SBGN-5.5
SBGN-5.5 will be held from April 21st to 23rd, 2010, in Wittenberg, Germany, at the Leucorea.
The meeting will be an opportunity for the SBGN community to meet face-to-face and to discuss SBGN development. The meeting will include presentations of SBGN specifications, implementations of support, as well as focused discussions about SBGN issues and future development.
The local organizers are Tobias Czauderna and Falk Schreiber. We gratefully acknowledge funding from IPK Gatersleben, Martin Luther University Halle-Wittenberg, and IMBIO e.V.
Contents |
Agenda
Wednesday April 21
| Time | Topic | Speaker | Slides |
|---|---|---|---|
| 8:00am | Breakfast in the cafeteria of the Leucorea | ||
| 9:00am – 9:10am | Introduction | Tobias Czauderna | (none) |
| 9:10am – 9:20am | Introduction | Nicolas Le Novère (via Skype) | (none) |
| 9:20am – 11:00am | Hacking (development of SBGN support) | ||
| 11:00am | Coffee break | ||
| 11:20am – 1:00pm | Hacking (development of SBGN support) | ||
| 1:00pm | Lunch | ||
| 2:00pm – 4:00pm | Hacking (development of SBGN support) | ||
| 4:00pm | Coffee break | ||
| 4:20pm – 6:00pm | Hacking (development of SBGN support) | ||
| 7:00pm | Dinner (self-funded): Restaurant Convivo
Neustraße 7-10 | ||
Thursday April 22
| Time | Topic | Speaker | Slides |
|---|---|---|---|
| 8:00am | Breakfast in the cafeteria of the Leucorea | ||
| 9:00am – 9:10am | Discussion around Wednesday activities | Tobias Czauderna | |
| 9:10am – 11:00am | Presentations & Software Implementations | Chair: Nicolas Le Novère | |
| Pathway diagrams in PathVisio: towards a richer model | Martijn van Iersel | slides | |
| SBGN-ED: Editing, Validating, and Translating of SBGN Maps | Tobias Czauderna | slides | |
| Quantifying SBGN-PD | Stuart Moodie | slides | |
| 11:00am | Coffee break | ||
| 11:20am – 1:00pm | Roadmap & Governance of SBGN | Chair: Nicolas Le Novère | |
| – SBGN competition – SBGN advertisement | |||
| 1:00pm | Lunch | ||
| 2:00pm – 4:00pm | Presentation & Entity Relationship Discussion | Chair: Nicolas Le Novère | |
| ER – nested entities | Nicolas Le Novère | slides | |
| Representing disease mechanisms in SBGN | Bernard de Bono (via Skype) | ||
| Software for Formalized Molecular Interaction Maps (MIM) | Augustin Luna (slides provided) | slides | |
| 4:00pm | Coffee break | ||
| 4:20pm – 6:00pm | Activity Flow Discussion | Chair: Nicolas Le Novère | |
| Biological Activity Node | Huaiyu Mi (via Skype) | slides | |
| 8:00pm | Dinner (self-funded): Restaurant Alte Canzley
Schlossplatz 3-5 | ||
Friday April 23
| Time | Topic | Speaker | Slides |
|---|---|---|---|
| 8:00am | Breakfast in the cafeteria of the Leucorea | ||
| 9:00am – 11:00am | libSBGN & SBGN-ML | Chair: Alice Villeger | |
| Update on the libSBGN/SBGN format effort and discussion | |||
| 11:00am | Coffee break | ||
| 11:20am – 1:00pm | Process Description Discussion | Chair: Stuart Moodie | |
| SBGN PD – What's Next – process cloning | Stuart Moodie | slides | |
| 1:00pm | Lunch | ||
Minutes
Participants
| Name | Affiliation | Group/Project |
|---|---|---|
| Tobias Czauderna | IPK Gatersleben (Germany) | VANTED, SBGN-ED, layout |
| Bernard de Bono* | EMBL-EBI (UK) | RICORDO |
| Damien Fleury | CNRS (France) | SIDR |
| Anja Hartmann | IPK Gatersleben (Germany) | RIMAS |
| Astrid Junker | IPK Gatersleben (Germany) | RIMAS |
| Christian Klukas | IPK Gatersleben (Germany) | VANTED, SBGN-ED |
| Nicolas Le Novère | EMBL-EBI (UK) | BioModels/KiSAO/ MIASE/MIRIAM/ SBO/SBGN/SBML/ SED-ML/TEDDY |
| Augustin Luna* | National Cancer Institute and Bioinformatics Department, Boston University (USA) | Molecular Interactions Maps (MIM) |
| Huaiyu Mi* | SRI International (USA) | PANTHER Pathway |
| Stuart Moodie | University of Edinburgh (UK) | Edinburgh Pathway Editor |
| Falk Schreiber | IPK Gatersleben & MLU Halle-Wittenberg (Germany) | VANTED, SBGN-ED, layout |
| Anatoly Sorokin | University of Edinburgh (UK) | Edinburgh Pathway Editor |
| Martijn van Iersel | BiGCaT Bioinformatics, Maastricht University (The Netherlands) | PathVisio, WikiPathways, BridgeDb |
| Alice Villeger | University of Manchester (UK) | Arcadia |
| Röbbe Wünschiers | University of Applied Sciences Mittweida (Germany) |
* could not attend in person because of cancelled flights
Accommodation
Some accommodation can be provided by the hosts of the meeting directly at the Leucorea (single rooms). The Leucorea is located in the city centre. If you travel in company and/or would prefer to stay in a hotel in Wittenberg, please visit Wittenberg Information - accommodation.
