Organisational Principles in Living Organisms

This Python package provides data structures to model and simulate the organisation at (unicellular) system scale.

• Genetic regulation (pyorganism.regulation)

  • Analog and digital control (cf. [1])
  • Transcriptional regulatory network (TRN): directed transcription factor-gene interaction network
  • Gene regulatory network (GRN): directed gene-gene interaction network (projection of the TRN)
  • Gene proximity network (GPN): undirected gene-gene proximity network
  • Couplons (intersection between sigma factor's and nucleoid associated proteins' targets)
  • Functional clusters (GO)
  • Metabolic control (cf. [2])
  • Continuous control (cf. [3])

• Metabolism (pyorganism.metabolism)

  • Metabolic systems
  • Network representations
  • Flux balance analysis (FBA)

Requirements

• future for Python2/3 compatiblity
• Cython
• networkx
• numpy
• pandas
• reading/writing SBML files requires libsbml or the PyPi package

• FBA requires either:

  • Gurobi (currently the only working interface),
  • GLPK,
  • MOSEK,
  • or any other linear programming solver that you are willing to provide the Python interface for (like gurobipy or cvxopt).

• KEGG interface requires SOAPpy
• (pytables for HDF5 storage can be replaced by pickling of numpy objects)

Authors

Former and current members of the Computational Systems Biology workgroup headed by Prof. Marc-Thorsten Hütt at Jacobs University Bremen. In alphabetical order:

• Beber, Moritz Emanuel
• Grigore, Alexandra Mirela
• Kölling, Nils
• Sonnenschein, Nikolaus

Relevant References

[1]	Marr, C., Geertz, M., Hutt, M.-T. & Muskhelishvili, G. Dissecting the logical types of network control in gene expression profiles. BMC Systems Biology 2, 18 (2008).

[2]	Sonnenschein, N., Geertz, M., Muskhelishvili, G. & Hütt, M.-T. Analog regulation of metabolic demand. BMC Systems Biology 5, 40 (2011).

[3]	Beber, M. E., Sobetzko, P., Muskhelishvili, G. & Hütt, M.-T. Interplay of digital and analog control in time-resolved gene expression profiles. BMC Systems Biology submitted, (2015).