From sherlock at genome.stanford.edu Thu Jun 5 14:53:55 2008 From: sherlock at genome.stanford.edu (Gavin Sherlock) Date: Thu, 5 Jun 2008 14:53:55 -0700 Subject: [Gofriends] MGED 11 Meeting, Trentino, Italy : Abstract Submission deadline for oral presentations is June 10th Message-ID: <0F9D2E1A-9456-4231-A913-0FDB0CDBE6C5@genome.stanford.edu> Dear Colleagues, Apologies if you receive this more than once. The MGED 11 abstract submission deadline for consideration for an oral presentation is next Tuesday, June 10th. Further information on MGED 11 is available at http://www.mgedmeeting.org/ and other key dates are: Notice of acceptance: June 25th Early registration ends: June 30th All abstract submission closes: August 5th The scientific focus of the meeting will be high throughput technologies - in particular microarrays and ultra high throughput sequencing - and associated data handling issues, analysis techniques and standards. We have lined up some outstanding speakers who will be giving talks on these topics. This year we will again be selecting half of the plenary speakers from submitted abstracts, to encourage greater participation in the MGED community. Continuing from last year, we will also be running a poster competition, with prizes for the best posters presented by graduate and postdoctoral students. Finally, we will be awarding up to seven $1500 travel grants to graduate or postdoctoral students who are US citizens traveling from the US. We look forward to seeing you all in Trentino, Sincerely, The Microarray and Gene Expression Data (MGED) Society ---------------------------------------------------------------------------------- MGED 11 Program Sunday 31st Aug. 15:00 - Registration and Exhibit Area are open Monday 1st Sept. 07:30- Registration opens 08:30- 09:00 Welcome, Introduction and organization details: Chris Stoeckert Catherine Ball, Cesare Furlanello ENCODE Session 09:00-10:00 Keynote Lecture: Ewan Birney 10:00-10:45 Plenary Lecture: Barbara Wold 10:45-11:15 Break 11:15-12:00 Plenary Lecture: Shirley Liu 12:00-12:30 Talks from Submitted abstracts (1) 12:30-14:00 Lunch Wine Genomics Session 14:00-14:45 Plenary Talk: Claudio Moser 14:45-15:30 Talks from Submitted abstracts (2) 15:30-16:00 Break 16:00-16:45 Plenary Talk: Duccio Cavalieri 16:45-17:45 Keynote Talk: Grant Cramer 18:00-20:00 Welcome cocktail 21.00 Public Science Conference I Tuesday 2nd Sept. Human Disease Session 09:00-10:00 Keynote Lecture: Joe Gray 10:00-10:45 Plenary Lecture: Mike Bittner 10:45-11:00 Break 11:00-11:45 Plenary Lecture: Nigel Carter 11:45-12:30 Talks from Submitted abstracts (3) 12:30-14:00 Lunch Quality and Standards in Action 14:00-14:15 Introduction and update on MGED Standards: Chris Stoeckert 14:15-14:30 MAGE-TAB Tools: Helen Parkinson/Tim Rayner 14:30-14:45 ISA-TAB and integrative standards: Susanna-Assunta Sansone 14:45-15:30 Title TBA (Semantic Web and Gene Expression): Alan Ruttenberg 15:30-16:00 Break 16:00-18:00 Poster Session I 19:00-21:00 Conference Dinner Wednesday 3rd Sept. Learning from Microarray Data 09:00-10:00 Keynote Lecture: Naama Barkai 09:45-10:30 Plenary Talk: Rainer Spang 10:30-11:00 Break 11:00-11:45 Plenary Talk: Atul Butte 11:45-12:30 Talks from Submitted Abstracts (3) 12:30-14:00 Lunch Functional Genomics and Systems Biology 14:00-15:00 Keynote Lecture : Stephen Oliver 15:00-15:30 Break 15:30-16:15 Talks from Submitted Abstracts (3) 16:15-17:00 Plenary Lecture TBA 17:00-19:00 Poster Session II Close of Meeting, Final Announcements, Award of Poster Prizes 20.15 Public Science Conference 2 Thursday 4th Sept. Workshops 8:30 - 11:30 Morning Parallel Sessions ? Data Analysis Tutorial: John Quackenbush and Roger Bumgarner ? Tutorial on using Bioconductor for Array Quality Assessment: Audrey Kauffmann and Wolfgang Huber 11:30 - 14:30 Gene Pattern