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README.md

20n/act/reachables

This project enumerates all bio-accessible chemicals. For each of those chemicals, it will design DNA blueprints. These DNA blueprints can bioengineering organisms with un-natural function.

20n/act/reachables contains many modules built from scratch in-house. Some: mine raw biochemical data, integrate heterogenous sources, learn rules of biochemistry, automatically clean bad data, mine patents, mine plain text, bioinformatic identification of enzymes with desired function.

Data integration, biochemical model, predictions, DNA design

This project holds most of the capabilities of 20n/act:

  • Data integrator
    • Integrates various heterogenous data sources containing enzyme function observations: BRENDA, MetaCyc, KEGG.
    • Chemical applications: Mines wikipedia, BING, ChEBI.
  • Biochemical model (chemoinformatics style)
    • Reaction operators (ROs): Model catalytic activity of enzymes
    • Structure activity relationships (SARs): Model substrate specificity
    • Inference of ROs and SARs
    • Uses of RO+SAR: Mechanistic validation of observations, prediction of new enzymatic chemistry
  • DNA design
    • Chemical to non-natural pathway (protein sequences and chemical intermediates)
    • Non-natural pathway to DNA design for microbial engineering (E. coli specific)
  • Untargeted metabolomics (LCMS analysis): Deep learning based automatic identification of comparative cellular changes
  • Bioinformatics: Infer enzymes with specified biochemical function (better than EC classifications)

Few modules outside of this project:

  • Front-end: Bio-reachables wiki that provides a human-accessible interface to all reachable chemicals, and their DNA designs.
  • Bioreactor: Preliminary designs for a home-grown DIY bio-reactor. Commercial versions cost upwards of $60,000. DIY bioreactors could be built for under $5,000 in total parts.