Spectacles, Eugene, and Kepler Managing Synthetic Biology Device Development Lesia Bilitchenko, Joanna Chen, Adam Liu, Richard Mar, Thien Nguyen, Nina Revko, Bing Xia Berkeley Software, iGEM 2009, MIT, November 1, 2009
Project Motivation
Project Motivation Teams are making MORE parts! Berkeley iGEM 2009 Wetlab made over 800 parts this summer!!!
Clotho Infrastructure DB Tool-to-tool Interaction Tool-to-database Interaction Reconfigurable Data Model
Reconfigurable Data Model Template Files Core Extension Datum Code Keywords Keywords Gen Sequence View XML Datum XML DB Clotho Tool Hibernate Core Data API Relational Clotho Data Core Databases Algorithm Manager
Design Flow Example Abstract design BBa_I13521 BBa_I763007 Device Specification BBa_J3901 BBa_J5526 Physical Assembly
Design Flow Example Abstract design Spectacles Clotho Core API Device Specification Revamped Clotho Core and Data Model Eugene Physical Assembly Kepler
Abstract Design Eugene Choose a part Modify name, sequence, or implementation Map to physical part in database Export to Eugene Clotho Tool - Sequence View API - Algorithm Manager
Spectacles Demo
Device Specification Realize an abstract design from Spectacles: Eugene Header Specify instances of Files physical parts <part declarations> Specify rules on how parts XML To can interact with each <rule declarations> Eugene other on devices Header Tool Construct devices while <device declarations> enforcing rules <function calls on devices> Perform functions on XML devices Database Eugene XML Tool X Of Compiler Parts
Eugene Demo
Physical Assembly Clotho Kepler Files for robot Assembly Graph
Assembly Graph R0040 R0051 R0011 J3901 R0010 B0034 E1010 B0010 B0012 Stage 1 J3901R0010 B0034E1010 B0010B0012 B0034E1010B0010B0012 Stage 2 R0040B0034E1010B0010B0012 R0011B0034E1010B0010B0012 Stage 3 R0051B0034E1010B0010B0012 J3901R0010B0034E1010B0010B0012
Stage 1 Processing J3901 R0010 B0034 E1010 B0010 B0012 J3901R0010 B0034E1010 B0010B0012 Stage 1 Stock Plate 1. Dilution file Assignments to wells for robot 3. File with human- Buffer readable instructions Dilution Plate pre-filled 2. Reaction file Assignment to wells for robot +Digestion Mix Reaction Plate +Ligation Mix
Kepler Workflow design environment • Visual • Extensible Director: controls the execution of actors Actor: a process step in the workflow
Kepler Demo
...and ~200,000 lines of code later… • Abstract device development, device specification, and physical assembly are key activities in Synthetic Biology. • Developed Spectacles, Eugene, and Kepler based software tools on top of a revamped Clotho framework. • Demonstrated the usefulness of these tools as a continued effort toward a complete design flow for Synthetic Biological Systems. • Collaborated with other institutions • Stanford, U Minnesota, SynBERC
Thanks Our Advisor Doug Densmore UC Berkeley 2009 “Wet team” In particular Sherine Cheung and Jenn Brophy J. Christopher Anderson Lab Josh Kittleson, Tim Hsiau SynBERC and QB3 Kate Spohr, Kevin Costa, Leonard Katz CHESS Christopher Brooks, Edward Lee Others Marlee Tishenor, Christine Tsin, Evan Yang, Nade Sritanyaratana, Armen Khodaverdian For more info be sure to stop by our poster and get a demo! Also be sure to check out: http://2009.igem.org/Team:Berkeley_Software Wiki http://2008.igem.org/Team:UC_Berkeley_Tools http://sourceforge.net/projects/clothocad/ http://sourceforge.net/projects/eugene/ Code and documentation http://sourceforge.net/projects/keplerclotho/
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