geuvadis_rnaseq September 2012

geuvadis_rnaseq@lists.crg.es

2 participants
5 discussions

by Mathias Brännvall

Dear colleagues, Here at last is the QC-survey for geuvadis. I kindly ask each partner to answer it and send back to me by *11 August* at the latest. As the survey covers both laboratory details and bioinformatics I suggest that each principal investigator at each site delegates the task to the appropriate person(s). For question 11 and 22: You don't have to describe every data analysis pipeline you have, that would be to much to ask. Please choose one or two you use the most and/or one that you have particular expertise in. Please don't hesitate to ask me if there is something that is unclear. Thank you and best summer greetings to all of you. Mathias -- _____________________________________________ Mathias Brännvall, PhD Project coordinator Dept. of Medical Sciences, sect. Molecular Medicine, Uppsala University Akademiska sjukhuset, ing. 70, 3 tr phone: +46-(0)18-6114934 mobile: +46-(0)70-1679446 e-mail: Mathias.Brannvall(a)medsci.uu.se

11 years, 9 months

[Geuvadis_rnaseq] GEUVADIS RNAseq paper -- TC doodle

by Gabrielle Anne Bertier

Dear all, Please fill in the following doodle for the next GEUVADIS RNAseq TC on the project's publication: http://www.doodle.com/pdeyynfz3rnwvtaf?lt=2<http://www.doodle.com/pdeyynfz3rnwvtaf?lt=1> Preliminary agenda would be: - outlines of the main paper and the QC companion paper - practicalities of publication - other companion papers Kind regards, Gabrielle Gabrielle Bertier Scientific Project Manager International and Scientific Affairs CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Tel: +34933160374 Mobile: +34639960656 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu; www.fliact.eu

11 years, 11 months

[Geuvadis_rnaseq] IMPORTANT NOTICE: GEUVADIS survey DEADLINE EXTENDED

by Gabrielle Anne Bertier

Dear all, I remind you that we would highly appreciate if you could fill in, and distribute our survey on NGS to all your relevant colleagues. Note that we've extended the deadline to the 10th October 2012 Full survey link: https://qtrial.qualtrics.com/SE/?SID=SV_bHJDue550PwdFrv To describe the survey please use freely the following text: ------------------ THE GEUVADIS PROJECT - More information on our website: www.geuvadis.eu<file:///C:\Users\gbertier\Documents\GEUVADIS\Annual%20Meeting%202\www.geuvadis.eu> The latest high-throughput next-generation sequencing technologies allow investigators to sequence entire human genomes and transcriptomes at an affordable price and within a short time frame. An increasing number of research centers in Europe have access to these technologies, in-house or through regional, national and international infrastructures. Storing, disseminating and analysing the large amount of data produced generate major challenges. Tackling these challenges requires extensive exchange of data, information and knowledge between sequencing centers, bio-informatics networks, the medical research community and the industry at the European level. The GEUVADIS (Genetic EUropean VAriation in DISease) Consortium has four main aims: 1. Develop standards in quality control and assessment of sequence data 2. Develop models for sequencing data storage, access and exchange 3. Develop standards for the handling, analysis and interpretation of sequencing data from DNA (and RNA) 4. Develop guidelines on the handling of ethical, legal and social implications of phenotype prediction from sequence variation * PURPOSE OF SURVEY 1. Collect quantitative and qualitative information on the current status of DNA sequence production, storage, exchange and analysis in Europe. 2. Collect feedback from research/clinical centers on their main challenges and difficulties regarding the management of these large data-sets potentially containing important medical information 3. Collect information on local standardization efforts, and avoid duplication of efforts throughout Europe 4. Create a road-map/policy document outlining the necessary steps to take national standards to the European level * POTENTIAL PUBLICATION OF RESULTS 1. Results of this survey will be presented at an internal GEUVADIS workshop, on October 30-31st 2012. 2. We will disseminate the road-map to potential funders (private of public), including the European Commission and other possible national public funders. 3. We will submit an abstract to the Joint Conference of Human Genome Meeting 2013 and 21st International Congress of Genetics. * DEADLINE: 30.09.2012 --------------------- If you have any question or comment regarding the Annual Meeting, the workshop and/or the survey please don't hesitate to contact me. Kind regards, Gabrielle.- Gabrielle Bertier Scientific Project Manager International and Scientific Affairs CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Tel: +34933160374 Mobile: +34639960656 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu; www.fliact.eu

