The SBOL Developers community meets approximately every 6 months. The discussion at these workshops is often convivial, collegiate, and interesting. In May 2014 the SBOL Developers group elected to co-locate future SBOL workshops with similar workshops hosted by the “Computational Modeling in Biology” Network (COMBINE). This creates an atmosphere where synthetic biologists and systems biologists can work toward a common goal of integrating biological knowledge through inter-operable and non-overlapping data standards. Our “COMBINE”d efforts empower exciting innovations like modeling whole cells.

We welcome participants from industry to these discussions, as the SBOL standard exists to support commercial as well as scientific innovation in synthetic biology and biotechnology.

EventsDate (YYYY/DD/MM)LocationPresenter(s)
COMBINE 20162016/19-24/09Newcastle University in Newcastle Upon Tyne, UK
Chris Myers: A Standard Enabled Workflow for Synthetic Biology
Robert Sidney Cox: The Visual Protein Design Language
Jacob Beal: Progress Report on Development of SBOL Visual 2.0
Anil Wipat: Overview of SBOL
James Alastair McLaughlin: sboljs: SBOL on the Web
Chris J. Myers: The Synthetic Biology Open Language (SBOL) Data Model
Bryan Bartley: libSBOL & pySBOL
Zhen Zhang: libSBOLj 2.0: A Java Library to Support SBOL 2.0
Anil Wipat: Introduction to SBOL Visual
Meher Samineni: CRISPR Tutorial
SBOL 142016/14-16/03Raytheon BBN Technologies in Boston, MA, USA
All Presenters: Program Document
COMBINE 20152015/12-16/10University of Utah in Salt Lake City, UT, USA
Anil Wipat: The Synthetic Biology Open Language (SBOL) - recent developments in SBOL tools and repositories
Anil Wipat: SBOL
Nicholas Roehner: Multiplicity of Representation in SBOL 2.0
Zhen Zhang: libSBOLj 2.0: A Java Library to Support SBOL 2.0
Tramy Nguyen: A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language
Jacob Beal: SBOL visual: introduction, recent developments, and current challenges
James Alastair McLaughlin: VisBOL: Web-based tooling for synthetic biology design visualization
Chris Myers: SBOL Infrastructure Discussion
Zach Zundel: Analysis of Weaknesses in SBOL/SBML Modeling through Creation of Use Cases
HARMONY 20152015/20/03Wittenberg, Germany, EU
Curtis Madsen: SBOL Stack: The One-stop-shop to Storing and Publishing SBOL Data
Tramy Nguyen: Synthetic Biology Open Language (SBOL) 2.0
COMBINE 20142014/18-22/08University of Southern California in Los Angeles, CA, USA
Herbert Sauro: Developing Standards in Synthetic Biology: the needs for a broad new engineering discipline
Jackie Quinn: Synthetic Biology Open Language Visual: graphical notation for forward engineering of biology
Jackie Quinn: SBOL Visual 2.0
Nicholas Roehner: Generating SBML models from SBOL
Nicholas Roehner: SBOL 2.0 Hierarchical Composition
Kevin Clancy: Vector NTI Express Designer as a demonstration of SBOL interoperability with COMBINE standards
Curtis Madsen: SBOL Stack: The One-stop-shop to Storing and Publishing SBOL Data
SBOL 102014//07-09/01UC Berkeley, CA, USA
Jackie Quinn: Brief Intro to SBOL and the Workshop
Matthew Pocock: Taking Stock, Code base tour
Ernst Oberortner: libSBOLj in Eugene + mapping
Nicholas Roehner: Using SBOL as a Genetic Data Model
Kevin: Lessons learned of NOT using libSBOLj
Ernst Oberortner: (mini)Eugene
Kevin Clancy: Vector NTI Express Designer
Nathan Hillson: TeselaGen and ICE + SBOL Visual and XML
Nicholas Roehner and Chris Myers: SBOL 2.0: Vision
Matthew Pocock and Goksel Misirli: Serialization (RDF Pickling)
Goksel Misirli: libSBOLj in Virtual Parts
Goksel Misirli: Exchanging synthetic biology data using SBOL and the Systems extension: A use case from the Flowers infrastructure
SBOL 92013/24-26/04Newcastle University in Newcastle, UK
Michal Galdzicki, Bryan Bartley: Host Context
Ryan, Jackie, Robert, Mike, Larisa, Bryan Bartley: Case Studies
Michal Galdzicki, Bryan Bartley, Evren Sirin, Nikhil Gopal, John Gennari: Demo of Version Control using the “SBOL Designer”
Raik Grünberg: Protein Parts in SBOL
Chris Myers, Nicholas Roehner: SBOL Modeling Extension
Ernst Oberortner, Matthew Pocock, Nicholas Roehner: SBOL Regulatory Interactions
Nicholas Roehner: Directed Acyclic Graph-Based Technology Mapping of Genetic Circuits
Goksel Misirli: Representing Biological Systems for the Flowers Consortium
Jacob Beal: SBOL in Action: The BBN BioCompiler
Ernst Oberortner, Michal Galdzicki: SBOL Compliance Working Group
Ernst Oberortner: SBOL Script
Larisa Soldatova: Towards an ontology for Synthetic Biology
SBOL 82012/07-08/11Boston University in Boston, MA, USA
Aaron Adler and Fusun Yaman: Synthetic Biology Tools from BBN
Michal Galdzicki and Bryan Bartley: Host Context
Matthew Pocock: Minimal Information
Nicholas Roehner: A Methodology to Annotate Systems Biology Markup Language (SBML) Models with the Synthetic Biology Open Language (SBOL)
Mandy Wilson: SBOL Extensions
Michal Galdzicki: I’m going to talk about SBOL Values
Jackie Quinn and Cesar Rodriguez: SBOL Visual
Jackie Quinn and Ernst Oberortner: SBOL in Action “Wetware Studio + Eugene”
Douglas Densmore: SBOL Compliance
Ernst Oberortner: SBOL Core
Michal Galdzicki: Using the Sequence Ontology
Michal Galdzicki: 3 Use Cases for SBOL
SBOL 72012/05/06Marriot Courtyard in San Francisco, CA, USA
Nicholas Roehner: Connecting SBML to SBOL via RDF/XML Annotation
Goksel Misirli, Matthew Pocock, J. Hallinan & Anil Wipat: A Repository of Standard Virtual Parts for Bacillus subtilis
Anil Wipat: Compiling a model to a Genbank file
Matthew Pocock: Newcastle SBOL Stack: A Service to the Community
Raik Grünberg: Protein Parts in SBOL
Ernst Oberortner, Cesar Rodriguez: SBOL Script
Michal Galdzicki: Serialization and use of SBOL
Michal Galdzicki: Tracking Sequence Verification Results