Travel
Leucorea, Wittenberg
As mentioned above, SBGN-5.5 will be held in Wittenberg, Germany, at the Leucorea.
Leucorea
Collegienstraße 62
06886 Lutherstadt Wittenberg
The maps below show the location of the Leucorea.
- Schloßkirche - Castle Church
- Cranachhöfe - Cranach Courtyards
- Altes Rathaus, Markt - Old Town Hall, Marketplace
- Stadtkirche - Town Church
- Leucorea
- Melanchthonhaus - Melanchthon House
- Lutherhaus - Luther House
- Luthereiche - Luther Oak
Travelling by air and train
If you plan to travel by air and train we would like to advise you either to go to Berlin (Airport Berlin Tegel TXL or Airport Berlin Schönefeld SXF) or to Leipzig (Airport Leipzig/Halle LEJ).
Airport Berlin Tegel TXL to Lutherstadt Wittenberg
- by bus (Bus TXL) or taxi from the airport to Berlin main station (Berlin Hauptbahnhof or short Berlin HBF)
- by ICE or IC from Berlin main station to Lutherstadt Wittenberg
- duration: 1 hour 15 minutes
- frequency: approximately one per hour
- by suburban train (S45) from the airport to Berlin Südkreuz station
- by ICE or IC from Berlin Südkreuz station to Lutherstadt Wittenberg
- duration: 1 hour 20 minutes
- frequency: approximately one per hour
- by regional train from the airport to Leipzig main station (Leipzig Hauptbahnhof or short Leipzig HBF)
- by ICE from Leipzig main station to Lutherstadt Wittenberg
- duration: 1 hour
- frequency: every 2 hours
Travelling by train
You can use the journey planner on the web page of Deutsche Bahn to plan your trip (please enter 'Lutherstadt Wittenberg' as destination and select then 'Lutherstadt Wittenberg' again from the pop-up menu). From Wittenberg main station to the Leucorea you can either take a taxi or walk. The Leucorea is in a 10 minutes walking distance from the station.
Travelling by car
The maps below show travel directions to Wittenberg.
For more information see also Leucorea, Wittenberg.
Weather
The weather in Germany during April can be unsettled, with temperatures ranging from 8°C to 18°C (46°F to 64°F). There is a chance of rain, so make sure to bring an umbrella and some wet weather clothes.
Miscellaneous
If you are traveling from outside of Germany, make sure to bring an appropriate power plug converter for your laptop and all other electrical devices you are bringing. Electric current in Germany is 50 Hz, 220 V. The plug types are depicted below. For more detailed information on the types of plugs that are used, as well as electrical standards in various countries, please visit Electricity around the world.
| Type C Plug | 
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| Type F Plug | 
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Local Organisers & Contact
SBGN-5.5 is organised by Falk Schreiber (IPK Gatersleben & MLU Halle-Wittenberg, Germany) and Tobias Czauderna (IPK Gatersleben, Germany).
If you have any queries please contact Tobias Czauderna czauderna<at>ipk-gatersleben.de.
Acknowledgement
We thank IPK Gatersleben and IMBio - Informationsmanagement in der Biotechnologie e.V. for financial support.
