Agenda
for Data Standards Meeting
 (pre-IWBDA meeting)

June
13,2010, 9am-6pm
Location:
Hilton meeting room Lido A

Attending:
   Chandran, Densmore, Dmytriv, Galdzicki, Ham,
Rodriquez, Peccoud, Sauro, Stan


Action Plans:
    1. RCN Proposal Deadline 18th
August. 

  
 http://www.nsf.gov/pubs/2010/nsf10566/nsf10566.htm

    2. Meeting Summary in Journal of Biological
Engineering

    3. Letter to Nature Biotechnology
    
Michal Galdzicki

1.
What I would like to get out of the meeting?
  • I hope
    to get a better understanding of the information sharing
    needs (use cases) in synthetic biology and how we can as a
    group respond to the needs.
2.
What I will talk about in two slides?
  • I will
    present SBOL semantic and how this exchange format can help
    mediate between different views of synthetic biology
    information.


Cesar
A. Rodriguez
1.
What I would like to get out of the meeting?

2.
What I will talk about in two slides?



Timothy
Ham
1.
What I would like to get out of the meeting?
  • Agreement
    on what should be included in the description of a part (not
    feature vs part debate, or format, but what specific
    information should be recorded)
  • How
    should part specifications (measurements and mathematical
    description) should be recorded

2.
What I will talk about in two slides?

  • Status
    of JBEIR


Zinovii
Dmytriv
1.
What I would like to get out of the meeting?

2.
What I will talk about in two slides?



Guy-Bart
Stan
1.
What I would like to get out of the meeting?
  • An
    overview of the envisioned data exchange standards and how
    these can directly be integrated in a unified Synthetic
    Biology CAD environment

2. 
What I
will talk about in two slides?
  • Our vision for
    data exchange standards: the SynBCOM information
    system

Douglas Densmore
1. What I would like to get out of the meeting?
  • Understand the
    current progress of all the efforts and what the current
    roadmap for the next year is.

2. What I will talk about in two slides?

  • Eugene/Spectacles/Clotho progress 

Herbert Sauro
1. What I would like to get out of the meeting?
  • Continued
    discussion on standards in synthetic biology.

2. What I will talk about in two slides?

Jean Peccoud
1. What I would like to get out of the meeting?
  • A funding plan
    to develop data exchange standards
  • Identify one or
    two other applications that could communicate with GenoCAD
    using available resources

2. What I will talk about in two slides?

  • Semantics of DNA
    sequences: can we reconcile ontology and grammars

Deepak Chandran
1. What I would like to get out of the meeting?
  • An overall
    picture of where we, as a group, are headed
  • Ideas on how
    I can make TinkerCell more useful in the
    community 

2. What I will talk about in two slides?

  • Current plans
    with TinkerCell and where I think it fits in the “big
    picture”


Others to keep updated:
Chris
Anderson

Drew Endy


Updates:

SBOL Semantic (Mike)

SBOL Visual (Cesar)

GenoCAD (Jean)

GD-ICE (Tim)

TinkerCell (Deepak)

Clotho (Doug) After 12pm
 
Emerging Topics:

features v parts? features and parts?

Case for a platform-independent data exchange standard: ie
implement this however you want, someone should write a
converter

Formally describe concrete use cases for an open and
platform-independent data exchange standard

Does SBOL build on the strengths of the Genbank format and
improve on the weaknesses?

The data exchange standards should be developed hand-in-hand
with real software tools 

how to go from a sequence centric design to a ‘modular’ then
to a ‘systems’ design?
 
Identifiers
Exchanging Data
Integrating Information
 
Parts, that are not parts: Segments of DNA sequence
independent of standards, independent of functional
connotation

Parts and DNA Sequence Features, can these concepts dance
together?
 
Lab data, how to represent experiments and the outcomes, not
just numbers; data have context

 
1. Use Cases

design the description, structural->sequence,qualitative
descriptions of interaction, functional dynamic
in silico dynamic simulation
in vivo validation by experiment

When I read a paper I want to be able to reuse the DNA
sequence or parts that the authors’ used:

To recreate a particular design, not a necessarily particular
behavior
Then to also make it work/ reproduce the results.

Tim related his experience of helping a outside group use his
inverter.
I want someone to be able to take a part from the BIOFAB
and its description so that the information can be moved into
a repository of their choosing.

An integrated environment to centralize the user’s
experience in design of parts, devices, and systems in such a
way that my tools can communicate between design,
simulation, storage
.

I want to be able to design a circuit and/or metabolic
pathway and get help in selecting parts and/or enzymes to
build the circuit.
I want to communicate a sequence based description from
one tool to another without using the GenBank
format. 
Why do we not want to use GenBank? can we
extend it?

What is the minimal information that you need to “reverse
engineer” the design of a system to know which part and
assciated parameter to modify based on a requirement based on
a system outcome / behavior. VERY HARD

A minimal experimental standard for the description for
synthetic  biology parts

The construct: DNA sequence
Strain particular genotype (ie lacI-), growth media

which Plasmid, genomic location

1.a. Part

Minimal Information Level 1 to create the device:

    Sequence (preferably annotated)

Minimal Information Level 2 to create and get the device to
operate:

    Sequence
    Growth Medium
    Temperature
    Strain
    Circuit Inputs, if any


MIBBI draft
define scope: 
enough to replicate a: 
A sequence (with some annotations?)

specify Strain, by convention

2. Funding Possibilities

    Research Coordination Network
(NSF) 
    Microsoft
    Google

    Life Technologies 

    Workshops, Meetings – companies

    Effort – NSF, NIH

    twice a year 2days

    Action Plan: RCN Proposal
Deadline 18th August. 
  
 http://www.nsf.gov/pubs/2010/nsf10566/nsf10566.htm

3. Software Tools

    Clotho
    Device Editor
    TinkerCell
    JBEIr2