Newcastle SBOL Workshop

24th – 26th April 2013, Newcastle University


The event will start 09.00 on Wednesday 24th and finish 17.00 Friday 26th April.

The event will be hosted by the School of Computing Science, The Newcastle Centre for Synthetic Biology and Bioexploitation and held at the Centre for Bacterial Cell Biology.

There will also be a joint seminar, titled “Standards, Networks and Evolution” by Dr. Herbert Sauro and Dr. Chris Myers on Tuesday, 23th April 2013 starting at 15:15. Click here for more details about this seminar. Please be aware that the location of this seminar has been changed to School of Computing Science, Room 701, Claremont Tower.

A copy of the agenda can also be accessed from Google Docs. Please feel free to add notes from the talks.


Click here for the PDF version of the programme.

Day 1 – Wednesday, 24th April – The State of SBOL

Location: Ground floor lecture theatre, Centre for Bacterial Cell Biology, Baddiley-Clark building.

9:00     Meet, greet & tea
9:30     Welcome and Introductions, Anil Wipat
9:35     Introduction to the workshop, Herbert Sauro
9:40     Matthew’s State of the SBOL Union Address, Matthew Pocock
10:00   SBOL in Action and Related Work [10 min Talk + 5 min Questions]
CHAIR: Matthew Pocock

    • Jake Beal – BioCompiler
    • Larisa Soldotova

10:30   Coffee Break
10:45   [Continue] SBOL in Action and Related Work [10 min Talk + 5 min Questions]
CHAIR: Matthew Pocock

    • Evan Appleton
    • Michal Galdzicki – SBOL Designer demo
    • Nicholas Roehner – Genetic Technology Mapping with SBOL in iBioSim
    • Goksel Misirli
    • Robert Cox
    • Kirtan Dave

12:00   Lunch
13:00   Working Group Updates & Rechartering [20 min – 10 talk, 5 discuss, 5 vote]
CHAIR: Goksel Misirli

    • Devices – Raik Grünberg (5 min, remote talk)
    • Modeling – Chris Myers
    • Visual – Jackie Quinn
    • Performance (characterisation) – Matthew Pocock
    • Regulatory – Ernst Oberortner, Matthew Pocock, Nicholas Roehner
    • Assembly – Ernst Oberortner

14:30   Coffee Break
14:45   [Continue] Working Group Updates & Rechartering [20 min – 10 talk, 5 discuss, 5 vote]
CHAIR: Goksel Misirli

    • Script – Ernst Oberortner
    • Compliance – Ernst Oberortner, Michal Galdzicki
    • Attribution – Michal Galdzicki
    • Host Context – Michal Galdzicki, Bryan Bartley (arriving 3pm)
    • Vector Express Designer (10 min)

16:00   Governance

17:00   Wrap up
19:00   Meal at the Marco Pierre White Steakhouse Bar & Grill
Address: 2-8 Fenkle Street, Newcastle upon Tyne, NE 1 5XN

Day 2 – Thursday, 25th April – Breakouts and Excursion

Location: Ground floor lecture theatre, Centre for Bacterial Cell Biology, Baddiley-Clark building.
8:30     Tea
9:00     Plan Breakout Sessions (make progress on specific tasks in small groups)
CHAIR: Chris Myers
Potential Topics:

    • SBOL Visual – Jackie Quinn
    • libSBOLj Hacking
    • Extension Method
    • IWBDA Abstracts
    • Technical Training (tutorials on Maven, GitHub)
    • Increasing Adoption
    • SBOL Primer – Jackie Quinn
    • Regulatory Elements – Robert Cox
    • SBOL Compliance – Michal Galdzicki
    • TBD – Please send breakout session ideas to the Editors

9:20     Talk by Ryan Cawood – Oxford Genetics provider of a catalogue of DNA components
9:30     Breakout Sessions
12:30   Wrap up / Lunch
13:00   Excursion
19:00   Meal at SIX at BALTIC Centre for Contemporary Art
Address: SIX Restaurant, BALTIC Centre for Contemporary Art Gateshead Quays, South Shore Road, Gateshead, NE8 3BA

Day 3 – Friday, 26th April – Breakouts and the Road Ahead

Location: Room 701, School of Computing Science, Claremont Tower.
09:00   [Continue] Breakout Sessions
12:30   Lunch
13:30   Breakout Groups Report Back
14:00   Roadmapping Discussion – Ernst Oberortner

    • Envisioning directions for SBOL
    • Setting goals and priorities for the next six months

16:30   Wrap up


We will be going to Corbridge on Thursday afternoon. Corbridge is a historical village, situated 16 miles west of Newcastle. The village includes beautiful walking routes and historical places such as Roman Site and Aydon Castle.

We will travel by a coach which will pick us from by the seminar room and will later drop us off the station. You may wish to bring rain coats and/or umbrellas.

View Corbridge in a larger map


Matthew Pocock will be waiting at Thistle Hotel at 8.30am on Wednesday, 24th April, to take editors to the SBOL Workshop. Even if you are not staying at Thistle Hotel, you can still join him. Alternatively, you can take the metro to Haymarket Metro Station and walk to the Centre for Bacterial Cell Biology.

