Two Weeks Until COMBINE/SBOL 11

posted Aug 4, 2014, 12:45 PM by Nicholas Roehner

We hope you'll join us for SBOL 11! This summer's workshop will be held Aug. 18-22 at USC as part of the 2014 COMBINE meeting. Registration and other details are on the COMBINE 2014 website and a schedule is linked from the SBOL meetings page.

SBOL 10 Starts Tomorrow!

posted Jan 6, 2014, 11:48 AM by Jackie Quinn   [ updated Jan 8, 2014, 1:28 PM by Herbert Sauro ]

We hope you're excited for the start of SBOL Workshop 10 tomorrow!

The workshop will start at 8:30 on Tuesday, Jan 7 in the Hearst Memorial Mining Building, room 290. A map of the points of interest relevant to the workshop can be found here.

The workshop agenda can be found hereIf you are connecting remotely, connection information can be found at the bottom of the agenda here.

List of attendees

Looking forward to seeing you all in Berkeley!

RSVP for SBOL 10 @ UC Berkeley, Jan 7-9, 2014

posted Dec 11, 2013, 10:39 AM by Jackie Quinn   [ updated Dec 11, 2013, 10:41 AM ]

SBOL Workshop 10 will be held Jan 7-9, 2014 at UC Berkeley. 

Please RSVP below. If you are interested in speaking on your project and how it relates to SBOL, please indicate your interest.


Call for Scholarship Applications

posted Oct 25, 2013, 3:51 PM by Jackie Quinn   [ updated Oct 31, 2013, 10:19 AM by Jackie Quinn ]

Travel scholarships will be available to students and post-docs who need funding assistance to travel to SBOL 10 at UC Berkeley Jan 7-9, 2014. Scholarships will be administered by the Bio-Design Automation Consortium. See attached file for the full scholarship description. 

To apply, submit the following to
  •  Your name and email address
  •  Your school and year of study (e.g., junior, 2nd year graduate student)
  • A brief summary of your scientific research and work experience
  • Your expected travel expenses
  • A short statement detailing why you seek support and how you plan to participate in the workshop and the SBOL effort.
Scholarship applications will be evaluated on a rolling basis starting November 8th. Questions can be directed to

10th SBOL Workshop: Jan 7-9, 2014 @ UC Berkeley

posted Oct 25, 2013, 2:06 PM by Jackie Quinn   [ updated Oct 31, 2013, 10:19 AM by Jackie Quinn ]

The 10th SBOL Workshop will take place at UC Berkeley on January 7-9, 2014. Info can be found here.

Looking forward to seeing you in January!

9th SBOL Workshop - Apr 24-26th, 2013 - Newcastle, UK

posted Mar 21, 2013, 10:26 AM by Ernst Oberortner   [ updated May 30, 2013, 11:33 AM ]

The SBOL community will held their 9th workshop from Apr 24th - 26th, 2012 at Newcastle University, Newcastle, UK. Further information is provided here.

If you are planning attending the Workshop, then please register here.

SBOL9 - Newcastle, UK - Apr'13

Sticker Competition

posted Feb 22, 2013, 9:26 AM by Ernst Oberortner   [ updated Jul 18, 2013, 11:16 AM by Nicholas Roehner ]

There is a possibility that one or more journals in the future will consider accepting SBOL files as part of manuscript submissions. In order to highlight authors who do submit SBOL information, it has been suggested that such papers be given some form of recognition through the use of SBOL compliance badges. It has been proposed to design two badges initially, these include:

1. “SBOL Standard” compliant which would mean that the design is available in SBOL format in a public repository.

2. "SBOL Visual" compliant which would mean that designs in the paper are depicted using SBOL Visual.

We would like to issue a competition to anyone who might wish to come up with the design for two badges that would correspond to the above categories. A $50 Amazon online gift card will be awarded to the winner, plus a free copy of the book "Enzyme Kinetics for Systems Biologists", 2nd Edition. Runner ups will be awarded honorable mentions. 

Submission of the compliance badges should preferably be in a vector format such as eps, AI, PDF or SVG. Competitors can submit badges in png format if this is unavoidable. An example of a set of icons but from a different domain, can be seen here 

The deadline for submitting the icons will be the 2nd April, 2013. The winner will be decided by an SBOL community vote by the end of April 2013. Anyone is welcome to submit icons for the prize!