tutorial: Ted Liefeld 14:30 - 17:30 Afternoon Parallel Sessions ? Using ArrayExpress Tutorial: Gabriella Rustici andMisha Kapushesky ? EMERALD Workshop on Array Quality Assessment Methods: Marc Salit and Wolfgang Huber From FMcCarthy at cvm.msstate.edu Wed Jun 11 15:23:06 2008 From: FMcCarthy at cvm.msstate.edu (Fiona McCarthy) Date: Wed, 11 Jun 2008 17:23:06 -0500 Subject: [Gofriends] survey of chicken & cow array usage Message-ID: Hi All, We are currently providing functional annotation (GO) for gene products represented on chicken & cow arrays. To prioritize our efforts, we would like know which arrays these communities are currently using. You can help us by completing the polls found here: Chicken Array Usage http://doodle.ch/participation.html?pollId=zwvmhpt5t23tvfv8 Bovine Array Usage http://doodle.ch/participation.html?pollId=ezwu46625934bzk4 These polls contain arrays in the Gene Expression Omnibus (GEO) Database. If the array you are using is not represented, please tell us by adding a comment underneath on the page. (If you are uncomfortable with adding your name, please feel free to use initials or etc.) Please help by passing this email on to your colleagues using arrays who are not members of this newsgroup. thanks Fiona McCarthy The AgBase Databases Department of Basic Sciences Box 6100 MS 39762-6100 Mississippi State University USA Tel: (+ 1) 662 325 5859 Fax: (+ 1) 662 325 1031 http://www.agbase.msstate.edu/ From dbarrell at ebi.ac.uk Fri Jun 20 01:16:31 2008 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Fri, 20 Jun 2008 09:16:31 +0100 Subject: [Gofriends] June 2008 GOA release In-Reply-To: <42690FC8.8010409@ebi.ac.uk> References: <42690FC8.8010409@ebi.ac.uk> Message-ID: <485B675F.5080603@ebi.ac.uk> GOA releases: June 2008 ============================ [Please see below for important proposed form at change] GOA (GO Annotation at EBI) is a project run by the European Bioinformatics Institute that aims to provide assignments of gene products to the Gene Ontology (GO) resource. The data can be obtained via: EBI FTP: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/ EBI SRS: http://srs.ebi.ac.uk. Search GOA data library GO FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/ GO CVS: http://www.geneontology.org/GO.CVS.help.html (the last two will be updated overnight) For further information read: http://www.ebi.ac.uk/GOA or contact goa at ebi.ac.uk. **Proposed GOA gene association file format change** The GOA group is intending to change the contents of columns 3, 10 and 11 in all GOA gene association files except gene_association.goa_pdb.gz. The changes being proposed are outlined below and will ensure that the format of the affected columns is in line with GO Consortium requirements. While the ordering of identifiers in these columns will change, no identifiers will be removed. These changes will come into effect at the end of July (Release 65 of GOA UniProt). *Column 3 (DB_Object_Symbol)* Current content: UniProt identifier (e.g. PRG4_HUMAN) Future content: Primary gene symbol when available (e.g. PRG4), otherwise will contain locus name or will repeat the value present in column 2 (either a UniProtKB accession, IPI, Ensembl, VEGA, HINV, TAIR or RefSeq peptide identifier). *Column 10 (DB_Object_Name)* Current content: A list of gene symbols and protein name. (e.g. PRG4, MSF, SZP: Proteoglycan-4 precursor) Future content: protein name only when available (e.g. Proteoglycan-4 precursor). Otherwise will be left blank. Column 11 (Synonym) Current content: IPI identifiers when available (e.g. IPI00024825) Future content: A pipe-delimited list of alternative gene symbol synonyms, IPI and UniProtKB identifiers (e.g. MSF|SZP|IPI00024825|PRG4_HUMAN). Please contact us if you have any concerns about these proposed changes. Regards The UniProt GOA Team