HUPO PSI Spring Workshop 2006 — Proteomics and Beyond

in association with the HUPO Publications Committee meeting

April 21st-23rd, San Francisco CA, USA

N.B. THIS MEETING OCCURRED IN THE PAST!

Contents

1. General Information
2. Meeting structure
3. Registration
4. Logistics
5. Sponsors

General Information

This page gives all information associated with the upcoming 2006 PSI Spring Meeting a the Hyatt Regency Hotel, San Francisco CA, USA.

Mainstream PSI activities

Since its conception in April 2002, the HUPO Proteomics Standards Initiative has contributed to the development of community standards for proteomics in a collaborative and very dynamic way, resulting in several published reports. Following the initial release in 2004, the MI work group has now released version 2.5 of the PSI MI standard for molecular interactions, and the mzData 1.05 standard for mass spectra has been widely implemented by instrument vendors, tool providers and public databases.

At its third spring meeting, the Proteomics Standards Initiative will formalise its structure, further develop its core standards, and provide a platform for scientific exchange with related fields beyond proteomics. Additionally, after initially operating in a very informal manner, PSI is now coming of age; with an increasing participation, increasing investment into standards by both academic and commercial entities, and growing interest by scientists, funders, and journals, the PSI needs to formalise its operations. A major topic in the common session will be a formal structure for PSI and its standardisation process.

• The PSI MI 2.5 standard for molecular interactions has been released, the MI activities will focus on tool implementation and curation aspects.
• The MS workgroup will discuss a backwards-compatible, incremental update of the mzData standard, and expects to finalise the analysisXML standard for protein identifications.
• The PSI MOD workgroup will finalise the proposed standard for the representation of protein modifications.
• The GPS workgroup will present the final, reviewed MIAPE: Gel Electrophoresis module, drafts of the gel informatics and sample preparation MIAPE modules, the beta release of the GelML format and drafts of spML (sample prep) and GIfML (gel informatics).

Additional events at the meeting

Metabolomics: The benefits of broad cross-domain input into the standardisation process are several; data intercompatibility, speed of development and design robustness are just three. The metabolomics community will most likely adopt the mzData format, with the obvious benefits for instrument vendors, tool and database providers; a productive collaboration is also being formed to jointly advance the spML format; the vocabularies to support both spML and mzData will similarly be advanced jointly. To promote this collaboration, representatives of the Metabolomics Society have been invited to participate in the meeting.

Minimum Information About a Cellular Assay: Advances in genomics and functional genomics have enabled large scale analysis of gene and protein function by means of high throughput cell biology. Cells are perturbed in vitro and induced effects are recorded and analysed. Perturbations can be in several flavours and induced by molecules (e.g. siRNA, expression construct, small chemical compound) or numerous other stresses (e.g. temperature shift, serum starvation). Standardisation of experimental descriptions and ontologies (adopting e.g. FuGE) with help of a Minimum Information About a Cellular Assay (MIACA) will provide means to compare, exchange, and integrate data that have been acquired in different and diverse setups. Working groups for MIACA modules will be established, towards the formulation of formats and ontologies, and their integration into a community standard data model. Scientists working in the generation or analysis of data acquired in cellular assays are invited to actively participate in this effort.

The FuGE OM/ML: PSI will continue to foster discussion of implementation issues for the FuGE model (now at milestone 2), both in its native form and as a parent schema for PSI formats.

The Functional Genomics Ontology (FuGO): The meeting will feature a half day session dedicated to issues around the growth and evolution of that ontology and the relationship between PSI-generated CVs and FuGO. Ontology issues will also arise throughout the meeting, and will in part be addressed in the context of FuGO.

PSI organising committee:

Henning Hermjakob
Randy Julian
Chris Taylor
John Garavelli

Local organizing committee:

Robert Barkovich, Thermo Corporation
David Horn, Agilent Technologies
Sean Seymour, Applied Biosystems

Meeting structure

How to register

Any queries regarding registration should be directed to Chris Taylor.

Logistics

The meeting will be held at the Hyatt Regency San Francisco, which is accessible from both the San Francisco (SFO) and Oakland (OAK) airports. Reduced rate rooms have been allocated at the Hyatt Regency ($195 per night). To reserve, dial (+1) 800 233 1234 and state that you are attending the "HUPO-PSI meeting". Please also indicate your intention to book at the Hyatt on the registration form, by checking the appropriate box.

By far the best way to travel to the Hyatt Regency is by using BART — the Bay Area Rapid Transit subway system (http://www.bart.gov/) — from either airport. The hotel is only feet away from the exit of the Embarcadero BART stop. There are maps of the whole BART system in all trains:

• SFO: BART departs directly from the international terminal of SFO. If you arrive at one of the domestic terminals you will have to take the AirTrain transport - a light rail loop that stops at various points within the airport - to reach the BART station. The cost from SFO is $5.15. From SFO, take any train in the direction of San Francisco/East Bay (Fremont, Richmond, Pittsburg/Baypoint).
• OAK: If you are arriving in Oakland, you must take a bus (AirBART) to reach the Coliseum/Oakland Airport BART station. The cost from OAK is $3.35 BART fare + $2.00 cash for AirBART. From OAK, take any train headed toward San Francisco (Colma, San Francisco, Milvia/SF Airport).

Alternately, you can take taxis or one of the many shared van transport services, although these are much more expensive ($25-45) and may well be rather slower, depending on traffic.

Sponsored (to date) by

Additional Sponsorship gratefully received from: Bruker [www.bruker.de], Cell Signaling Technology [www.cellsignal.com]