Code
Meeting Minutes for 7/3/09
Attendees
Drew Endy
Cesar
Alexander
Marnia
Tad
20 or so others...
Overview
Drew talked about the origin of synthetic biology. Drew then talked about the current state of synthetic biology. He then talked about the future of synthetic biology. Cesar then gave a talk about his project and the goals of that project. A video archive of these talks can be found here: www.justin.tv/xp_prg
The overall algorithm at a high level is:
At low granularity this is the essence of the problem:
1. A BioBrick standard specifies two DNA cutting enzymes (restriction endonucleases or restriction enzymes)
http://en.wikipedia.org/wiki/Restriction_enzyme
that can be used for composing basic parts into composite parts
- A wildtype DNA sequence is likely to have sites in the middle of the sequence that allow for the restriction enzyme to make a cut.
- The algorithm has to identify those sites in the wildtype DNA sequence
- The algorithm has to mutate the sites but must adhere to three constrains
a. The mutation eliminates the restriction site (the location where the restriction enzyme makes the cut)
b. The mutation does not change the amino acid that is suppose to be encoded if the sequence is a protein generating one (aka an open reading frame)
http://en.wikipedia.org/wiki/Open_reading_frame
c. The mutation does not change the function of the sequence. For example, a mutation in a ribosome binding site (RBS) may lower or increase the affinity of the ribosome to the site
http://en.wikipedia.org/wiki/Ribosomal_Binding_Site http://en.wikipedia.org/wiki/Ribosome
A tool that does work similar to what I'm describing, but not exactly is GeneDesigner:
https://www.dna20.com/tools/genedesigner.php'>https://www.dna20.com/tools/genedesigner.php
It's proprietary and closed-source, but gives you access to a real tool in this domain.
Action Items
#DescriptionNotesDifficultyAssignedPriorityDue Date 1 Find individuals who want to form a team to code for the projects: http://code.google.com/p/biobrickstudio/'>http://code.google.com/p/biobrickstudio/ which involves objective c which will be the interface and http://code.google.com/p/synbiopython/wiki/SynBioPython'>http://code.google.com/p/synbiopython/wiki/SynBioPython which involves python which will be the back endAlexander Castro, Meredith L. Patterson, and David Saches appear to want to be on the team so far. Cesar said he would meet with Drew on Monday and then wanted to meet with members on the current team. Low Tim Heath High 7/8/09 2 Find a way to interface from objective C to pythonCesar wrote: The core problem right now is having the BioBrick Studio GUI (Objective-C/Cocoa) interact with Python-based "DNA Sequence Refinement" (DSR) algorithms. It appears the python will exist on google app engine so an webservices xml wrapped in http approach could be used. The only problem is google app engine will not work for long running applications and cannot keep an internet socket open.Medium All High 7/8/09 3 Convert a wild-type DNA sequence into a standard basic partThis is the #1 requirement of the entire project. Cesar wrote: The specification of the first standard is located here: http://dspace.mit.edu/handle/1721.1/45138'>http://dspace.mit.edu/handle/1721.1/45138Extremely Hard All Highest 1/1/2010 4 Study http://dspace.mit.edu/handle/1721.1/45138'>http://dspace.mit.edu/handle/1721.1/45138This is the first specification of the projectLow All High 7/8/09 5 Study http://openwetware.org/wiki/The_BioBricks_Foundation:RFC'>http://openwetware.org/wiki/The_BioBricks_Foundation:RFCThis is the emerging standard for the bio bricks specificationLow All High 7/8/09 6 Setup a meeting to discuss http://dspace.mit.edu/handle/1721.1/45138'>http://dspace.mit.edu/handle/1721.1/45138Cesar considers this extremely important to the projectLow Tim Heath High 7/8/09 7 Study http://openwetware.org/wiki/Endy:Notebook/BioBrick_Studio'>http://openwetware.org/wiki/Endy:Notebook/BioBrick_StudioCreated to assist with the projectLow All High 7/8/09 8 Study https://www.dna20.com/tools/genedesigner.php'>https://www.dna20.com/tools/genedesigner.phpCesar says this is close to how he wants the software to work but not exactHigh All High 7/8/09 9 Study http://en.wikipedia.org/wiki/Restriction_enzyme'>http://en.wikipedia.org/wiki/Restriction_enzymeA BioBrick standard specifies two DNA cutting enzymes (restriction endonucleases or restriction enzymes) that can be used for composing basic parts into composite partsLow All High 7/8/09 10 Study http://en.wikipedia.org/wiki/Open_reading_frame'>http://en.wikipedia.org/wiki/Open_reading_frameThe mutation does not change the amino acid that is suppose to be encoded if the sequence is a protein generating one (aka an open reading frame)Low All High 7/8/09 11 Study http://en.wikipedia.org/wiki/Ribosomal_Binding_Site'>http://en.wikipedia.org/wiki/Ribosomal_Binding_Site and http://en.wikipedia.org/wiki/Ribosome'>http://en.wikipedia.org/wiki/RibosomeThe mutation does not change the function of the sequence. For example, a mutation in a ribosome binding site (RBS) may lower or increase the affinity of the ribosome to the siteLow All High 7/8/09 12 Study http://syntheticbiology.org/BioBricks/mRNA_design_rules.html'>http://syntheticbiology.org/BioBricks/mRNA_design_rules.htmlDavid thought this was an important concept to understandLow All High 7/8/09 13 Allow for wiki and svn access to http://code.google.com/p/synbiopython/wiki/SynBioPython'>http://code.google.com/p/synbiopython/wiki/SynBioPython to all members on teamNeed access to contribute code and documentation!Low Cesar High 7/8/09 14 Figure out weekly meeting timeThe tech shop is offering us Friday nights. I can't be there until 9:30 PMLow All High 7/8/09