5th GSC Workshop
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The 5th GSC Workshop
This workshop is being funded by NERC with organisational support provided by NIEeS and the EBI.
[edit] Dates
Date: 12 - 14 December 2007
[edit] Venue
The Venue for this 5th workshop will be the European Bioinformatics Institute (EBI), Cambridge, UK. The local host is Peter Sterk and the workshop will take place within the new and state-of-the-art IT training suite at the EBI.
[edit] Background
This 5th workshop will focus on finalizing a stable version of the MIGS checklist for publication. It will also focus heavily on hands on work with the newly created "Genomic Contextual Data Markup Language" (GCDML). This is a much richer XML schema that also implements MIGS/MIMS in addition to containing a wider range of additional elements for describing genomes and metagenomes.
[edit] Agenda and Presentations
The agenda is packed with great talks, and yet we need to make sure we have time for group discussions. There are many 10 minute talks because we want people to be able to provide a diversity of views, ideas, and material for seeking group consensus on several key issues.
All speakers should aim for no more than 1 slide for each 2 minutes of your talk. For example, a 10 minute talk should only be 4-5 slides of significant content. Chairs will be strict when it comes to sticking to the timetable. These talks are designed to introduce a topic/project and specific progress towards GSC goals.
If you have any questions about the content or scope of your talk/session, or would like to suggest a change to the agenda, please write to the chair of your session (or to dfield 'at' ceh.ac.uk to pass any query along to the right person/people).
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[edit] WHAT YOU CAN DO AT THE 5th GSC WORKSHOP TO HELP THE GSC REACH ITS GOALS
The purpose of these GSC workshops is to involve the wider, international community in the goal of describing our collection of genomes/metagenomes in more detail. This means extending the type of information captured through a new specification (MIGS/MIMS), setting up a way to capture data (GCDML, the Genome Catalogue), the generation of a unified list of genomes/metagenomes (The Genomic Rosetta Stone), and the development of appropriate ontologies (e.g. EnvO).
The workshop will be a mix of updates since the last workshop (e.g. GCDML, the Environment Ontology) and introductory talks from new communities also interested in describing/analyzing genomes/metagenomes (e.g. Sequencing Centres) or with broad and relevant experiences capturing metadata (e.g. Encyclopedia of Life, BarCode of Life Project, the Ecological Metadata Language (EML), MINIMESS proposal).
[edit] Add to the Wiki
The GSC Wiki is open for anyone to edit and many of you have. Please feel free to make an account and contribute at any time.
[edit] Changes to MIGS checklist
This page in the wiki has been set up to hold feedback on the MIGS checklist and will be resolved at the workshop. The proofs will be resumitted to Nat Biotech on Monday the 17th. Please feel free to add comments!
[edit] OUTCOME OF WORKSHOP: Final MIGS checklist
OUTCOME OF WORKSHOP: Here is the online outline of the checklist built by George Garrity and used at the workshop to discuss the checklist and add additional examples. This is a final version of the checklist: http://gensc.sourceforge.net/docs/migsmims/
[edit] Create MIGS Compliant Genome Reports
Our main goal will be to finalize the checklist for publication. Hopefully we can do this in the time allotted on the first day (to be led by George Garrity) and then spend lots of time on getting to grips with the Genomic Contextual Data Mark Up Language (GCDML) for the rest of the meeting.
If you are willing, you can print out the checklist and try to describe your own genome or metagenome. This would be invaluable as it would guide which elements you think work/don't work. Any data you provide can then be put into the Genome Catalogue and you will get credit for being among the first to fill out a report!
As soon as MIGS is stabilized and we can finish the corresponding XML, we have promises of batch uploads of all Sanger microbial genomes and a large set of phage genomes among other reports. We are looking for more contributions.
[edit] GCDML
Renzo Kottmann, with input from many, has released a first version of GCDML and we are hoping it will be considered by any genomic/metagenomic database for the capture of curated and calculated information. A key part of the development of GCDML in the future will be its extension beyond capture of MIGS/MIMS to additional sources of curated data to calculated data. Nikos Kyrpides has put together an excellent session with representatives of the major sequencing centres to discuss the standardization of gene calling and genomic annotation.
Here is more information available
[edit] Work on the Genomic Rosetta Stone
We will be looking, now that EMBL genomes are mapping to Genome Project Identifiers (PIDs), to proceed with the mapping of local identifiers across genomic databases. As a start, we have a mapped set of the first 500 published genomes from GOLD as collated by Paul Swift and mapped to PID by Peter Sterk. This file has the PIDs in green on the worksheet "Micro_genomes_first_500" along with RefSeq IDs and accession numbers for all chromosomes. This is a real milestone and a great start to jumpstarting the bigger project. Several groups have already agree to join the effort and are working to map their local identifiers to PID (have been doing so for a long time now). We need to update information on who wants to be involved, whether webservices are available for harvesting the mappings, and how we intend to build a central 'resolver' system. An online prototype is available from Tanya Gray and more information can be found here:
More information available here: http://gensc.org/gc_wiki/index.php/Genomic_Rosetta_Stone#A_Genomic_Rosetta_Stone
[edit] Catalogue any sequence datasets not found in the INSDC
There are an increasing number of large sequence-based datasets that are not found in the INSDC. This page aims to provide a comprehensive list of such datasets to flag up the growing issue of a need for a unified list of all genomes and metagenomes.
- The Marine Viromes of Four Oceanic Regions: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368
REASON: No flowgrams, unassembled. The first published pyrosequencing data sets (4 pooled samples) from natural viral communities. Unique identifiers given for CAMERA, SCUMS, and GCat but could not submit unassembled pyrosequencing data to GenBank and not in Trace Archive as flowgrams no available.
