Meeting NOV 3, 2015

Date: Nov 3, 2015

Participants: Dagmar, Frank, Ilya, Kyle, Denis, Leandro, Jonathan, Yin Hoon

Location: Hangout

Report

• Ilya

  • imported Leandro's model and ran it
  • Question is if the results are good, Leandro wanted to check it
  • finalised toy model

• Denis

  • Script to generate subset model for translation
  • still working on protein decay subset generator

• Seems we now have three toy models available right now/being worked on

  • Matthias model (dFBA)
  • Leandro's model
  • Ilya's model

Open issues/questions

• Denis needs examples of SBO annotation in order to prepare conversion to SBGN

  • Frank has some code from Metabolism group (using libSBML API), could also be done with COPASI
  • The example for SBO is here

• Frank pointed out that we need annotations about the model history before submission to BioModels DB

  • an example for history of SBML files is here

Goal for next time

• Frank: Get SED-ML script done
• add SBO term to all modules (example in: https://github.com/whole-cell-tutors/whole-cell-reduced/blob/master/Metabolism/full_model/Metabolism_matrices_annotated_08_L3V1.xml)
• Dagmar: Get SBGN-ML files in Git repository
• start generating model history (annotations, see Frank's example above)