BioCompiler

From WaterlooiGEM

Contents 1 Action Items 2 Abstract 3 Introduction 4 Flowchart of Previous Works

Action Items

• Rob -> research "little b" find the papers its based on and any papers using it
• Matt -> research SBML, etc.
• Deon -> Synthetic Biology Workbench: what's it do, how's it used?

• Come up with a better project name than BioCompiler
• Write the abstract/intro/background flowchart of the project.
• Download Eugene and the Clotho suite from Berkeley -- play with them and figure out what they can do
• Download SynBioSS and figure out what it does
• Distill information from this paper into an human-undergrad-readable form: http://research.microsoft.com/apps/pubs/default.aspx?id=79443
• Add projects/papers to the list below in the Flowchart of Previous works section. Include dependencies of that project/paper on relevant projects/papers so that we can eventually transform the list of bullets into a flowchart.

Abstract

Introduction

Flowchart of Previous Works

Obviously, this isn't in flowchart form yet, but:

• Synthetic Biology Markup Language (SBML): this is an important foundation for synthetic biology software in that it is a markup language that describes synbio constructs at the biochemical level.
  • Dependencies: none - language spec.

• Systems Biology Workbench (SBW): refers to a framework for tying together systems biology modules (applications) and the modules themselves. The SBW download itself consists primarily of a "SBW Broker" which only routs messages, a SBML support module, Jarnac (a simulator of reaction networks), and JDesigner (a front-end for reaction network simulators, uses Jarnac as a backend).
  • Dependencies: SBML, Jarnac

• Jarnac: a Basic-based language that describes a "any physical system that which can be described in terms of a network and associated flows". Although it's nominally a language, it comes with computational support for various forms of simulation which is why it's used as the simulation module of SBW.
  • Dependencies: it's a successor to SCAMP. Simulation component has dependencies on the LSODAor CVODE integrator, the NLEQ solver, and the IMSL library.

• Berkeley Software 2009: Clotho, Eugene, Spectacles, Kepler
  • Dependencies: SBW for simulation, compatible with Stanford's SBOL Visual project.

• SynBioSS: "users enter BioBrick numbers and the software pulls DNA sequence information from the Registry, then builds a network of reactions that represent all the biomolecular interactions, then simulates the network of reactions in time and generates probability distributions of molecules, such as GFP"
  • Dependencies: can import Eugene-exported XML from Berkeley, generates SBML or NetCDF files, pulls sequence data directly from the Registry

• Microsoft Research: GEC: Genetic Engineering of living Cells.
  • Dependencies: the Registry (compatible, not a direct interface), based on the Language for Biochemical Systems (LBS) which is Michael Pederson's thesis project, simulation uses SBW or can export to SBML, cites GenoCAD as the only other "formally defined programming language for genetic engineering of cells" and uses GenoCAD as a grammar checker.

• SBOL
• GenoCAD
• NetCDF
• little b