- "Roesch et al The ISME Journal Pyrosequencing enumerates and contrasts soil microbial diversity (2007) 1, 283 – 290
REASON: Sequences too small. "As Genbank does not provide accession numbers for sequences of this length, these 562 sequences are provided in the supple-mentary material (Table S1). "
Note: Small read archives under development
[edit] Contribute to the upcoming special issue of OMICS from the 5th GSC Workshop
Dawn Field and George Garrity have been asked by the OMICS Editor and Chief Eugene Kolker to produce a special issue of OMICS based on the 5th GSC Workshop.
Background and how to contribute: GSC Special issues of OMICS
[edit] Travel to the EBI (workshop venue)
A coach/bus will be provided each day to transport delegates from the accommodation at Jesus College, Cambridge, to the EBI and back again in the evenings. Pick-up location will be from Victoria Avenue within the college, and times will be shown in the agenda that can be downloaded from this wiki page, but are likely to be 9.30am on Wed 12th and 8.30am on Thurs 13th and Fri 14th. Return times from the EBI to Cambridge will be 6.00pm on the 12th and 13th, and 3.30pm on the 14th.
For those delegates travelling directly to the EBI: Maps and directions are available from the EBI website
If you are travelling directly to the EBI, please be aware that you will need to check in at the main gate reception. Your names have already been registered with security, please tell them you are visiting the EBI and your contact person is Peter Sterk. Security passes and workshop badges can be collected from the EBI reception desk.
Additional information on the Wellcome Trust Genome Campus, facilities and local weather can be found at http://www.ebi.ac.uk/Information/Site_Info/site_info.html.
[edit] Accommodation
11, 12 and 13 December
Accommodation will be paid for by the GSC and provided for participants on the nights of Wednesday 12th and Thursday 13th December at Jesus College, Cambridge. Please indicate on your registration the nights that you require accommodation.
Accommodation can also be provided on Tuesday 11th December for those participants travelling long distance. Please indicate on your registration if you require accommodation for Tuesday 11th December.
Breakfast is included at the college and will be available from 7.30am - 8.30am.
Jesus College is situated in the heart of Cambridge and is easily accessible by bus, rail or car. A map of Jesus College and travel directions can be found on their college website at http://www.jesus.cam.ac.uk/contacts/travel.html.
On arrival at Jesus College, please contact the Porters Lodge to obtain a key to your room. A map of the college is available here.
Transport from Jesus College to the workshop venue at the EBI is provided as stated above.
[edit] NOTE: Internet Access
If require Internet access in your room accommodation at the college, then we will need your laptop "Machine Address" 3 weeks before the event to register access. Please email the Machine Address to Ms Caroline Wills-Wright, email CARLIS@wpo.nerc.ac.uk. before 20th November. This is not wireless access, so you will need to provide your own Internet cable to connect to the College ethernet.
14 December
Accommodation for the 14th December in Cambridge can also be arranged, but you will need to request this by sending a request by email to Ms Caroline Wills-Wright, email CARLIS@wpo.nerc.ac.uk. Accommodation for the 14th will necessitate a move from Jesus College as rooms are not available at the college.
If you have an early flight booked on Saturday and require accommodation closer to the airport for the night of Friday 14th, then please book this yourself and the expense will be reimbursed to you.
[edit] Travel to Cambridge
The above Jesus College link to their travel page has details on how to get to Cambridge from most airports and local cities. A summary for Heathrow to Cambridge is:-
Rail
Take the Heathrow Express rail service to Paddington rail station (departs every 15 mins), then the underground tube to Kings Cross rail station (departs every 30 mins), then a train to Cambridge (departs every 30 mins). Then take a taxi from Cambridge rail station to Jesus College. Total cost about £35.00 and takes just over 2.0 hours if you get your timing right.
Coach
Take the National Express Jetlink coach from the Central Bus Station at Heathrow airport direct to Cambridge Drummer Street bus station. Coaches run every hour - tickets from the coach driver. Then from the Cambridge bus station walk 10 mins to Jesus College. Total cost about £25.00 and takes about 2.5 - 3.0 hours. A timetable with pick-up points is available here Image:Bus heathrow.pdf.
[edit] Workshop Lunches and Dinners
During the workshop, we will have a buffet lunch outside the meeting room on Wednesday. On Thursday and Friday, lunch will be at the site restaurant. Lunch vouchers will be provided.
There are two scheduled dinners for the workshop delegates, both are held in the Upper Hall at Jesus College. Dinner is at 7.30pm on Wednesday 12th and 7.30pm on Thursday 13th December. Please indicate any special dietary requirements during the registration process.
We are also arranging dinner for the 11th at a local Cambridge seafood restaurant (like last time!).
Dinner on the 11th will be at the Loch Fyne Restaurant in central Cambridge (http://www.lochfyne.com/Restaurants/Locations.aspx). The reservation (~20 people!) is for 8:30 and we will meet at the Porter's Lodge at Jesus College at 8 pm to walk into Town. It is a set meal with a Christmas theme and is sponsored by the GSC.
[edit] Reimbursement of Expenses
Reasonable travel costs will be reimbursed to the delegates on submission of a signed NERC T&S form along with all original receipts for the expenditure being claimed. Travel can include all travel to and from the venue. A NERC T&S form can be downloaded from here.
Completed forms with receipts must be posted to Ms Caroline Wills-Wright, CEH Oxford, Mansfield Road, Oxford, OX1 3SR. email CARLIS@wpo.nerc.ac.uk.
[edit] Two Page Summary
You can download and print a two page summary of the venue, accommodation, travel and T&S claim form from here.
[edit] MIGS/MIMS and GCDML - Outstanding Issues
MIGS/MIMS and GCDML - Outstanding Issues