SBOL 62012/05-06/01Univeristy of Washington in Seattle, WA, USA
Herbert and Mike: Organization of materials for the workshop
Deepak Chandran: TinkerCell
Mandy Wilson: GenoCAD/SBOL Visual Implementation
Nathan: Device Editor
Alan and Marc: Gene Designer acquiring BIOFAB part design and performance from the Data Access Web Service
Chris Myers and Nicholas Roehner: iBioSim
Neil and Matthew Pocock: Neil’s Group Software System
Doug Densmore and Cassie: Clotho, Hermes Tool
Drew: Statement of community values of what is expected of SBOL Developers and Editors
Herbert Sauro and Cesar Rodriquez: SBOL Governance
Mike: Host Context
Jake and Sridhar: Connection between Clotho and a DNA Component Repository
Matthew Pocock: OBI Standard
Darren: Amyris Experience
Chris Myers and Deepak Chandran: Modelling
Trevor: libSBOLxml
Mike: RDF
Eduardo: JSON
Cesar Rodriquez: SBOL Visual
Doug Densmore: Assembly
Cesar Rodriquez: Controlled English for Genetic Design Specification
Nathan J. Hillson: DeviceEditor: implications for SBOL
Chris Myers: SBOL Serialization
Michal Galdzicki, Raik Gruenberg, Herbert Sauro, Allan Kuchinsky, Anil Wipat: Host Context
SBOL 52011/08/06The Omni Hotel in San Diego, CA, USA
All Presenters: Program Document
SBOL 42011/07/01The Inn at Virginia Tech in Blacksburg, VA, USA
Michal Galdzicki: SBPkb & libSBOL
Cesar A. Rodriguez: SBOL visual
Cesar A. Rodriguez: BIOFAB Data Access Web Client and Service
Guy-Bart Stan: BIOFAB UK-US “Bit-to-Atom-to-Bit” Exchange
Douglas Densmore: BioCompiler
Mandy Wilson: GenoCAD
Deepak Chandran: TinkerCell
Cesar A. Rodriguez: OpenSequenceAssembler
Chris Myers: iBioSim
Barry Moore: The Sequence Ontology
Jean Peccoud: Knowledge representation frameworks: ontologies and grammars
SBOL 32010/13/06Hilton Anaheim in Anaheim, CA, USA
All Presenters: Program Document
SBOL 22009/26/07Stanford University in Stanford, CA, USA
Vincent Rouilly: Existing DNA sequence standards + their associated tools (database / analysis)
Vincent Rouilly: Description of the current Minimum Information Required effort
Raik Grünberg: Relevant technologies — RDF
Cesar Rodriguez: Relevant Technologies: Unified Modeling Language (UML)
Michal Galdzicki: Update on PoBoL
Raik Grünberg: RFC 30 — data exchange architecture
Douglas or Cesar: Update on BioBrick Open Language (BOL)
Cesar Rodriguez: Synthetic Biology Data Transfer Process (SB/DTP) and Standard Biological Part Web Service
SBOL 12008/27/04University of Washington in WA, USA
All Presenters: Program Document