Sponsored by: Autodesk, Department of Bioengineering, Biomedical and Health Informatics, UW and Boston University


January 5-6, 2012


Location: Foege Building, University of Washington, Seattle,
WA


Time: 8:30 am – 6:00 pm


Contacts:

Herbert M Sauro: hsauro@u.washington.edu
Michal Galdzicki mgaldzic@uw.edu

Sponsored
by:

Autodesk, Department of Bioengineering, Biomedical and Health
Informatics, UW and Boston University

Location

The 6th SBOL Workshop will take place in William
H. Foege building
 which hosts the Bioengineering and
genome sciences departments. We have reserved a number of
rooms for the 2 day event, including the main seminar room on
the ground floor of the lobby of the Bioengineering
department and a number of smaller rooms for breakout
sessions. The physical address 

UW Department of Bioengineering
N107 William H. Foege Building
1705 NE Pacific Street
Seattle, WA 98195-5061

About
the University of Washington

The University of Washington (UW, and commonly called
“U-Dub”) was founded in 1861. It is one of the oldest
universities on the west coast of the United States. Its main
campus is in Seattle.

The map below shows the location
of coffee/Tea and Lunch/Dinner locations:

Yellow circles mark UW sites. Filled red marks are
non-UW sites. The lower filled mark is a very good Mexican
restaurant that also serves coffee at an open hatch. The
upper filled mark points to the University Avenue where there
are a wide range of food
locations. 


Accommodation

A block of rooms has been reserved at the University Inn
under the group name SBOL Workshop. These room cost $126
dollars per night (this includes all taxes)

University
Inn

4140 Roosevelt Way NE
Seattle, WA 98105
(206) 632-5055 

The map below shows the hotel in relation to the Department
of Bioengineering

Transport

Directions from SeaTac Airport to the University
District

There are three ways to get to the University district:

  • By Taxi ( for about $45-$50 + tip )
  • By Shuttle ( for $19 (if registered) +tip )
  • By Public Transport ( for $2-$2.50 )

For the shuttle you may either book online with Shuttle
Express or call them at 425-981-7000.

Public transport can include a bus or more recently light
rail. The light rail is quite frequent and takes about 40
mins to get to downtown Seattle. You want to stay aboard
until the end (which is Westlake Center in the Seattle
downtown Tunnel). 

Once you arrive at Westlake Center, just get out of the
Train and simply walk to the front, where you can take any of
the buses 71, 72, 73 and 74. The thing to keep in mind is
that you want to take the express buses. (Express buses take
the freeway for part of the way and its exit is closest to
the two hotels).

You will need to pay the fare when you leave the bus at
the destination (if the driver does not accept the ticket you
got from the machine before). They only accept exact fare,
which has to be fiddled into the machine next to the
driver.

The express bus will take the I-5 (the freeway) and once
you get onto the bridge, you will see the university district
on your left. The copper coloured building is the
William-Foege Building where the workshop will be
held. 

Once you are on the bridge you want to signal the driver,
that you want to get out at the next stop, by pulling a cord
on the left and right of the bus cabin. The driver should
know where the University Inn is, the hotel itself is located
at the corner of Roosevelt Way and 42rd Street. Once the bus
stops you will have to go to the front of the bus, show them
your ticket, and if he is not happy with that pay the fare of
$2.




Workshop Goals:



  1. Review Use Cases


  2. Review SBOL 1.0 Deployments


  3. Define SBOL Compliance



    1. Strategies for Development of Test Cases


    2. How to use SBOL?


  4. Develop Guidelines for SBOL Extensions


  5. Identify and Form Data Exchange Partnerships


  6. Identify New Use Cases and Requirements for SBOL Version
    2.0


Schedule:


Please click here to view the workshop
agenda

Goals:

  1. Review Use Cases
  2. Review SBOL 1.0 Deployments
  3. Define SBOL Compliance
    1. Strategies for Development of Test Cases
    2. How to use SBOL?
  4. Develop Guidelines for SBOL Extensions
  5. Identify and Form Data Exchange Partnerships
  6. Identify New Use Cases and Requirements for SBOL Version 2.0

