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Computational synthetic biology: Predicting DNA edits for bioengineering

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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](http://20n.com/blog.html#bio-acetaminophen). 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](https://preview.bioreachables.com/) (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](mailto:act@20n.com?Subject=Purchase%20request%20for%20Enterprise%20Edition%20of%20Bioreachables%20Wiki).

#### Building the project
Checkout the repo. Follow [instructions to run](wikiServices#1-wiki-content-generation) to create the database and prediction corpus. If you'd rather get a pre-packaged DB without creating it yourself [please contact us](mailto:act@20n.com?Subject=Purchase%20request%20for%20pre-packaged%2020n-act%20DB.). 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](reachables/src/main/scala/initdb.scala) Run:[Instructions](wikiServices#create-an-act-db)
 | 2 | Reaction operator (RO) inference | Mines rules of enzymatic catalysis | Code:[biointerpretation module](reachables/src/main/java/com/act/biointerpretation)
 | 2 | Structure Activity Relationship (SAR) inference | Mines substrate specificities | Code:[biointerpretation module](reachables/src/main/java/com/act/biointerpretation)
 | 3 | Biointerpretation | Mechanistic validation of enzymatic transforms (using ROs) | Code:[com.act.biointerpretation.BiointerpretationDriver](reachables/src/main/java/com/act/biointerpretation/BiointerpretationDriver.java) Run:[Instructions](wikiServices#run-biointerpretation)
 | 4 | Reachables computation | Exhaustively enumerates all biosynthesizable chemicals | Code:[com.act.reachables.reachables](reachables/src/main/scala/reachables.scala) Code:[com.act.reachables.postprocess_reachables](reachables/src/main/scala/postprocess_reachables.scala) Run:[Instructions](wikiServices#run-reachables-and-cascades)
 | 5 | Cascades computation | Exhaustively enumerates all enzymatic routes from metabolic natives to bioreachable target | Code:[com.act.reachables.cascades](reachables/src/main/scala/com/act/reachables/cascades.scala) Run:[Instructions](wikiServices#run-reachables-and-cascades)
 | 6 | DNA designer | Computes protein & DNA design (coli specific) for each non-natural enzymatic path | Code:[org.twentyn.proteintodna.ProteinToDNADriver](reachables/src/main/java/org/twentyn/proteintodna/ProteinToDNADriver.java) Run:[Instructions](wikiServices#building-dna-designs)
 | 7 | Application miner | Mines chemical applications using web searches [Bing] | Code:[act.installer.bing.BingSearcher](reachables/src/main/java/act/installer/bing/BingSearcher.java) Run:[Instructions](wikiServices#augment-the-installer-with-bing-search-data)
 | 8 | Enzymatic biochemistry NLP | Text -> Chemical tokens -> Biologically feasible reactions using ROs | Code:[act.shared.TextToRxns](reachables/src/main/scala/act/shared/TextToRxns.scala) Frontend:[TextToRxnsUI](reachables/src/main/r/TextToRxnsUI) |
 | 9 | Patent search | Chemical -> Patents | Code:[act.installer.reachablesexplorer.PatentFinder](reachables/src/main/java/act/installer/reachablesexplorer/PatentFinder.java) Run:[Instructions](wikiServices#enrich-the-reachables-with-patents)
 | 10 | Bioreachables wiki | Aggregates reachables, cascades, use cases, protein and DNA designs into a user friendly wiki interface | [Documentation](wikiServices#2-new-wiki-instance-setup-steps)
 
 <img width=65% src="http://20n.com/assets/video/making-apap-20n%3Aact-small.gif">

#### 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](reachables/src/main/python/DeepLearningLcmsPeak) Code:[com.act.lcms.UntargetedMetabolomics](reachables/src/main/scala/com/act/lcms/UntargetedMetabolomics.scala)
 | 2 | LCMS: Comparative visualization | Visualizing traces side-by-side from untargeted evaluation of over and underexpressed peaks | Doc:[LCMSDataVisualisation](reachables/src/main/r/LCMSDataVisualisation)

<img width=65% src="http://20n.com/assets/img/lcms-viz.png"> 
 
#### 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](reachables/src/main/scala/costmodel.scala) Code (viz server):[costModelUI](reachables/src/main/r/costModelUI) Source model:[XLS](http://20n.com/assets/spreadsheet/cost-model.xlsx)

License and Contributing
===
Code licensed under the GNU General Public License v3.0.
If an alternative license is desired, [please contact 20n](mailto:act@20n.com?Subject=Purchase%20request%20for%2020n-act%20codebase%20under%20commercial%20license).

Original Authors
===
* [Saurabh Srivastava](http://saurabh-srivastava.com/)
* [J. Christopher Anderson](https://www.linkedin.com/in/j-christopher-anderson-682b0594/)
* [Mark T. Daly](https://www.linkedin.com/in/marktdaly/)
* [Michael Lampe](https://www.linkedin.com/in/michael-lampe-57750761/)
* [Thomas Legrand](https://www.linkedin.com/in/thomaslegrand1/)
* [Vijay Ramakrishnan](https://www.linkedin.com/in/viramakrishnan/)
* [Gil Goldshlager](https://www.linkedin.com/in/gil-goldshlager-a78aa4b8/)
* [Nishant Kakar](https://www.linkedin.com/in/nishant-kakar-44937b74/)

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