SBML.org — the global portal for all things SBML

The 7th SBML Hackathon

(Day 1 (Thursday, March 26))
(Day 1 (Thursday, March 26))
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| style="padding-left: 1em" | LibSBML 4.0 API tutorial + Q&A session
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| colspan="2" | <font color="#888">''Lunch (provided) and poster viewing time''</font>
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| style="border-right: 1px dotted #bbb" | Hacking, collaboration, ad hoc discussions
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| style="padding-left: 1em" | SBML Test Suite tutorial & discussion
| style="padding-left: 1em" | SBML Test Suite tutorial & discussion

Revision as of 23:50, 24 February 2009

ebi.ac.uk/ European Bioinformatics Institute]
//ebi.ac.uk/ European Bioinformatics Institute]

March 26–28, 2009

ebi.ac.uk EBI] in Hinxton, UK, which was also the site of the 2004 SBML Hackathon. The EBI is the home of the Le Novère group and their many efforts and resources, which include the BioModels Database, the Systems Biology Ontology, MIRIAM Resources, and more.//ebi.ac.uk EBI] in Hinxton, UK, which was also the site of the 2004 SBML Hackathon. The EBI is the home of the Le Novère group and their many efforts and resources, which include the BioModels Database, the Systems Biology Ontology, MIRIAM Resources, and more.

www.surveymonkey.com/s.aspx?sm=R3lHlmttN6H5ZnoTWajO_2fQ_3d_3d the registration form] if you plan on attending!//www.surveymonkey.com/s.aspx?sm=R3lHlmttN6H5ZnoTWajO_2fQ_3d_3d the registration form] if you plan on attending!

SBML Hackathons are annual meetings of developers of SBML software, tools, and other resources and facilities. The Hackathons are hands-on work sessions providing an opportunity to discuss software interoperability and other practical matters involving SBML. All interested persons are welcome to attend.

conferences.theiet.org/biosysbio/ BioSysBio] (March 23–25 in Cambridge, UK) and will itself be followed immediately afterwards by the 2009 BioModels Meeting on March 28–30, also at the EBI. Persons interested in these events may also want to take note of the CellML-SBGN-SBO-MIASE-BioPAX super-workshop, which will be held shortly afterwards in Auckland, New Zealand, April 5–9.//conferences.theiet.org/biosysbio/ BioSysBio] (March 23–25 in Cambridge, UK) and will itself be followed immediately afterwards by the 2009 BioModels Meeting on March 28–30, also at the EBI. Persons interested in these events may also want to take note of the CellML-SBGN-SBO-MIASE-BioPAX super-workshop, which will be held shortly afterwards in Auckland, New Zealand, April 5–9.

This year, for the first time in the SBML Hackathon series, we are introducing the option for people to bring and display posters about their work. The purpose is to compensate for the fact that the hackathons do not provide opportunities for people to give oral presentations about their software and other projects, yet not everyone at a hackathon is familiar with all the work going on by other people. We will therefore arrange poster display space near the hackathon rooms, and attendees can use the posters to provide information about ongoing projects as well as opportunities for face-to-face conversations about their work.

www.elixir-europe.org/ ELIXIR] project.//www.elixir-europe.org/ ELIXIR] project.


We are also grateful for additional sponsorship from the following organizations: www.embl.org European Molecular Biology Laboratory (EMBL)]//www.embl.org European Molecular Biology Laboratory (EMBL)] www.embl.org European Molecular Biology Laboratory (EMBL)]//www.nigms.nih.gov/ National Institute of General Medical Sciences (NIGMS)], USA bnmc.caltech.edu Biological Network Modeling Center], USA//bnmc.caltech.edu Biological Network Modeling Center], USA

Agenda :updated:

In order to accommodate different people's level of experience and different goals, we will go back to using two rooms this year (something that we did in past SBML Hackathons, though not in the most recent two). The following agenda may still change somewhat as we get closer to the actual event.

Arrival day (Wednesday, March 25)

conferences.theiet.org/biosysbio/ BioSysBio 2009]). See below on this page for information about accommodations in Cambridge.//conferences.theiet.org/biosysbio/ BioSysBio 2009]). See below on this page for information about accommodations in Cambridge.

