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Saturday, October 8, 2011

SED-ML Web Tools & KISAO

SED-ML uses KISAO to annotate simulation algorithms with information of what kind of simulation should be performed. Until today the SED-ML Web Tools only displayed the term identifier. This has changed, now the terms will be resolved and displayed:


To make this work I’ve modified LibSedML to resolve all KISAO terms found. This is now part of the Algorithm object, and can be accessed through the Term property.

Unfortunately KISAO is now only available in OWL format. This means people have to ‘reason’ over the document in order to find out even the most basic things. While the EBI provides a ‘libKISAO’, this library is only available for Java. 

In the end I’ve decided to convert the OWL file periodically in a more readable format:

 <term id='KISAO:0000377' 
name='one-step method'>
<definition> <![CDATA[A numerical method
for differential equations which uses one
starting value at each step.]]>




I will update that file periodically and have it compiled into libSedML, if you would like to have a look at it, you can access it here:


Friday, October 7, 2011 web applications down

The web site of the Saurolab was moved to a different machine the domain has been transferred to that machine. As a result, all applications that previously ran on are no longer available via their old URLs. The old server is still available via its IP:

That web site also still hosts the web applications:

In the coming weeks I will update these applications and move them over to

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