MIBBI workshop 2010

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PLEASE NOTE THAT THIS MEETING HAS NOW TAKEN PLACE

Contents

Meeting outputs

The presentations from the second MIBBI workshop can be found here.

Date and location

November 30th to December 3rd, 2010 @ Hotel Jagdschloss Niederwald, Ruedesheim/Rhein, Germany.

N.B. This workshop has already taken place.

Meeting Agenda

Tuesday, 30th November

19.30 Welcome reception
20.00 Dinner

Wednesday, 1st December

09.00 Welcome and introductions
  • Welcome and logistics (Susanna Sansone, Carsten Kettner, Martin Hicks)
  • Round-the-table self-introductions
10.00 MIBBI and beyond: towards BioSharing (Susanna Sansone)
10.30 Break
10.45 MIBBI Portal: project updates and user communities (Chair: Susanna Sansone)
  • MI project briefings (by presenter surname)
  1. Scope of guidelines (technologies, biology, etc.).
  2. Level of implementation (tools, formats, CVs, databases, enforcement).
  3. Activity status, contributors, funding.
12.15 Discussion: MI Projects (Drawing on topics common across the MI specifications presented)
  • Overlaps in domains covered by Portal-registered checklists
  • Level of uptake of individual checklists
  • What challenges face each project?
  • Would externally-sourced tools/databases/formats/CVs help
  • Will DOIs & ORCIDs (supporting data citation and enabling the recording of data set reuse [=impact]) affect uptake in each represented community?
  • The user communities (consumers) for MI projects
  • Researchers, developers, funders, journal editors, vendors, ..?
  • How to best cater to their (different) needs?
13.00 Lunch
14.30 MIBBI Foundry: rationale, status and next steps (Chair: Dawn Field)
  • Serving communities operating in many domains: the challenge of implementing several MIs (Philippe Rocca-Serra)
  • The MIBBI Foundry and its modules (Chris Taylor)
15.15 Discussion: Foundry (On the Foundry development approach and the content produced)
  • Discuss ways of working on content as a group, such as:
  • Specific groups for particular assays, organisms, environments, etc.; joint groups on shared areas (sample description, referencing, etc.)?
  • Possible strategies for the MI community:
  • Work jointly on the Foundry while maintaining each project's specifications?
  • ‘Replace’ individual projects with collaborative work on the Foundry?
  • How best to serve the needs of several user groups, namely:
  • experimentalists (reporting), journals (publications), funders (policy)
16.10 Instructions for breakout sessions (Dawn Field)
  • Group ‘wet’ (lead: TBA; rapporteur: TBA; guide: Dawn Field)
  • Group ‘dry’ (lead: TBA; rapporteur: TBA; guide: Chris Taylor)
  • Group ‘biosharers’ (lead: TBA; rapporteur: TBA; guide: Susanna Sansone)
16.15 Break
16.30 Breakout groups: Foundry (Vision statement: “By 2012 a scientist, developer, funder, journal editor, etc. will be able to seamlessly navigate between MI specification components and use them or recommend them in a modular way according to domain(s) of interest and needs”.)
  • Pros and cons for modular versus community-specific checklists, e.g.:
  • Inter-compatibility of MI specifications
  • The need to serve MI specifications to diverse users
  • Procedures for the management of changes and updates
  • Collaborative development, ownership and governance, e.g.:
  • Is it tenable? How would it affect uptake?
  • Do useful models for working exist (e.g., GO, OBI, other successful groups)?
  • Development of a Foundry Charter: binding commitments to enable communities to demonstrate their commitment to develop their MI requirements within MIBBI
  • Recommending the MIBBI Foundry as their preferred source of guidelines
  • Agreeing to work towards consensual solutions with respect to shared areas (e.g., organism, person, geographic location, sample preparation, etc.)
18.00 End of main session
20.00 Dinner