Day 1 (Thursday, March 26)

Time Activity (Main room) Activity (2nd room)
07:00–08:00 Breakfast at Arundel Hotel (provided)
08:00–08:30 Buses to the EBI from the hotel in Cambridge
08:30–09:00 Computer set up & poster mounting
09:00–09:10 Introduction by Nicolas Le Novère
09:10–09:30 Introduction by Michael Hucka
09:30–12:00 Hacking, collaboration, ad hoc discussions LibSBML 4.0 API tutorial + Q&A session
12:00–14:30 Lunch (provided) and poster viewing time
14:30–18:00 Hacking, collaboration, ad hoc discussions SBML Test Suite tutorial & discussion
18:00–19:00 Social time in pub (self-funded)
19:00–19:30 Buses back to the hotel in Cambridge
Dinner (self-organized and self-funded)

Day 2 (Friday, March 27)

Time Activity (Main room) Activity (2nd room)
07:00–08:00 Breakfast at Arundel Hotel (provided)
08:00–08:30 Buses to the EBI from the hotel in Cambridge
08:30–12:00 Hacking, collaboration, ad hoc discussions SBML Level 3 Core specification hacking
12:00–13:30 Lunch (provided)
13:30–18:00 Hacking, collaboration, ad hoc discussions SBML Level 3 Core specification hacking
19:00–22:00 Buses to Cambridge
Dinner at Trinity College in Cambridge (provided)

Day 2.5 (Saturday, March 28)

Time Activity (Main room) Activity (2nd room)
07:00–08:00 Breakfast at Arundel Hotel (provided)
08:00–08:30 Buses to the EBI from the hotel in Cambridge
08:30–11:00 Hacking, collaboration, ad hoc discussions (To be determined)
11:00–12:00 Discussions, conclusions & future plans
12:00–13:30 Lunch (self-funded)


biomodels.net/meetings/2008/index.html BioModels Annual Meeting] will begin on the afternoon of March 28 and go through March 30th. Please consult the BioModels meeting page for more information about it. For those not attending the BioModels meeting, we will arrange transportation back to the hotel in Cambridge, or to airports, or elsewhere, depending on your needs.//biomodels.net/meetings/2008/index.html BioModels Annual Meeting] will begin on the afternoon of March 28 and go through March 30th. Please consult the BioModels meeting page for more information about it. For those not attending the BioModels meeting, we will arrange transportation back to the hotel in Cambridge, or to airports, or elsewhere, depending on your needs.

Attendees :updated:

The following is the list of attendees registered as of 2009-02-23:

Name Institution Project(s)
Frank Bergmann University of Washington, USA

sys-bio.org/ SBW]//sys-bio.org/ SBW]

Vijayalakshmi Chelliah EMBL-EBI, UK

sys-bio.org/ SBW]//www.ebi.ac.uk/biomodels-main/ BioModels Database]

Mike Cooling University of Auckland, New Zealand

sys-bio.org/ SBW]//www.cellml.org/ CellML]

Andreas Dräger University of Tübingen, Germany

sys-bio.org/ SBW]//www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX/ SBML2LATEX]

Lukas Endler EMBL-EBI, UK

sys-bio.org/ SBW]//www.ebi.ac.uk/biomodels-main/ BioModels Database]

Christoph Flamm University of Austria, Austria

sys-bio.org/ SBW]//www.tbi.univie.ac.at/~raim/odeSolver/doc/api.html SBML ODE Solver]

Akira Funahashi Keio University, Japan

sys-bio.org/ SBW]//celldesigner.org/ CellDesigner]

Ralph Gauges University of Heidelberg, Germany

sys-bio.org/ SBW]//copasi.org/ COPASI]

Martin Golebiewski EML Research gGmbH, Germany

sys-bio.org/ SBW]//sabio.villa-bosch.de/SABIORK/ SABIO-RK]

Stefan Hoops Virginia Bioinformatics Institute, USA

sys-bio.org/ SBW]//copasi.org/ COPASI]

Michael Hucka California Institute of Technology, USA

sys-bio.org/ SBW]//sbml.org SBML], BioModels.net

Akiya Jouraku Keio University, Japan

sys-bio.org/ SBW]//www.celldesigner.org/ CellDesigner]

Nick Juty EMBL-EBI, UK

sys-bio.org/ SBW]//www.ebi.ac.uk/compneur-srv/miriam/ MIRIAM], SBO

Sarah Keating California Institute of Technology, USA

sys-bio.org/ SBW]//sbml.org SBML]

Christian Knüpfer University of Jena, Germany

sys-bio.org/ SBW]//www.ebi.ac.uk/compneur-srv/teddy/ TEDDY]

Falko Krause Humboldt University, Germany

sys-bio.org/ SBW]//sysbio.molgen.mpg.de/semanticsbml/ semanticSBML]

Camille Laibe EMBL-EBI, UK

sys-bio.org/ SBW]//www.ebi.ac.uk/compneur-srv/miriam/ MIRIAM], SBO

Nicolas Le Novère EMBL-EBI, UK

sys-bio.org/ SBW]//sbml.org SBML], BioModels Database, MIRIAM, SBO, BioModels.net

Chen Li EMBL-EBI, UK

sys-bio.org/ SBW]//www.ebi.ac.uk/biomodels-main/ BioModels Database]

