Templates

Wiki as a template for the documentation

This Wiki is our template for the documentation during the project. It organizes the tasks and manages the documentation.

Wiki's structure

Introduction

Administrative-Overview

Executive-Summary

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Group 1

• Synopsis Group 1
• Sources of Bachmann model
  • SBML and extra formats
  • Reproducibility
• Software tools for simulation
• How to build a Fully Featured COMBINE Archive?
• Communication channels
• Provision of a template for documentation
• Schedule (draft)
• Review of results
• COMBINE Archive (Testversion!)

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Group 2

• Finding of SBML models
• Comparison of SBML models
• The chosen one
• Simulation tools
• Metadata
• Improving metadata annotations
• Finalization SBML-Code
• Synopsis Group 2

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Group 3

• SBGN Maps for Bachmann model
• Choice of SBGN language
• Tool to draw the SBGN Map
• SBGN-Map Drawing & Orientation by the 10 simple Rules

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Group 4

• Selection of experiments
• Selection of SED-ML tool(s)
• Generation of SED-ML file(s)
  • Generation in SED-ML Webtools and COPASI
  • Generation in Tellurium
  • Validation of SED-ML files
• Integration into COMBINE Archive
• Test of SED-ML files and COMBINE Archive

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• Methods / Toolbox
• Discussion / Limitations / Results
• Glossary