SSSB Liveblog: Saturday Afternoon

Raik Gruenberg - BrickIt: An open source solution for local BioBrick management

Raik drank the BioBrick cool-aid and decided he loved it.  He ended up with hundreds of biobricks in different assemblies in his freezer - and disappointed the Registry at MIT didn’t help him keep track of their physical location.

So he built a tool to help track of local sample: BrickIt

Check it out and improve it - we sure will.  Let’s install a public version - we’ll just need to fix up some new views and perhaps implement some kind of user management & authentication system. 

Jean Peccoud - From Registries to an IDE of genetic systems

Analyzed MIT registry to try and visualize the abstraction hierarchy at work by finding inclusion of sequences in other sequences: i.e. compositions.  Lots of surprising stuff - “devices” [not sure how they categorized parts into devices] being used in compositions with basic parts, and no more than a few parts used in more than 10 compositions.

Parts Warehoue - how do you actually manage a bunch of clones?  Jean’s team sequenced the 2007 iGEM parts kit (I made all of them) and found that 471 of the wells contained undocumented DNA, 1011 contained documented DNA, and 7 contained no DNA (I’m curious how many contained the *wrong* DNA).

One business model for the Warehouse might be to have the submitter pay a submission fee for adding a part to the DNA registry to keep it maintained and to enable its reuse.

Main idea: Lack of clear understanding of what’s a part?  Basic parts / atomic parts particularly important.  IDE: develop problem-dependant design strategies, and dream of a portable and abstract description language.

Ralph Santos - PICA (part interaction and Composition Assertion)

A Composable template to describe parts in a loose way.  Abstraction vs. Models: all A are M, but not all M are A.  But let’s describe parts/devices in terms of terminals and state spaces - the terminals describe the input and output, how it interacts with the world.  See PICA

Andrew Miller - CellML for modeling Synthetic Biology

CellML is a community effort, and has a process to get people involved (with a public issue tracker).  Drafts are developed by contributors and shared and discussed early and often.  CellML is an XML language.  It’s useful for exchange b/w programs and researchers, but not a good human-computer interface.  Tools and input languages are the solution there.  CellML models can be broken into components, which themselves represent variables. The core requires all units be specified for real number variables and constants. Models can be composed by importing components from other CellML files.  This lends itself to a library or registry of models, perhaps the models associated with a collection of biobricks.

Michael Pederson LBS - Textual description language for modeling synthetic biology.

LBS is a text based description language that lets you define parallel modules of sequential processes, as reaction rates of various species.  Species have typed parameters (i.e. “is this species phosphorylated?”)  You can define typed patterns that identify specific species, with types, and then modules that relate the transition from pattern to the next.

LBS currently is defined as a language syntax and semantics, and a current project is to compile LBS to petri nets or CellML models.

Questions: is it possible to compile a high-level model (like LBS) down to specific BioBricks?  For this, we’d need a formal model of the BBs’ semantics.