Synthetic Biology @ BBN

Metrology for Mammalian Synthetic Biology

Registration: email biotools@bbn.com

Modularity is one of the fundamental tenets of synthetic biology: the notion that we can effectively engineer biological organisms by combining or modifying known biological components, such as DNA, RNA, and proteins.  

Putting this vision into practice, however, has been hampered by a lack of quantitative models capable of making accurate predictions about what components will do when combined to form novel biological circuits, except in a few particular narrow domains.

The problem may be understood as one of metrology: effective engineering requires a system of measurements that are focused on delivering the specific types of information needed for design of functional systems.  Consider, for example, the use in mechanical engineering of properties such as stiffness, stress and strain, and rigidity.  These sorts of quantities are precisely focused on questions that need to be answered by designers of physical structures and are measurable through well-defined and standardized experiments.

In synthetic biology, despite the excellent work done by many researchers, the field has not yet converged on an appropriate system of measurements that can support the needs of biological circuit designers.  Until it does, the engineering of complex circuits will tend to be a black art requiring much costly trial and error.

With recent improvements in tools for measurement, analysis, and modeling, however, the time is ripe to revisit the question of metrology for synthetic biology.  This is particularly true for work in mammalian cells, which are relatively robust to the introduction of engineered circuits and where large libraries of orthogonal components are beginning to emerge.

Workshop Goals:

The goal of this workshop is to bring together both producers and consumers of synthetic biology component models, with the aim of laying out a roadmap for metrology in mammalian synthetic biology.  Participants will be invited to contribute to a whitepaper to be produced after the workshop, summarizing the conclusions of the workshop and recommendations for metrology investigations that will advance synthetic biology.

Agenda for Discussion:

The use that measurements are put to will dictate what it makes sense to measure, and how we know whether we are measuring the right things with high enough precision and accuracy.
Fluorescence? PoPS? RiPS? Single element  (e.g. terminator, 5'UTR) or "device" complex (e.g, rtTA + pTRE)?  When are population measurements sufficient and when are single cell measurements necessary? What model priors should be assumed? What types of context are important?
When data has an unexpected form, do we debug our models or our experiments or our materials? How much do duplicate sample points matter? What resolution of sampling is necessary to determine variation? How do we decide when to throw data away?  When is it time to think we've discovered a new phenomenon?  Can we learn anything systematic about biology?
Fluorimetry? Optical imaging? Flow cytometry, HCS microscopy? HT mass spec? Others?
How do we share data, with a lab, or with our peers, or publicly? How do we represent it?  How do we protect it?

Schedule and Location:

Location
Patil/Kiva Seminar Room (32-G449)
MIT Stata Center (Building 32)
32 Vassar Street
Cambridge, Massachusetts

Time
Sunday, May 12th, 2013, 1-5pm

Schedule:

Dial-in participation will be provided via GoToMeeting:

  1. https://www2.gotomeeting.com/join/336632202
  2. Use your microphone and speakers (VoIP) - a headset is recommended.Or, call in using your telephone.
  3. Dial +1 (805) 309-0010
  4. Access Code: 336-632-202
  5. Audio PIN: Shown after joining the meeting
  6. Meeting ID: 336-632-202

Registration:

Registration is free.
To register, email: biotools@bbn.com

Sponsors:

Bio-Design Automation Consortium
Raytheon BBN Technologies