Plan

Understanding the intricacies of metabolism is the central focus for many diseases, particularly cancer. Pathways, reactions, and fluxes are key factors to consider when modeling the outcome and preventability of metabolic diseases. However, an important and underrepresented aspect is the atom transitions between reactions. These transitions are characteristic of cancer metabolism and are tell­tale signals of co­factor behavior, particularly when looking at the transition of hydrogen between metabolites and co­factors. The current model is under several assumptions: the TCA cycle goes through one cycle, the Pentose Phosphate Pathway has a linear path, the ambiguous fates of specific atoms are not considered (one fate is chosen), and the mammalian cell is represented by carbon transitions of three pathways (Glycolysis, TCA cycle, and Pentose Phosphate Pathway).

High-level goals

• Represent carbons with circles
  • some inspiration: https://github.com/escher/escher-demo/tree/gh-pages/structures
• Establish data structures with the following content. At first, 1 JSON file with this info:
  • Carbon numbers for metabolites
  • Atom (carbon) transitions
  • Which metabolites are clickable and which ones are measurable
  • Based on doc: https://docs.google.com/document/d/113XzkAclohIjc585FO-mKbvCgu5WVgXolY8XQ_Ir5Ro/edit?usp=sharing
    • parse this doc and make it JSON (see example in the doc)
• initial mockup

Development priorities

• Look through a few D3.js tutorials
• Refresher of SVG syntax
• Start with this map: RECON1.Glycolysis TCA PPP.json
• Start by forking the structures demo and commit to escher-trace repository
• Put together a nice set of mockups and run them by the tracing experts
• Can we load the JSON file and draw carbon circles with it?
• [later: Play around with escher-test, webpack, babel, ES6, etc.]

Inspiration

• https://github.com/d3/d3/wiki/Gallery
• https://www.omix-visualization.com/examples/timedependent2.jsp#sthash.l8ur4IQH.dpbs

Style guide

• http://standardjs.com/