COMBINE Notebooks GSoC Project Preparation

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of various community standards and formats in systems biology and related fields. The goal of this project is to create several interactive Jupyter notebooks that showcase these standards and their libraries around one common theme; the repressilator model. More information about this project can be found on the Github issue (https://github.com/nrnb/GoogleSummerOfCode/issues/192). I am preparing myself for this project and being mentored by Dr. Matthias König.

The first month of learning taught me some great things, some new and some known (e.g. the COMBINE structure, history, abstract and core ideas). I have gone through the following resources have reached a good understanding of the core ideas:
  1. COMBINE webpage: http://co.mbine.org/standards
  2. https://pypi.org/project/libsbgnpy/ (accessed 02-April-2022)
  3. https://pypi.org/project/python-libsbml/ (accessed 02-April-2022)
  4. https://pypi.org/project/pyNeuroML/ (accessed 02-April-2022)
  5. https://pypi.org/project/libcellml/ (accessed 02-April-2022)
  6. https://pypi.org/project/python-libsedml/ (accessed 02-April-2022)
  7. https://github.com/SynBioDex/pySBOL3 (accessed 02-April-2022)
  8. https://pypi.org/project/python-libcombine/ (accessed 02-April-2022)
  9. https://github.com/sys-bio/libOmexMeta (accessed 02-April-2022)

Studying the resources provided a good overview of the core ideas of combine and I got a good overview of its needs, use cases, its basic functionality, hierarchy of different constructs and various object-oriented features. 

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