Wolfram Liebermeister Humboldt University, Germany

sys-bio.org/ SBW]//sysbio.molgen.mpg.de/semanticsbml/ semanticSBML]

Allyson Lister University of Newcastle, UK SAINT
Catherine Lloyd University of Auckland, New Zealand

sys-bio.org/ SBW]//www.cellml.org/ CellML]

Timo Lubitz Humboldt University, Germany

sys-bio.org/ SBW]//sysbio.molgen.mpg.de/semanticsbml/ semanticSBML]

Ion Moraru UCHC, USA

sys-bio.org/ SBW]//vcell.org/ VCell]

Chris Myers University of Utah, USA

sys-bio.org/ SBW]//www.async.ece.utah.edu/BioSim/ iBioSim]

Anika Oellrich EMBL-EBI, UK

sys-bio.org/ SBW]//www.pdn.cam.ac.uk/groups/comp-cell/StochSim.html StochSim]

Brett Olivier University of Amsterdam, The Netherlands

sys-bio.org/ SBW]//pysces.sourceforge.net/ PySCeS]

Nicolas Rodriguez EMBL-EBI, UK

sys-bio.org/ SBW]//www.ebi.ac.uk/biomodels-main/ BioModels Database]

Sven Sahle University of Heidelberg, Germany

sys-bio.org/ SBW]//copasi.org/ COPASI]

Herbert Sauro University of Washington, USA

sys-bio.org/ SBW]//sys-bio.org/ SBW]

Maria Schilstra University of Hertfordshire, UK

sys-bio.org/ SBW]//strc.herts.ac.uk/bio/maria/Apostrophe/index.htm NetBuilder]

Lucian Smith University of Washington, USA

sys-bio.org/ SBW]//sys-bio.org/ SBW]

Jacky Snoep Stellenbosch University, South Africa

sys-bio.org/ SBW]//jjj.biochem.sun.ac.za/index.html JWS Online]

Neil Swainston University of Manchester, UK

sys-bio.org/ SBW]//www.mcisb.org/ MCISB]

Darren Wilkinson Newcastle University, UK

sys-bio.org/ SBW]//www.calibayes.ncl.ac.uk/ CaliBayes]

Location


View Larger Map

ebi.ac.uk/ EMBL-EBI]. Address and contact details://ebi.ac.uk/ EMBL-EBI]. Address and contact details:

EMBL Outstation - Hinxton
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
United Kingdom
Tel: +44 (0)1223 494 444

www.ebi.ac.uk/embl/ EMBL-Bank] and what is now known as UniProt) to the research community. Although geographically separated from EMBL's main headquarters and other sites, the EMBL-EBI is an integral part of EMBL.//www.ebi.ac.uk/embl/ EMBL-Bank] and what is now known as UniProt) to the research community. Although geographically separated from EMBL's main headquarters and other sites, the EMBL-EBI is an integral part of EMBL.

Arundel House Hotel
Arundel House Hotel

Accommodations

www.arundelhousehotels.co.uk/ Arundel House Hotel] in nearby Cambridge. The accommodations will be complimentary for attendees from academic/non-commercial organizations. (Please contact the organizers if you are affiliated with a commercial group.)//www.arundelhousehotels.co.uk/ Arundel House Hotel] in nearby Cambridge. The accommodations will be complimentary for attendees from academic/non-commercial organizations. (Please contact the organizers if you are affiliated with a commercial group.)

Breakfast is included as part of the accommodations on the mornings of March 26–28 inclusive. Lunches and coffee/tea/soda breaks will also be provided on the meeting days at the EBI.

Transportation

Transportation to and from the airports will be arranged for everyone by the meeting organizers. biomodels.net/meetings/2008/index.html BioModels Annual Meeting] will begin on the afternoon of March 28 and go through March 30th. Please consult the BioModels meeting page for more information about it. For those not attending the BioModels meeting, we will arrange transportation back to the hotel in Cambridge, or to airports, or elsewhere, depending on your needs.//www.surveymonkey.com/s.aspx?sm=R3lHlmttN6H5ZnoTWajO_2fQ_3d_3d registration page] purposefully requests your arrival and departure details, so that the organizers can schedule your pick up and drop off.

Transportation to and from the Arundel hotel in Cambridge will be arranged by the organizers for the meeting days. We anticipate arranging mini-buses leaving for Hinxton at around 8:00, and then returning in the evenings between 18:00 and 19:00.

For transportation in and around Hinxton on occasions when you want to go out but no group outing is prepared, the following options are available:

  • Hinxton and Ickleton are within walking distance. As mentioned below, they each have a pub.

www.ebi.ac.uk/Information/Travel/shuttle_timetable.html leave regularly] for nearby areas.//www.ebi.ac.uk/Information/Travel/shuttle_timetable.html leave regularly] for nearby areas.

