SBOL Meetup San Francisco, CA, 2012



SBOL Meetup

Date: June 5th, 2012

Time: 9:00 am – 6:00 pm


Marriot Courtyard in Downtown San Francisco




JC Anderson, Swapnil Bhatia, Joanna Chen, Douglas Densmore,
Michal Galdzicki, Raik Gruenberg, Jennifer Hallinan, Nathan J.
Hillson, Cassie Huang, Allan Kuchinsky, Florencio Mazzoldi,
Ernst Oberortner, Sunny Park, Darren Platt, Matthew Pocock,
Cesar Rodriguez, Nicholas Roehner, Almer van der Sloot, Anil

Remote Attendees

Aaron Adler, Jacob Beal, Jeffrey Johnson, Chris Myers, Umesh P,
Hector Plahar, Mandy Wilson



  1. 9:00 am –  

    1. Presenter:  Ernst

      1. Organization of materials for the

      2. Present (and eventually edit) the Agenda


  1. 9:15 am –
    SBOL in

    [10 min. live demo + 5 min. discussion each]

    1. Demonstrations [Session Chair: Raik]

      1. Michal Galdzicki

        1. Converter for the iGEM Registry – Provide
          information from a parts registry in SBOL RDF/XML

        2. Distributed Repositories

          1. WikiDust and Magpie

      2. Nicholas Roehner

        1. SBOL and SBML

        2. Tool: iBioSim

      3. Jen

        1. Newcastle’s Parts Repository

      4. Matthew

        1. SBOL Stack

      5. Cesar

        1. Towards SBOL XML Compliance in a Commercial

        2. Tool:  Genome Compiler


  1. 10:15 am –


  1. 10:30 am –
    Sessions [10 min. presentation + 5 min. discussion

[Session Chair: Darren Platt]


  1. SBOL Serialization [Michal]

    1. Integrated XML and RDF combined

    2. Experience

  2. SBOL Visual [Aaron/Cesar]

    1. Quick Overview of the Temme paper

      1. Discuss pros and cons

      2. What’s next?

    2. Process for approving new and retiring old

  3. SBOL Modeling  [Nicholas / Neil]

    1. iBioSim / MoSeC

    2. Discuss: approaches to cross-annotating SBOL and SBML

  4. SBOL Performance [Nicholas / Neil]

    1. Need to discuss what performance information is

  5. SBOL Script [Cesar & Ernst]

    1. Needed syntax, vocabulary, and grammar

  6. New Extension Idea  [Michal]

    1. Tracking Sequence Verification Results

  7. Protein (& Chassis) Extension [Raik]

    1. Capture Amino Acid sequences and codon


  1. ~12:30 pm –


  1. 1:00 pm –

    [Session Facilitator: Cesar]

    1. Discussion driven mainly by imagination and a lot less by
      technical details

    2. Suggested

      Topics – Emphasis on Suggested

      1. How do we gather and respond to experimental
        synthetic biologist’s needs and

      2. How do we stimulate more industry uptake?

      3. SBOL sequence publication guidelines for

      4. CAD fetching DNA components from a

        1. Specific Instances

          1. Clotho fetching parts from the iGEM

          2. Gene Designer fetching parts from the

          3. Genome Compiler providing fetched parts from
            the iGEM Registry

        2. What’s next?

      5. Sending a genetic design to a wetware construction

      6. Specifying genetic designs simultaneously with
        graphical and textual languages

        1. Specific Instance

          1. Clotho Spectacles and Eugene

        2. What’s next?

      7. Connecting a genetic design editor with a
        simulation framework

        1. Specific Instances

          1. TinkerCell

          2. iBioSim

        2. What’s next?


  1. 2:30pm –

    Workflows to define case studies

    [Session Facilitator: Doug]

    1. Currently, we have one nice workflow of how SBOL members
      exchange SBOL files (i.e. Utah, Newcastle, BU).  We
      should discuss about other possible examples/workflows of
      exchanging SBOL files


  1. 3:00 pm –

    [Session Chair: Anil Wipat]

    1. SBOL entering maintenance phase

      1. Steady funding is needed

      2. Acknowledgement of sponsorship on the

    2. What is the relationship with DARPA?

    3. Potential Grant targets

      1. NIST, NIH, and DOE

      2. What is the best approach for each?

    4. Should we consider Kickstarter-type funding?


  1. 4:00 pm –
    Publications /


  1. 4:30 pm –

    [Session Chair: Mike]

    1. SBOL Values

    2. Looking for a new editor to replace Cesar after he
      completes his term


  1. 5:30 pm –
    Meeting at
    Imperial College

    1. What should be the goal of the next meeting?


  1. Dinner

    1. Organized during meeting

    2. Pay individually

Meeting Notes:


Doug: how do we let people put their own flavor on SBOLv while
being compliant.

Chris A: there is an established iconography for genetics/
molec bio ~50 yrs of history. There is an established

Anil: But, there is no “standard” .

Chris A: ~The technical issues need to be fixed.

Modeling Extension

Nic: proposed a SBML annotation and then package to embed SBOL
into SBML.

Raik: proposed a diagram showing connections between


Doug more centralized, workshop grants, but work should be

Education and promotion:

Doug:  Establish an SBOL YouTube channel to place


Allan:  It would be useful to have SBOL as [part of] a
formal non-profit organization.  It would facilitate
gathering donations from corporate entities.

Doug: Problem with using Kickstarter for fundraising is that
large corporate entities are unlikely to use this approach.
Allan agreed.

Layout goals and tangible 3 month or so long SBOL projects.
Keep a list for professors to use for interested

Doug: We need to secure a sizable amount of funding to afford
professional software developers.  Inconsistent, small
amounts won’t get the job done.


Michal:  The SBOL paper is being targeted as a Nature
Biotechnology Perspective.

General preference for higher impact papers.

Compliance/ Acknowledgement:

Doug: Provide award stickers to iGEM students if there tools
are SBOL compliant.  Provide compliance icons

Matthew: Possible compliance icons.  The promoter symbol
for SBOL Visual.  Arrow pointing out for export.
Arrow pointing in for import.

-proposed design due at next meeting, if only 1 proposal accept
at next meeting by default otherwise vote to

Raik: Establish demonstrations at scientific and trade


SBOL Core Values:

  • Useful

    • Does what is needed, doesn’t get in the way


  • Useable

    • TBD

      • Who is envisioned as the eventual user? different
        cultures, backgrounds of training

      • Added value for the user

      • Community should be the users

    • Educational /feedback forum at a synbio conf

  • Used

    • Becomes the de-facto standard for data exchange in
      Synthetic Biology and Genetic Engineering

      • Maybe this should be higher on the order of

  • Agile

    • Changes to reflect the changing needs of the

  • Free

    • Beer and Speech

  • Transparent and Accountable Governance

  • For the Community by the Community

    • Diversity of the community

      • participation by underrepresented

      • Welcoming and inclusive of all

      • and industry and academia, non-profit

    • Recognizing that diversity is a strength


  • capture the next generation of thinkers

    • iGEM

Next meeting:

Workflows will be due at ICL meeting

precanned presentations on extensions

start discussion on mailing list prior to meeting

Needed for next workshop:

Mnady: If providing Remote Access to meeting get

Spreed USB Conference Speaker Microphone