Tobias Czauderna edited this page Jun 11, 2016 · 3 revisions

SBGN 9 will be held from April 29th to May 2nd, 2013, in Edinburgh, Scotland.

The meeting will be an opportunity for the SBGN community to meet face-to-face and to discuss SBGN development. In particular we want to discuss not only the current SBGN specifications, but also the future development of SBGN. Since it will be dedicated to just SBGN and will take place over 4 days it will be arguably the most important meet we have had since the Okinawa Hackathon in 2008.

The meeting will be hosted by Prof Igor Goryanin of Edinburgh University and the local organiser is Stuart Moodie. We gratefully acknowledge funding from the BBSRC.

Registration

Registration is now closed for this event.

Agenda

Monday April 29

Time Topic Speaker
12:00pm – 1:00pm Lunch
1:00pm – 1:30pm Welcome / Introduction (pdf) Stuart Moodie
1:30pm – 2:15pm SBGN overview and status update (pdf)
SBGN issues to discuss (community feedback) Chair: Anatoly Sorokin
2:15pm – 2:30pm Status update: LibSBGN (pdf) and SBGN.org (pdf) Tobias Czauderna
2:30pm – 3:30pm AF development - issues (pdf) Chair: Falk Schreiber
3:30pm – 4:00pm Coffee break
4:00pm – 6:30pm ER development - issues and L1V2 (pdf) Chair: Anatoly Sorokin
8:00pm Dinner - Abden Rm, Abden House

Tuesday April 30

Time Topic Speaker
8:30am – 10:00am ER development continued Chair: Anatoly Sorokin
10:00am – 10:30am Morning tea
10:30am – 12:30pm PD development - issues and L1V2 (pdf) Chair: Stuart Moodie
Identity gates and generics in SBGN PD (pdf) Anatoly Sorokin
12:30pm – 1:30pm Lunch
1:30pm – 3:00pm PD development continued Chair: Stuart Moodie
3:00pm – 3:15pm SBGN using rxcon and Biographer (pdf) Ulrike Münzner
3:15pm – 3:30pm SBGN in CellDesigner (pdf) Akira Funahashi
3:30pm – 4:00pm Coffee break
4:00pm – 6:30pm The future of SBGN - lessons learned from SBGN Level 1 Chair: Frank Bergmann
SBGN from the user's perspective (pdf) Astrid Junker
SBGN in use (pdf) Alexander Mazein
Reillustrating Reactome (pdf) Robin Haw
Describing rule-based modeling: SBGN PD and SBGN ER (pdf) Michael Blinov
Apply SBGN AF in the LEGO project (pdf) Huaiyu Mi
Software for Graphical Notations in PathVisio and Lessons from its Usage (pdf) Augustin Luna
8:00pm Dinner - Nelson Rm, St Leonards House

Wednesday May 01

Time Topic Speaker
8:30am – 10:30am Proposals for SBGN Level 2 Chair: Michael Blinov
Ideas for Level 2 (pdf) Stuart Moodie
Ideas for Level ER Michael Blinov
10:00am – 10:30am Morning tea
10:30am – 12:30pm Discussion based on ideas from early morning session Chair: Huaiyu Mi
12:30pm – 1:30pm Lunch
1:30pm – 3:30pm Discussion based on ideas from early morning session continued Chair: Katja Wengler
3:30pm – 4:00pm Coffee break
4:00pm – 6:00pm Discussion based on ideas from early morning session continued Chair: Katja Wengler
7:30pm Dinner: Wedgwood the Restaurant

Thursday May 02

Time Topic Speaker
8:30am – 10:00am LibSBGN - issues and milestone 3 (pdf) Chair: Tobias Czauderna
Exchanging rendering information with SBGN-ML (pdf) Frank Bergmann
Reactome and LibSBGN (pdf) David Croft
10:00am – 10:30am Morning tea
10:30am – 12:30pm Funding - sustainability of SBGN Chair: Huaiyu Mi
Conclusions from discussions, closing remarks Chair: Falk Schreiber
Next SBGN meeting / HARMONY / COMBINE
12:30pm Lunch

Meeting Minutes

Minutes of the discussions were captured in this Google Doc.

Workshop Participants

The following will be attending the meeting.

