insert Value Here...]]></activators>

<inhibitors><![CDATA[...Insert Value Here...]]></inhibitors>

<alpha><![CDATA[...Insert Value Here...]]></alpha>

<A><![CDATA[...Insert Value Here...]]></A>

<nlp><![CDATA[...Insert Value Here...]]></nlp>

</document>

Description of input values

stoich
Stoichiometry data (required): each row has format rateID,metaboliteID,value
keqs
Equilibrium constants: each row has format rateID,value. Reactions not supplied are irreversible.
kcats
Turnover numbers (required)
kms
Michaelis constants
metfixed
Fixed metabolite levels
rates
List of flux modes (required): each row has format efmnumber,rateID1,rateID2,... The efmnumber should be an integer.
boundse
Bounds on enzyme levels (optional)
boundsx
Bounds on metabolite levels (optional)
moietymet
Metabolites in moieties (optional)
moietyval
Total moiety concentrations (optional)
weights
Enzyme weights (optional): taken as value of 1 if not specified.
activators
Optional: only provide if activator exists
inhibitors
Optional: only provide if inhibitor exists
alpha
alpha values (optional): advanced option for custom rate equations
A
A values (optional): advanced option for custom rate equations
nlp
Select an NLP solver