  • Taxis are also available.

www.ebi.ac.uk/Information/Travel/travel.html EBI's directions to the campus] page.//www.ebi.ac.uk/Information/Travel/travel.html EBI's directions to the campus] page.

Other notes

The following information may be useful to first-time travelers to the EBI and the surrounding region.

Poster details :updated:

As mentioned above, this year we are going to experiment with having posters as a means for people to inform each other about their software and other projects. The maximum poster size is 1.7 meters (66 inches) wide by 1 meter (39 inches) tall. We will provide poster boards together with tacks/pins to attach posters to the boards. Posters will be displayed in the EBI "IT breakout area" during the Hackathon. Posters can be hung at any time following your arrival at the EBI. (See also the agenda above.)

Electrical supply

en.wikipedia.org/wiki/Domestic_AC_power_plugs_and_sockets#Type_G_.28British_3-pin.29 elsewhere].//en.wikipedia.org/wiki/Domestic_AC_power_plugs_and_sockets#Type_G_.28British_3-pin.29 elsewhere].

Internet networking

The EBI is covered by a wireless network that reaches pretty much everywhere on campus, so make sure to bring a wireless card if you need one. In some rooms, wired ethernet jacks are also available. (For example, in the IT training room where most Hackathon activities will take place, there is an Ethernet plug on every desk.)

Weather

In the Cambridge, region, the weather in late March tends toward cool and often overcast. Rain often comes in short but heavy bursts. Average daytime temperatures range in the 10–15 degree Celsius, while at night, temperatures sometimes dip below freezing. Please bring suitable outdoor clothing and shoes. On the bright side, this time of year is the beginning of spring, so you may seen flowers blossoming and some bouts of warm sunshine.

The widget on the right shows the current weather in Cambridge.

www.bbc.co.uk/weather/5day.shtml?id=1413 BBC weather page for Cambridge, UK].//www.bbc.co.uk/weather/5day.shtml?id=1413 BBC weather page for Cambridge, UK].

Around the campus

www.ebi.ac.uk/Information/Site_Info/ campus information page] provides detailed information about the Wellcome Trust Genome Campus.//www.ebi.ac.uk/Information/Site_Info/ campus information page] provides detailed information about the Wellcome Trust Genome Campus.

www.ickletonvillage.co.uk/ Ickleton]. When we say "villages", we mean it—these are very small places. They each have a pub serving quite decent food and drink, but unfortunately, that's all you will find in these two villages.//www.ickletonvillage.co.uk/ Ickleton]. When we say "villages", we mean it—these are very small places. They each have a pub serving quite decent food and drink, but unfortunately, that's all you will find in these two villages. www.redlionhinxton.co.uk/ Red Lion Hinxton]//www.redlionhinxton.co.uk/ Red Lion Hinxton] www.redlionhinxton.co.uk/ Red Lion Hinxton]//myweb.tiscali.co.uk/ickleton/Services.htm#bmPub Ickleton Lion]

It should be noted that the Genome Campus has been designated as a non-smoking environment. Smoking is not permitted within any buildings on the campus. Smoking outside is only permitted in certain designated areas on the Campus.

About Cambridge

Cambridge is less than 10 miles away from Hinxton. The city is the home of the University of Cambridge, which in 2009 celebrates its 800th anniversary. For more information about the city and the university, please visit the following websites:

www.redlionhinxton.co.uk/ Red Lion Hinxton]//www.gwydir.demon.co.uk/cambridgeuk/ Cambridge (UK) Web Sites] www.redlionhinxton.co.uk/ Red Lion Hinxton]//www.cam.ac.uk/CambArea/index.html General Cambridge information] www.embl.org European Molecular Biology Laboratory (EMBL)]//www.fitzmuseum.cam.ac.uk/ Fitzwilliam museum] (very nice!) www.cam.ac.uk/cambuniv/finding/addresses/college.html Cambridge colleges] (with websites). Colleges are at the heart of Cambridge history, architecture and current student life.//www.cam.ac.uk/cambuniv/finding/addresses/college.html Cambridge colleges] (with websites). Colleges are at the heart of Cambridge history, architecture and current student life.

Contacts

Nick Juty Nicolas Le Novère Linda Taddeo Michael Hucka
juty at ebi.ac.uk lenov at ebi.ac.uk ltaddeo at caltech.edu mhucka at caltech.edu
Tel: +44 (0) 1223 494 418 Tel: +44 (0) 1223 494 521 Tel: +1 626 395 3375 Tel: +1 626 395 6911
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD
UK
Beckman Institute 139-74
California Institute of Technology
Pasadena, California 91125
USA


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