Schedule:

The main workshop room is N130 (bottom floor) all session are held there unless specified otherwise.
Unconfirmed Presenters are in square brackets [Name]
First Day

  1. 8:30 am – Welcome
    1. Presenter:  Herbert and Mike
      1. Organization of materials for the workshop
        1. Use the SBOL 2.0 Use Cases & Requirements document for ideas that come up during the workshop http://v2.sbols.org)
  2. 8:45 am – SBOL in Action
    1. Guidelines
      1. Moderator: Mike
      2. 5 min. live demo + 5 min discussion each
    2. Demonstrations
      1. Use Case: Design specification with SBOL Visual
        1. TinkerCell
          1. Presenter: Deepak
        2. GenoCAD
          1. Presenter: Mandy
        3. Device Editor
          1. Presenter: Nathan via Pre-recorded Screencast
      2. Use Case: BioCAD retrieves part information from a BIOFAB
        1. Gene Designer acquiring BIOFAB part design and performance from the Data Access Web Service
          1. Presenter: Alan and Marc
      3. Use Case: Pending
        1. iBioSim
          1. Presenter: Chris, Nic
      4. Use Case: Pending
        1. Neil’s Group Software System (name pending)
          1. Neil and Matthew
      5. Use Case: BioCAD reads and writes an SBOL 1.0 file
        1. Clotho, Hermes Tool
          1. Presenters: Doug and Cassie
  3. 10:00 am – Break
  4. 10:30 am – SBOL Community
    1. Statement of community values of what is expected of SBOL Developers and Editors
      1. Discussion Facilitator:  Drew
    2. SBOL Governance
      1. Discussion Facilitator: Herbert
      2. Chairperson
        1. Discussion Facilitator: Cesar
  5. 12:00 pm – Lunch
  6. 1:30 pm – Extensions Breakout Sessions
    1. Guidelines
      1. Elect a presenter for the next day, potentially the Extension Lead
      2. Prepare slides as notes to present to the group in the “Results from Breakout Sessions” session
    2. Breakout Session A in Room N503
      1. 1:30 pm – Host Context
        1. Discussion Facilitator: Mike
      2. 3:00 pm – Performance
        1. Discussion Facilitators: Cesar, Sridhar
        2. Connection between Clotho and a DNA Component Repository
          1. Discussion Facilitators: Jake and Sridhar
      3. 4:30 pm – Experiment
        1. OBI Standard
          1. Presenter: Matthew
        2. Amyris Experience
          1. Presenter: Darren
    3. Breakout Session B in Rm. N303
      1. 1:30 pm – Modelling
        1. Discussion Facilitators: Chris and Deepak
      2. 3:00 pm – XML/RDF/JSON serializations
        1. libSBOLxml Presenter: [Trevor]
        2. RDF Presenter: Mike
        3. JSON Presenter: [Eduardo]
    4. Breakout Session C in Rm N230
      1. 1:30 pm – Visual
        1. Discussion Facilitator: Cesar
      2. 3:00 pm – Assembly
        1. Discussion Facilitator: Doug
      3. 4:30 pm – Script: Controlled English for Genetic Design Specification
        1. Discussion Facilitator: Cesar
  7. 6:10 pm – Dinner

 

Second Day (Room N130)

  1. 8:30 am – IdeaStudio by Autodesk
    1. Presenter: Deepak
  2. 9:00 am – SBOL and DICOM SB
    1. How do we work together?
    2. Presenters: Richard and Guy
  3. 10:00 am – Results from Breakout Sessions
    1. Facilitator: Mandy
    2. Guidelines
      1. For each Breakout Session 1 person presents
      2. Slides as notes from the previous day’s discussion
    3. Discussion
    4. Ratifying Extensions
      1. Develop a set of guidelines for the first iteration
      2. Evaluate the guidelines at the next SBOL Workshop
  4. 12:00 pm – Lunch
  5. 1:00 pm –  SBOL Compliance
    1. Facilitators: Mandy, Mike, and Cesar
  6. 3:00 pm – SBOL Core Finalization
    1. Strand Issue/Orientation Semantics
      1. Discussion Facilitators: Matthew and Darren
  7. 6pm – Dinner

Meeting Notes:
SBOL in Action
SBOL visual
Deepak: SBOLv: remove the line, Jake: move the horizontal zero line to bottom of symbol. Darren: suggested that the SBOLvisual to SBOLsemantic connection should be strict, where the meaning of the symbol is well defined, to reduce/ remove ambiguity.