Name Affiliation Group/Project Joining Remotely
Frank Bergmann California Institute of Technology (USA) SBML Layout
Michael Blinov University of Connecticut Health Center (USA) BioNetGen@VCell BioPAX@VCell
David Croft EBI-EMBL (UK) Reactome
Tobias Czauderna IPK Gatersleben (Germany) SBGN-ED
Ugur Dogrusoz Bilkent University (Turkey) ChiBE
Akira Funahashi Keio University (Japan) Cell Designer
Robin Haw Ontario Institute of Cancer Research (Canada) Reactome
Astrid Junker IPK Gatersleben (Germany) SBGN Bricks
Augustin Luna Center for Cancer Research, NIH (USA) Molecular Interaction Maps and PathVisio plugins
Alexander Mazein OIST (Japan) Cholesterol biosynthesis regulation via SREBP transport
Huaiyu Mi USC (USA) PANTHER Pathway
Stuart Moodie EBI-EMBL (UK) SBGN
Ulrike Münzner Humboldt-Universität zu Berlin (Germany) rxncon biographer
Nicolas Le Novère Babraham Institute and EBI-EMBL (UK) SBGN Yes
Falk Schreiber IPK Gatersleben & University of Halle-Wittenberg (Germany) SBGN-ED
Anatoly Sorokin Institute of Cell Biophysics(Russia), University of Edinburgh (UK) SBGN
Stephen Waterson University of Edinburgh (UK) SBGN User
Katja Wengler University of Hertfordshire (UK) NetBuilder

Accommodation

Delegates will stay in Edinburgh University's Pollock Halls campus area. This is a 5 minute walk from the meeting venue.

The Salisbury Green Hotel 18 Holyrood Park Road Edinburgh EH16 5AY‎ 0131 651 2189 Google Map

Venue

The meeting will be on the Edinburgh University's Pollock Halls campus at St Leonards Hall.

Meeting Room: St Trinnean’s

Venue Info and Map

Meals

We provide refreshments, lunch and dinner during the meeting, if you have advised any specific requirement on your registration we will pass this information to our caterers.

Workshop Dinner

On Wed 1 May, 7:30pm we will be having a workshop dinner in Wedgewood's on Edinburgh's Historic Old Town.

Wedgwood the Restaurant Royal Mile, 267 Canongate, Edinburgh, EH8 8BQ.

Phone: 0131 558 8737

http://www.wedgwoodtherestaurant.co.uk

Travel Information

Edinburgh

The city of Edinburgh is the capital of Scotland, and the second largest city in Scotland. It is a dynamic and fascinating city with a rich history and many sights worth seeing.

The official Edinburgh tourist board website and the Edinburgh city council website both list good information about Edinburgh festivals and other events, as well as museums and galleries.

Of course, no visit to Edinburgh would be complete without a visit to Edinburgh Castle.

Getting out and about in Edinburgh is relatively easy and most places in the centre of the city are walkable. There is a very good bus service with bus timetables and route maps at each bus stop. The bus fare cost a flat rate of £1.40. A day ticket cost £3.50. All tickets can be purchased from the driver on the bus. Note that no change is given and only cash is accepted so if you are going to use the bus then think ahead and save your small change. For more information go to: http://lothianbuses.com.

Generally Edinburgh is a friendly place and the locals are very proud of their city and keen to show it off. So if in doubt ask a local they will invariable be only to pleased to help. You may find they speak took quickly for you to understand. If so ask them to repeat and to slow down and you should be OK.

Travelling by air and train

Many airlines fly direct from the US or Europe to Edinburgh Airport, and from the airport there is a frequent bus service to the city centre. A taxi from the airport will costs just under £20 (GBP).

An alternative is to fly to Glasgow Airport and take the train from Glasgow Queen Street station (in Glasgow city centre) to Edinburgh Waverley Station (in Edinburgh city centre). The journey time is 45 mins.

Ryan Air have many flights from the Continent to Prestwick airport, which is South West of Glasgow. You can travel by train direct from the airport to Edinburgh (using changing in Glasgow). The journey takes about 2 hours.

Edinburgh Airport connects to the major Western European hub airports and it can often be cheaper (and less traumatic) to travel via Schiphol (Amsterdam) or Frankfurt airports rather than Heathrow. The cheapest flights often fly via Charles de Gaul (Paris).

Getting to Pollock Halls Campus

Pollock Halls 18 Holyrood Park Road Edinburgh EH16 5AY

By road

If you're coming to Edinburgh from the South, take the A720; City of Edinburgh Bypass, then take the A7 Old Dalkeith Road exit at the Sheriffhall Roundabout going towards the City Centre. Continue straight for approximately 3 miles. Just past the Royal Commonwealth Pool at the lights, turn right onto Holyrood Park Road. Pollock Halls is the second turning on the right.

There is on-site parking.

By taxi

A taxi from St. Andrew Square Bus Station or Princes Street to Pollock Halls will cost approximately £7 and take 5-10 minutes.

By Bus

From the shop side of Princes Street; take a bus to the Royal Commonwealth Pool on Dalkeith Road, Pollock Halls is a short walk down Holyrood Park Road from the stop. Due to current tram works there may be route changes, all Lothian Buses can be picked up from North Bridge.

Lothian buses

Nos 2, 14, 30, 33; £1.50 is the standard adult one-trip fare. You'll need exact change.

By Rail

Pollock Halls is 2 miles from Edinburgh Waverley, our main station. A taxi or a bus will take around 10 minutes.

By Air

Pollock Halls is about 8 miles from Edinburgh International Airport. A taxi will cost around £20, or take the Airlink bus service to Waverley Bridge, an adult open return is £6 and a single £3.50.

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