The Centre for Bacterial Cell Biology
Baddiley-Clark Building
Medical School
Newcastle University
Richardson Road
Newcastle upon Tyne
United Kingdom

It is around 15 minute walk to the Centre for Bacterial Cell Biology from Haymarket Metro Station.

View Centre for Bacterial Cell Biology, Baddiley-Clark Building in a larger map

Click here to view a detailed map of the university campus.

On day 3, the workshop will be held at the School of Computing Science, Claremont Tower. The directions are shown with the red colour on the map.

School of Computing Science
Claremont Tower
Claremont Road


Situated in the North East of England, Newcastle has excellent transport links with major UK and international cities.

Newcastle is easy to get to:

  • Road – the A1(M) running north to south passes close by the city centre
  • Rail – Newcastle is about 3 hours from London
  • Air – Newcastle International Airport is only seven miles away. Newcastle International Airport has direct links to many European airports and can also be reached via hubs at Amsterdam, Brussels, London and Paris airports. Destinations can be found at the
  • Coach/Bus – the main coach station is located in the city centre
  • Sea – ferries run from nearby North Shields to Holland

Newcastle is a compact city so it’s easy to cycle or walk around. The Metro rail network offers fast, efficient travel from the Newcastle International Airport and Newcastle Central Railway Station.

We have a number of maps to help you find your way around the city and campus.

About Newcastle

Newcastle is the cosmopolitan capital of the North East. Famous for its welcoming character, with the University at the heart of the city, it’s a great place to live.

Take a virtual tour around the city of Newcastle.


Newcastle was named after the Norman castle in its centre. However, the city can trace its history back to Roman times. Remnants of Hadrian’s Wall exist alongside a medieval cathedral, and impressive Victorian buildings.

Newcastle lies at the heart of the ancient kingdom of Northumbria, renowned for its glorious unspoilt countryside and rich heritage. The region is at the northern limit of the Roman Empire and has been the location of many border battles with Scotland.


Newcastle is great for shopping with around 600 shops in the city centre.


The Quayside is a cultural hub bringing together the best of Newcastle and Gateshead. The Sage Gateshead music centre and the BALTIC art gallery share the river with many bars, cafes and restaurants.


Newcastle has lots to offer:


St James’ Park, home to Newcastle United Football Club, is just a short walk from the University. The city is also home to Newcastle Falcons rugby club and has first-class basketball and ice hockey teams. Newcastle also hosts the world’s biggest half marathon, the Great North Run.

Find out more


The following hotels are available at reduced prices for the meeting by quoting the reference (usually Newcastle University). Prices are correct at time of publication but may change. You may also find cheaper deals on the web for these hotels so check the web first:

Hotel Standard Single Standard Double /Twin Standard Double /Twin Executive Single Executive Double /Twin Executive Double /Twin
Sole Occupancy Sole Occupancy 2 Person Sole Occupancy 2 Person
Copthorne – Newcastle N/A £88.00 £98.00 N/A £113.00 £123.00
Hilton – Gateshead N/A £85.00 £95.00 N/A £135.00 £145.00
Jurys Inn – Newcastle N/A £85.00 £95.00 N/A N/A N/A
Jury’s Inn NewcastleGateshead Quays N/A £85.00 £95.00 N/A N/A N/A
Holiday Inn Newcastle Jesmond (formally Imperial) N/A £70.00 £75.00 N/A £92.00 £98.00
Caledonian Hotel – Jesmond £72.00 £82.00 £88.00 N/A £90.00 £95.00
Malmaison – Quayside Newcastle N/A £125.00 £135.00 N/A £130.00 £140.00
Thistle Hotel – Newcastle * £72.00 £79.00 £89.00 N/A £109.00 £119.00
Hotel Du Vin Quayside £125.00 £125.00 £125.00 £125.00 £125.00 £125.00
Premier Inn – Newcastle £68.00 £68.00 £77.00 N/A N/A N/A
Grey Street Hotel £89.00 £89.00 £99.00 £109.00 £109.00 £119.00
Sandman Signature Hotel £85.00 £85.00 £95.00 N/A £95.00 £105.00

* SBOL editors will be staying at Thistle Hotel.

A wider range of accommodation is available on the Visit NewcastleGateshead website, but select hotels in the centre of Newcastle or Jesmond.

Further details

We thank the School of Computing Science, the UK Flowers Consortium, Newcastle Centre for Synthetic Biology and Bioexploitation, AutoDesk and Turing ate my hamster LTD for funding.

There is travel bursary pot for non-academic (non-faculty) members available – the SBOL editors will be in touch about how it will be allocated and how to apply.

This meeting is a workshop to promote the active development of SBOL. If you are not a member of the SBOL development team and you would like to join in with this meeting please see details of how to join the SBOL community on the SBOL website.

For queries and travel advice please contact[at]

If you are attending the workshop please send an email to[at] by March 31st stating your arrival and departure dates together with any special dietary requirements, so that we can gauge numbers.




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