Mandy: The current version is a reduced, some symbols are not present.
GenoCAD
Mandy suggests an SBOL Grammar. Deepak: a rule that says 5’UTR comes before a CDS and after a promoter. Jake pointed out that this is true in some organisms

DeviceEditor (screencast)
Nathan: a generic symbol is used and needed. Icon selection process is not standardized. The
Desired is the stable XML serialization. DNA template context is not preserved .

GeneDesigner
Cesar: pulls BIOFAB data
Darren: suggests an optional (owa) type approach to the serialization.

iBioSim
Nic: needs the model extension (ie parameters) to automate the process.

Unnamed tool
Neil; Goksel using RDF for integration

SBOL community – Facilitated by Drew

0. Why
-big deal
– scaling
– you wont know everybody
1. values
eg What does open mean
(open to anything)
(open to everyone)

2. expectations
– of developers
– of editors
– of users
(eg a company that releases a software tool that exports a closed format “SBOL”)
———————————————-
3. mechanics
– copyright
– trademark
– partner organizations

Present our values to other in a form that those
Make our values explicit, as the SBOL standard scales up we wont be able to personally communicate
Open
– open development
– open access (Documentation & Source )
Principles
– enabling
– no taxation on its use.
Licenses
– GPL (hard give back)
-LGPL (librayr+core)

Best Case Scenario
– software company perspective (keep it open, but dont constrain to the give back)
– not slow/ hindered by core model
– Provide enough expressiveness in the core to allow the “users” of it not to have to change it
– standards are about commerce/ exchange of goods. Now companies in syntheticbiology/ metabolic engineering lives in a closed world. They produce hydrocarbons, that’s their output. They can benefit from doing so, using SBOL.
. Enforcement, certification, compliant.
– practically useful

We do not have a statement that it is free ($) and what open is.

Raik:Not just the standard, but also the data. Sharing the designs themselves. Â
Matthew: Should we constrain use? eg Dangerous things? Restrictions on how you use it? Drew: there are normative values. Jake/Drew: a statement of values is needed!

Drew: Send a synthesis request to a company, a web of registries.
Doug: common vocabulary, to facilitate communication
Swapmil: document provenance extension could help.
Jake: expectation for developers, volunteer time, expected.
Daren: SBOL needs to be contagious, it needs to attract people.

Darren and Matthew presented their challenge to strand orientation. Darren asks about Gal1 yeast promoter. Matthew about the example he gave on the list (dual direction promoter)

SBOL Chairperson
Consensus is to have a chairperson.

SBOL Ratification
Darren Platt and Matthew Pocock presented a case that reveals ambiguity in strand orientation.  Cesar will follow-up with Darren and Matthew to collect concrete use cases.  The use cases will be reviewed by the Editors.

Discussion on cases
re: Circular
– Not included because a component can be circular in one use, and not circular in another use. eg a subComponent can never be circular
Partially Realized Design Template example:

*Outcomes of the 6th SBOL Workshop, Seattle 2012*
– Demonstrated successful exchange of SBOL v1.0.0 data using libSBOLxml
– Received feedback on use of SBOL visual
– Needed is a statement of values of SBOL community
– Recommended a single serialization
– Nominated 2 additional SBOL editors, for 5 editors total
– Elected Herbert Sauro as chair of SBOL
– Recommended to establish extension working groups
– Established centralized test case management (coordinated by Matthew)

*Deadlines agreed to: *
– Specification revisions due Friday 1/13/2012
– Java library and XSD due in 1 month (Evren)
– Call for SBOL v1.1.0 ratification vote – Mon 1/16/2012 following release of final pdf on 1/13/12