1. EUGENE A Basic Structural Language for describing biological systems By Adam Liu and Lesia Bilitchenko

2. What is the problem? Biological systems need to be Explained Described Interpreted This requires textual representation, which can Describe algorithms Automate processes Enforce rules Interact with graphical version (BOGL) Accepted and used by Community

3. How can it be solved? Design a structural programming language Direct relationship to BOGL symbols Predefined data types Ability to create new data types Data abstraction, hierarchy Procedures for data manipulation Promoter p; EUGENE:BOGL: RBS rs;

4. What is the new technical idea Most existing languages specify species, reaction Low level of abstraction Limited in scope, hard to create large designs Geared towards modeling and are computer readable Systems Biology Markup language (SBML) BioNetGen (BNGL) Antimony (human readable, but for modeling) EUGENE Abstraction based on parts Hierarchy Rule based description

5. What is the impact if successful? Launch of a textual language to describe standard biological parts that Is human-readable and human- writable Is portable and customizable Raises the level of abstraction Incorporates interactive visuals Establishes a standardized method of describing complex systems and interactions Garners support from the community Is easily maintained if changes are needed

6. How will the program be organized? Loop indefinitely Parse language with a parser generator Bison, ANTLR, etc. Write context-free grammar Parse language with a custom parser in Java Integrated quickly into Clotho Needs extensive documentation

7. How will intermediate results be generated? New syntax and documentation will be constantly updated on the RFC The interpreter will be updated to parse and handle new syntax Currently the Pictoparts plug-in in Clotho’s main toolbar New name? Lachesis, BOL, BOTL, Eugene, Ugene, ALFS, etc.

8. How will you measure progress? Progress will be measured by how well we follow the timeline*: Week 1-2: brainstorm primitives and develop basic syntax Week 3-5: investigate parsers and get a basic interpreter working Week 6-8: get feedback, implement functionality, test, repeat Week 9-11: integrate with visualizations and workflows Week 12-13: finalize documentation Week: 1 2 3 4 5 6 7 8 9 10 11 12 13 Month:June July August *will probably change

9. What will it cost?