11 years, 11 months

Re: [Geuvadis_rnaseq] [Geuvadis_wpl] GEUVADIS RNAseq paper -- TC doodle

by Gabrielle Anne Bertier

Dear all, yes that's right, the doodle is set up at CET. Thanks, Gabrielle -----Original Message----- From: Alvis Brazma [mailto:brazma@ebi.ac.uk] Sent: 26 September, 2012 17:51 PM To: Gabrielle Anne Bertier Cc: geuvadis_rnaseq(a)lists.crg.es; geuvadis_wpl(a)lists.crg.es; geuvadis_rna_analysis(a)lists.crg.es Subject: Re: [Geuvadis_wpl] GEUVADIS RNAseq paper -- TC doodle Dear Gabrielle, Am I right to think that this is CE time zone? Thanks, - Alvis Gabrielle Anne Bertier wrote: > Dear all, > > Please fill in the following doodle for the next GEUVADIS RNAseq TC on > the project's publication: > > http://www.doodle.com/pdeyynfz3rnwvtaf?lt=2 > <http://www.doodle.com/pdeyynfz3rnwvtaf?lt=1> > > > > Preliminary agenda would be: > > > > - outlines of the main paper and the QC companion paper > > - practicalities of publication > > - other companion papers > > > > > > Kind regards, > > Gabrielle > > > > */Gabrielle Bertier/* > > /Scientific Project Manager > International and Scientific Affairs > CRG, Center for Genomic Regulation > Carrer Dr. Aiguader, 88/ > > /08003 Barcelona, España > /Tel: +34933160374 > Mobile: +34639960656 > email: gabrielle.bertier(a)crg.es <mailto:gabrielle.bertier@crg.es> > > web: www.geuvadis.eu; www.fliact.eu > > > > > ---------------------------------------------------------------------- > -- > > _______________________________________________ > Geuvadis_wpl mailing list > Geuvadis_wpl(a)lists.crg.es > http://davinci.crg.es/mailman/listinfo/geuvadis_wpl

11 years, 11 months

[Geuvadis_rnaseq] IMPORTANT REMINDER: GEUVADIS survey to fill in and distribute !

by Gabrielle Anne Bertier

Dear all, I remind you that we would highly appreciate if you could fill in, and distribute our survey on NGS to all your relevant colleagues. I have attached a PDF describing all questions you will face in the survey Deadline to respond to the survey: 30th September 2012 Full survey link: https://qtrial.qualtrics.com/SE/?SID=SV_bHJDue550PwdFrv To describe the survey please use freely the following text: ------------------ THE GEUVADIS PROJECT - More information on our website: www.geuvadis.eu<file:///C:\Users\gbertier\Documents\GEUVADIS\Annual%20Meeting%202\www.geuvadis.eu> The latest high-throughput next-generation sequencing technologies allow investigators to sequence entire human genomes and transcriptomes at an affordable price and within a short time frame. An increasing number of research centers in Europe have access to these technologies, in-house or through regional, national and international infrastructures. Storing, disseminating and analysing the large amount of data produced generate major challenges. Tackling these challenges requires extensive exchange of data, information and knowledge between sequencing centers, bio-informatics networks, the medical research community and the industry at the European level. The GEUVADIS (Genetic EUropean VAriation in DISease) Consortium has four main aims: 1. Develop standards in quality control and assessment of sequence data 2. Develop models for sequencing data storage, access and exchange 3. Develop standards for the handling, analysis and interpretation of sequencing data from DNA (and RNA) 4. Develop guidelines on the handling of ethical, legal and social implications of phenotype prediction from sequence variation * PURPOSE OF SURVEY 1. Collect quantitative and qualitative information on the current status of DNA sequence production, storage, exchange and analysis in Europe. 2. Collect feedback from research/clinical centers on their main challenges and difficulties regarding the management of these large data-sets potentially containing important medical information 3. Collect information on local standardization efforts, and avoid duplication of efforts throughout Europe 4. Create a road-map/policy document outlining the necessary steps to take national standards to the European level * POTENTIAL PUBLICATION OF RESULTS 1. Results of this survey will be presented at an internal GEUVADIS workshop, on October 30-31st 2012. 2. We will disseminate the road-map to potential funders (private of public), including the European Commission and other possible national public funders. 3. We will submit an abstract to the Joint Conference of Human Genome Meeting 2013 and 21st International Congress of Genetics. * DEADLINE: 30.09.2012 --------------------- If you have any question or comment regarding the Annual Meeting, the workshop and/or the survey please don't hesitate to contact me. Kind regards, Gabrielle.- Gabrielle Bertier Scientific Project Manager International and Scientific Affairs CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Tel: +34933160374 Mobile: +34639960656 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu; www.fliact.eu

11 years, 11 months

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geuvadis_rnaseq September 2012