Julian West
posted 4 months ago

Open-source platform for Systems Bio : "Life123"

As a PLATFORM for SYSTEMS BIOLOGY, the open-source project LIFE123 (https://life123.science) offers a growing set of tools to wrestle with the complications of numerical solutions to complex dynamical systems, such as cycles of biochemical reactions.

  • ONLY 1/2 OF THE BATTLE, is to offer functions to set up and simulate webs of reactions, optionally with spatial components and diffusion (plus - upcoming - membranes...)
  • The OTHER 1/2 OF THE BATTLE is a battery of tools, to tame numerical instabilities, to visualize & analyze the results, and to integrate high-performance computing: a collaboration of software engineering, data science, numerical methods, biochemistry & biology, among other fields.

=> Pleased to announce version Beta 22 of this collaborative open-source project.

Explore it all with just a few lines of Python code in convenient Jupyter notebooks! (optionally in a 1-click hosted environment)

VIEW THE NOTEBOOK with this experiment: https://nbviewer.org/github/BrainAnnex/life123/blob/main/experiments/reactions_single_compartment/large_time_steps_1.ipynb

BRIEF INTRO VIDEO: https://www.youtube.com/watch?v=TCvQUKPVimE

1-CLICK to RUN IT LIVE! (say "Cancel" to the prompt; see brief vid, above, for explanation): https://mybinder.org/v2/gh/BrainAnnex/life123/main

INTERACTIVE VERSION OF THE GRAPH DIAGRAM of the chain of reactions of this example: https://brainannex.github.io/life123/experiments/reactions_single_compartment/large_time_steps_1.log.htm

#medicine #systemsbiology #insilico #reactomics #biology #chemistry #biochemistry

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