Please send your stickers to the SBOL Editors.

SBOL Workshop, November 7-8, 2012 @ BU

posted Oct 4, 2012, 6:02 AM by Mandy Wilson   [ updated Nov 16, 2012, 10:39 AM by Ernst Oberortner ]

For the latest details on this upcoming Workshop, please check out the SBOL Workshop 8: November 7-8, 2012, Boston University webpage.


SBOL Meetup @ IWBDA'12

posted Jun 7, 2012, 6:30 AM by Ernst Oberortner   [ updated Jun 13, 2012, 11:59 AM ]

Location: Marriott Courtyard Hotel, San Francisco, CA
Date: June 5th, 2012

The major outcomes are:
- Discussion on the relationship between SBOL and SBML for the SBOL Modeling extension
- Tendency to a "centralized" development team for libSBOL
- The brainstorming sessions emphasized the need for maintaining and then stimulating more industry involvement

JC Anderson (University of California, Berkeley)
Allan Kuchinsky (Agilent Technologies)
Darren Platt (Amyris Biotechnologies)
Swapnil Bhatia (Boston University)
Joanna Chen (Joint BioEnergy Institute)
Douglas Densmore (Boston University)
Cassie Huang (Boston University)
Ernst Oberortner (Boston University)
Cesar Rodriguez (Genome Compiler)
Raik Grünberg (University of Montreal)
Anil Wipat (Newcastle University)
Matthew Pocock (Newcastle University)
Nicholas Roehner (University of Utah)
Michal Galdzicki (University of Washington)
Jennifer Hallinan (Newcastle University)
Nathan J. Hillson (Joint BioEnergy Institute)
Florencio Mazzoldi (Autodesk)
Sunny Park (Newcastle University)
Almer van der Sloot (University of Montreal) 

Remote Attendees:
Mandy Wilson (Virginia Bioinformatics Institute)
Aaron Adler (BBN)
Jacob Beal (BBN)
Jeffrey Johnson (University of Washington)
Chris Myers (University of Utah)
Umesh P. (University of Kerala)
Hector Plahar (Joint BioEnergy Institute)

SBOL Meetup @ IWBDA - June 5th, 2012

SBOL Developers meet for 6th SBOL Workshop

posted Jan 14, 2012, 8:12 PM by Michal Galdzicki   [ updated Feb 22, 2012, 12:30 PM by Ernst Oberortner ]

January 5-6, 2012
University of Washington
Seattle, WA

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

Deadlines agreed to:
- Specification revisions due Friday
- Java library and XSD due in 1 month
- Call for SBOL v1.1.0 ratification vote - Mon 1/30/2012 following release of final pdf on 1/27/12

Thirty-three SBOL developers met at the University of Washington, Seattle to discuss the development of SBOL extensions. The workshop was attended by U.S. and U.K. academic researchers as well as industry representatives.

Allan Kuchinsky (Agilent Technologies) Cesar Rodriguez (Genome Compiler) Chris Myers (University of Utah)
Darren Platt (Amyris Biotechnologies) Jackie Quinn (Harvard University) Nicholas Roehner (University of Utah)
Carlos Olguin (Autodesk) Guy-Bart Stan (Imperial College London) Daniel Cook (University of Washington)
Jake Beal (BBN Technologies) Richard Kitney (Imperial College London) Deepak Chandran (University of Washington)
Marc Juul Christoffersen (BIOFAB) Raik Grünberg (University of Montreal) Jeff Johnson (University of Washington)
Cassie Huang (Boston University) Yizhi (Patrick) Cai (Johns Hopkins) John Gennari (University of Washington)
Doug Densmore (Boston University) Sridhar Ranganathan (Life Technologies) Kyung Kim (University of Washington)
Ernst Oberortner (Boston University) Anil Wipat (Newcastle University) Wilbert Copeland (University of Washington)
Swapnil Bhatia (Boston University) Goksel Misirli (Newcastle University) Michal Galdzicki (University of Washington)
Evren Sirin (Clark & Parsia) Matthew Pocock (Newcastle University) Herbert Sauro (University of Washington)
Alan Villalobos (DNA2.0) Drew Endy (Stanford University & BIOFAB) Mandy Wilson (Virginia Bioinformatics Institute)

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