The ZBIT Systems Biology Software and Web Service Collection

COMBINE 2016

Andreas Draeger

In systems biology, people want to perform dynamic simulations, steady-state analyses and others. SBML is the format to use for the model, but you also need a data structure for use in the software, and as such they developed jSBML.

People build models from KEGG, textbooks and more. They try to rebuild KEGG diagrams in CellDesigner, which is very time consuming. Is there a better way to do this? And, indeed, there are even difficulties with this manual method, as some reaction participants present when you study the record aren’t visible in the associated diagram (e.g. the addition of ATP), which can cause issues for novices. Therefore they developed KEGGtranslator to convert KEGG pathways to various file formats. Another way to add a data source to your model is through BioPAX2SBML. Additionally, they’ve created ModelPolisher which can augment models with information from the BiGG database, which is available as a command-line tool and as a web service. For dynamic simulation, they have a tool called SBMLSquezer, which generates kinetic equations automatically and also reads information from SABIO-RK.

This system was applied to all networks in KEGG. They use SBMLsimulator to run the simulations. They’ve developed a documentation system called SBML2LaTeX which helps people document their models.

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

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