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.

20n / act

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