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README.md

README.md

20n/act: An open source platform for bioengineering

20n/act is the data aggregation and prediction system for bioengineering. For a target molecule, 20n/act predicts DNA insertions into cells (usually a microbe such as E. coli or S. cerevisiae) that modify the cell. These modified cells make the target molecule by fermentation from sugar. We call these "target molecules/chemicals" the bioreachables. The system predicted/invented the first bio-route to Acetaminophen/Tylenol/APAP. Read more on our blog post. The technical details of the APAP work can be found in patents applications on coli and yeast fermentation.

Getting started

Live preview

See predicted DNA for 11 sample molecules at Bioreachables Preview (Login:Pass = public:preview). Due to limitations we can only make a preview version available. If you'd like the full version please contact us.

Building the project

Checkout the repo. Follow instructions to run to create the database and prediction corpus. If you'd rather get a pre-packaged DB without creating it yourself please contact us. The codebase is public to further the state-of-the-art in automating biological engineering/synthetic biology. Some modules are specific to microbes, but most of the predictive stack deals with host-agnostic enzymatic biochemistry.

Components of 20n/act

Predictor stack

Answers "what DNA do I insert if I want to make my chemical?"

Module Function Code
1 Installer Integrates heterogeneous raw data Code:com.act.reachables.initdb
Run:Instructions
2 Reaction operator (RO) inference Mines rules of enzymatic catalysis Code:biointerpretation module
2 Structure Activity Relationship (SAR) inference Mines substrate specificities Code:biointerpretation module
3 Biointerpretation Mechanistic validation of enzymatic transforms (using ROs) Code:com.act.biointerpretation.BiointerpretationDriver
Run:Instructions
4 Reachables computation Exhaustively enumerates all biosynthesizable chemicals Code:com.act.reachables.reachables
Code:com.act.reachables.postprocess_reachables
Run:Instructions
5 Cascades computation Exhaustively enumerates all enzymatic routes from metabolic natives to bioreachable target Code:com.act.reachables.cascades
Run:Instructions
6 DNA designer Computes protein & DNA design (coli specific) for each non-natural enzymatic path Code:org.twentyn.proteintodna.ProteinToDNADriver
Run:Instructions
7 Application miner Mines chemical applications using web searches [Bing] Code:act.installer.bing.BingSearcher
Run:Instructions
8 Enzymatic biochemistry NLP Text -> Chemical tokens -> Biologically feasible reactions using ROs Code:act.shared.TextToRxns
Frontend:TextToRxnsUI
9 Patent search Chemical -> Patents Code:act.installer.reachablesexplorer.PatentFinder
Run:Instructions
10 Bioreachables wiki Aggregates reachables, cascades, use cases, protein and DNA designs into a user friendly wiki interface Documentation

Analytics

Answers "Is my bio-engineered cell doing what I want it to?"

Module Function Code
1 LCMS: Untargeted metabolomics Deep-learnt signal processing to identify all chemical [side]effects of DNA engineering on cell Code:DeepLearningLcmsPeak
Code:com.act.lcms.UntargetedMetabolomics
2 LCMS: Comparative visualization Visualizing traces side-by-side from untargeted evaluation of over and underexpressed peaks Doc:LCMSDataVisualisation

Unit economics of bioproduction

Answers "Can I use bio-production to make this chemical at scale?"

Module Function Code
1 Cost model: Manufacturing unit economics for large scale production It backcalculates cell efficiency (yield, titers, productivity) objectives based on given COGS ($ per ton) of target chemical. From cell efficiency objectives it guesstimates the R&D investment (money and time) and ROI expectations Code:act.installer.bing.CostModel
Code (viz server):costModelUI
Source model:XLS

License and Contributing

Code licensed under the GNU General Public License v3.0. If an alternative license is desired, please contact 20n.

Original Authors