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SBGN 5.5

cannin edited this page Jun 10, 2016 · 1 revision

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.

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
                Lutherstadt Wittenberg

                \[<http://maps.google.de/maps?f=q&source=s_q&hl=en&geocode>=&q=Neustra%C3%9Fe+7-10+06886+Lutherstadt+Wittenberg&sll=51.866489,12.647959&sspn=0.011554,0.019419&ie=UTF8&hq=&hnear=Neustra%C3%9Fe+7,+06886+Wittenberg,+Lutherstadt,+Wittenberg,+Sachsen-Anhalt&ll=51.866488,12.643869&spn=0.011554,0.027595&z=16 Map and directions\]  |

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 Lutherstadt Wittenberg

                \[<http://maps.google.de/maps?f=q&source=s_q&hl=en&geocode>=&q=Schlossplatz+3-5+06886+Lutherstadt+Wittenberg&sll=51.151786,10.415039&sspn=20.141655,42.758789&ie=UTF8&hq=&hnear=Schlo%C3%9Fplatz+3,+06886+Wittenberg,+Lutherstadt,+Wittenberg,+Sachsen-Anhalt&z=16&iwloc=A Map and directions\]  |

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
                – TM proteins
                – moving compartments                                    | Stuart Moodie
                                                                           
                                                                           
                                                                                                 | [slides](/media:SBGN5.5-PDWhatsNext.pdf "wikilink")
                                                                                                   
                                                                                                   
                                                                                                                                                       |

| 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 [center|thumb|425px|Leucorea](/Image:Sbgn_5_5_leucorea_800x600.jpg "wikilink")

The maps below show the location of the Leucorea.

center|thumb|425px|Leucorea

1. Schloßkirche - Castle Church 2. Cranachhöfe - Cranach Courtyards 3. Altes Rathaus, Markt - Old Town Hall, Marketplace 4. Stadtkirche - Town Church 5. Leucorea 6. Melanchthonhaus - Melanchthon House 7. Lutherhaus - Luther House 8. Luthereiche - Luther Oak
<iframe width="425" height="350" frameborder="0" scrolling="no" marginheight="0" marginwidth="0" src="=&q=Collegienstra%C3%9Fe+62+06886+Lutherstadt+Wittenberg+&ie=UTF8&hq=&hnear=Collegienstra%C3%9Fe+62,+06886+Wittenberg,+Lutherstadt,+Wittenberg,+Sachsen-Anhalt,+Deutschland&t=h&ll=51.865057,12.649662&spn=0.004638,0.00912&z=15&output=embed"></iframe> <a href="=&q=Collegienstra%C3%9Fe+62+06886+Lutherstadt+Wittenberg+&ie=UTF8&hq=&hnear=Collegienstra%C3%9Fe+62,+06886+Wittenberg,+Lutherstadt,+Wittenberg,+Sachsen-Anhalt,+Deutschland&t=h&ll=51.865057,12.649662&spn=0.004638,0.00912&z=15" class="external text" title="View Larger Map">View Larger Map
### 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 [Airport Berlin Schönefeld SXF](http://www.berlin-airport.de/EN/index.html) to Lutherstadt Wittenberg - 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 [Airport Leipzig/Halle LEJ](http://www.leipzig-halle-airport.de/en/index.html) to Lutherstadt Wittenberg - 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 For more information see also [Travelling by train](http://www.sbgn.org/Events/SBGN-5.5#Travelling_by_train).

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.

<iframe width="425" height="350" frameborder="0" scrolling="no" marginheight="0" marginwidth="0" src="=&q=Collegienstra%C3%9Fe+62+06886+Lutherstadt+Wittenberg+&ie=UTF8&hq=&hnear=Collegienstra%C3%9Fe+62,+06886+Wittenberg,+Lutherstadt,+Wittenberg,+Sachsen-Anhalt,+Deutschland&ll=51.865057,12.649662&spn=1.18722,2.334595&z=7&iwloc=A&output=embed"></iframe> <a href="=&q=Collegienstra%C3%9Fe+62+06886+Lutherstadt+Wittenberg+&ie=UTF8&hq=&hnear=Collegienstra%C3%9Fe+62,+06886+Wittenberg,+Lutherstadt,+Wittenberg,+Sachsen-Anhalt,+Deutschland&ll=51.865057,12.649662&spn=1.18722,2.334595&z=7&iwloc=A" style="color:\#0000FF;text-align:left">View Larger Map
[center|Wittenberg travel directions](/Image:Sbgn_5_5_wittenberg_travel_500x317.gif "wikilink")

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.

<iframe width="210" height="170" marginheight="0" marginwidth="0" frameborder="0" src=""> </iframe>
### 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 |
           </html>                                                                               |

|-------------|--------------------------------------------------------------------------------------|

| Type F Plug |

           </html>                                                                               |

|-------------|--------------------------------------------------------------------------------------|

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 czaudernaipk-gatersleben.de.

Acknowledgement

We thank IPK Gatersleben and IMBio - Informationsmanagement in der Biotechnologie e.V. for financial support.

[Image:Sbgn_5_5_IPK_logo.png](/Image:Sbgn_5_5_IPK_logo.png "wikilink")       [Image:Sbgn_5_5_IMBio_logo.png](/Image:Sbgn_5_5_IMBio_logo.png "wikilink")
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