Thursday, 2nd December

09.00 Breakout groups report back (Chair: Chris Taylor)
  • Group ‘wet’ (rapporteur: TBA)
  • Group ‘dry’ (rapporteur: TBA)
  • Group ‘biosharers’ (rapporteur: TBA)
10.00 MICheckout: status and next steps (Chair: Susanna Sansone)
  • MICheckout: status and next steps (Chris Taylor)
10.20 Discussion: MICheckout (Simple Q&A based on the preceding presentation)
  • Suitability of current list of output types
  • HTMLs, XML, XML Schema, tab-delimited, ISA config file (and wikis)
  • What choices should the interface offer to experimentalists
  • Extremely simple at present: self-ordered list of largely ‘raw’ content
  • Offer only high-level views of domains and techniques/technologies?
  • 'Off-the-peg' lists keyed by existing community MI specifications?
  • How should the next interface look and function?
10.50 Instructions for breakout sessions (Susanna Sansone)
11.00 Break
11.15 Breakout groups: MICheckout (Generating ideas for the next version of MICheckout)
  • What concepts are useful for scientists describing workflows
  • Granularity; world view (e.g., 'omics'); language use (e.g., assay, species)
  • Desirability and availability of appropriate controlled vocabularies
  • What choices should the interface offer to experimentalists
  • High-level views of domains and techniques/technologies?
  • 'Off-the-peg' lists keyed by existing community MI specifications?
  • Are there additional output types that we need?
  • What are the main features that the new interface should have?
12.15 Breakout groups report back (Chair: Chris Taylor)
13.00 Lunch
15.00 Beyond MIBBI (Chair: Dawn Field)
  • BioSharing: goals, activities and plans (Susanna Sansone)
15.20 Discussion: BioSharing (From policies to checklists, terminologies, formats and...)
  • Towards a ‘one-stop-shop’ for (candidate/emerging) standards
  • Entering core information de novo or importing from / linking to other resources?
  • Specialisation for each type of standard
    • Which fields to display, what is missing etc.
  • Beyond standards: listing compatible tools, journal endorsements, etc.
  • Providing searches and views for diverse users
  • Managing updates
  • Encouraging 'joined-up' projects and maximising reuse
  • Use of MI specifications, CVs/ontologies and formats
16.00 Break (Chairs prepare final summary)
16.45 Summary and wrap up
  • Major points, next steps and action list (Chairs)
  • Final comments, if any arise
18.00 End of main session
20.00 Dinner

Meeting Objectives

  1. Review and advise on current state of project
    • Website and Portal: state of website, suggested changes.
    • Foundry: review of content and methods of working.
    • MICheckout: fitness for purpose, how to improve it.
  2. Formalise ownership and upkeep of MIBBI Foundry module content
    • Recording of member projects’ interest areas (ownership).
    • Development (often collaborative) of modules covering projects’ interest areas.
    • Recommendation to communities to use only Foundry guidelines.
  3. Reach a position on interactions with other standards projects and resources
    • Implementing ontology links in Foundry modules (and taking a position on ‘choice’).
    • Encoding of Foundry content in tools, formats and databases; use of identifiers.
    • Beyond checklists: working in the context of the BioSharing initiative.

Organising Committee and Support

Dawn Field, NERC Environmental Bioinformatics Centre, UK.

Carsten Kettner, Beilstein-Institut, Frankfurt, Germany.

Susanna-Assunta Sansone, University of Oxford, UK.

Chris Taylor, European Bioinformatics Institute, UK.

Attendees

Jan Aerts MIQAS
Nigel Binns MIARE
Andy Blake MIMPP
Cedrik Britten MIATA
Ario de Marco MIPFE
Dawn Field MIBBI
Jennifer Fostel TBC
Pascale Gaudet ISBiocuration / BioDBCore
Alejandra Gonzalez-Beltran GIATE
Nigel Hardy CIMR
Jan Hellemans MIQE
Henning Hermjakob PSI, EBI databases
Nick Juty MIRIAM / MIASE
Carsten Kettner STRENDA
Jim Leebens-Mack MIAPA
Eamonn Maguire MICheckout
Steffen Neumann Plant metabolomics
Sandra Orchard MIMIx / MIABE / MIAPAR
Helen Parkinson MIAME / MINSEQE
William Piel MIAPA
Shoba Ranganathan MIABi
Philippe Rocca-Serra MIAME/Nutr / MIAME/Tox
Susanna-Assunta Sansone MIBBI
Annapaola Santarsiero BioSharing
David Shotton MIIDI
Peter Sterk MIGS/MIMS/MIENS
Chris Taylor MIBBI / MIAPE
Andreas Untergasser MIqPCR (/MIQE)
Trish Whetzel NCBO


Then workshop is supported by Beilstein-Institut; MIBBI activities are part of the BioSharing network and supported by BBSRC and NERC funds to the ISA project.

General Information

The workshop will take place in the historic Hotel Jagdschloss Niederwald in Rüdesheim, Germany. The setting and the limited number of participants provide a very convivial atmosphere for the ready exchange of thoughts and ideas. The meeting will be held 30th November - 3rd December 2010 with the 30th and 3rd for travelling. On the evening of the 30th there is a reception followed by dinner. The workshop, lunches and dinners will take place at the hotel. The scientific program will take place over two days and will start at 09.00 on Wednesday, 1st December and end in the late afternoon on Thursday, 2nd of December 2010. If you wish to extend your stay, please contact the hotel directly. The language of the workshop is English. The dress of the workshop is casual/informal.

Reimbursement of Travel Expenses

The Beilstein-Institut will cover reasonable expenses of invited and registered guests.

Board and lodging: The foundation will pay the full board rate at the hotel including all meals (ca. 400,- EUR per person for three nights) (extras, such as drinks or telephone, are excluded).

Travel: if requested, we will meet your expenses, including coach (economy) air travel, 2nd class rail travel or travel by car. The anticipated limit will be 500,- Euros.

German tax regulations allow us to reimburse travel expenses only if:

  • We are given the original invoice(s) and/or,
  • We are given all original tickets used:
    • For air travel - the original passenger coupons.
    • For rail travel - the original ticket(s).
    • For those travelling by car, please note the exact number of kilometres travelled.

Please help us to ensure rapid repayment of your travel expenses by using this PDF form.

Instructions for Project Briefings

Attendees representing projects that have generated one or more minimum information specifications are requested to prepare a three-minute presentation to describe the scope and status of those specifications. We suggest that speakers prepare three slides:

1. The name and scope of the specification(s) they represent.
Acronym and its expansion; list of topic areas addressed (technologies and techniques, biology, etc.) -- no need for the background on the techniques beyond a single-sentence explanation -- can be got later.
2. The status of the specification(s) and any associated resources.
Whether it is a draft or mature, and whether databases, tools, CVs and formats exist to support it.
3. A summary of contributors and their means of support.
Just as it says. Could cram significant publications in here.

Questions will form part of the subsequent discussion.

We will have an LCD projector (XGA) connected to a Windows or Apple Macintosh PC available. A detailed running order for these brief presentations will be decided shortly.

Accommodation & Travelling

Accommodation will be reserved for registered participants (upon receipt of the completed and returned registration form) for four three nights at:

Jagdschloss Niederwald Hotel
Fam. Mueller
Am Niederwald 1
D-65385 Ruedesheim
Germany.
 
Phone: +49-6722-7106-0
Fax: +49-6722-7106-666
Email: jagdschloss@niederwald.de
Web: http://www.niederwald.de/


A special rate of about EUR 400,- per person for lodging (3 nights) and full board has been negotiated with the hotel. The full board at the hotel covers from dinner on 30th November to breakfast on 3rd December and includes all coffee breaks during the conference, pool and sauna use as well as free WLAN access.

Extras, such as drinks, telephone calls etc. are not included in the price.

The hotel accepts MasterCard and Visa.

Please notify the organizers about changes of your travel plans. Cancellation fees are at the expenses of the participants.

Accompanying participants are responsible for settling their hotel bills directly with the hotel on departure.

How to Reach the Conference Site

The hotel is located on top of the Rheingau heights of Ruedesheim. Hotel website.

By air

Ruedesheim is located ca. 50 km north of Frankfurt airport which can be reached by almost all airlines from Europe and Overseas. Other airports close to Ruedesheim are Cologne and Dusseldorf. From these cities, it is then possible to travel by train via Mainz and Wiesbaden to Ruedesheim. Low-price airlines fly to Hahn airport from where bus connections to Koblenz, Mainz and Frankfurt are available.

By rail

Travel to Ruedesheim via Wiesbaden (from Frankfurt airport) or Mainz (from Cologne or Dusseldorf airport) and take a taxi or the hotel shuttle to the Jagdschloss Niederwald Hotel.

By car

Coming from Koblenz or Cologne: Take the autobahn A61, exit Bingen and take the ferryboat to Ruedesheim. Or take autobahn A61, change at "Dreieck Nahetal" to the A60 and drive in the direction "Mainz". Change at "Dreieck Mainz" to the A643, in the direction "Wiesbaden, Frankfurt", cross the river Rhine and change at "Autobahnkreuz Schierstein" to the A66/B42, in the direction Ruedesheim.

Coming from Frankfurt airport: Take the autobahn A3 and drive in the direction Cologne. Change at "Wiesbadener Kreuz" to the A66, in the direction Wiesbaden. The autobahn A66 becomes the B42 and leads you directly to Ruedesheim. Both the Niederwald Monument and the Jagdschloss Niederwald are sign posted.

Liability and Insurance

The Beilstein-Institut will not be liable for any accident, theft or damage to property, nor for any delays or modification in the program due to unforeseen circumstances. Participants and accompanying persons are advised to arrange for their personal travel and health insurance.

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