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DTSTAMP:20260711T114628Z
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DTSTART:20171001T230000Z
DTEND:20171001T230000Z
DESCRIPTION:\nIn this course\, participants will receive an introduction to
  EMBL-EBI and its public data resources\, with a focus on functional genom
 ics (e.g. microarray expression profiling\, RNA-seq\, ChIP-seq). \nDuring
  the course\,participants will acquire skills in the effective use of func
 tional genomics databases: ArrayExpress (one of the ELIXIR core data re
 sources) and Expression Atlas.  Such skills will include searching\, ret
 rieving and interpreting data relevant to their research areas of interest
 s.  There will be interactive presentations\, demonstrations and practica
 l exercises to give trainees hands on experiences.To complement the sessio
 ns on functional genomics\, there will be brief presentations on some rela
 ted EMBL-EBI resources: EBI metagenomics and Reactome. \nSince many EM
 BL-EBI resources are built to facilitate reproducible research\, there wil
 l also be a session discussing the obstacles and barriers to data reproduc
 ibility in the research environment\, illustrated by real-life examples. 
  Participants will learn about some handy data management techniques that 
 help to alleviate reproducibility problems\, many of which have already be
 en implemented for over a decade at EMBL-EBI.\nPlease note this course doe
 s not cover microarray\, sequencing\, metagenomic or network data analysis
 .\n \nCourse Organizers:​\n\nCymon Cox is a senior researcher at  CCM
 AR in Faro. He is the leader of  the Plant Systematics and Bioinformatic
 s group. \n           Affiliation: Fundação para a Ciência (FCT
 ) / CCMAR\, Faro\, PT\n \n\nAmy Tang studied Human Genetics at the Univer
 sity of Nottingham for her bachelor degree.  She did her PhD at the Broc
 kdorff's lab\, then at MRC Clinical Sciences Centre / Imperial College Lon
 don\, working on the epigenetic control of X-chromosome inactivation in mo
 use early development. The project was split 50:50 into wet-lab and bioinf
 ormatics\, this is when she first got interested in bioinformatics. After 
 a short postdoc in the same lab\, she returned to study at Imperial for a 
 MSc in Bioinformatics and Systems Biology\, which helped her move laterall
 y from wet-lab to bioinformatics.\nAmy now leads the curation efforts for
  ArrayExpress and Expression Atlas databases in the Gene Expression T
 eam\, promoting reproducible research by maintaining curation quality\, an
 d also by driving the development of the user-friendly ArrayExpress data s
 ubmission tool Annotare. To allow users make the most out of the database
 s and to educate researchers on best practices for reproducible research\,
  she also manages all training activities for the Team\, delivering most o
 f the hands-on courses on functional genomics resources at EMBL-EBI and wo
 rldwide.  Through listening to Annotare submitters' needs and gathering f
 eedback at training courses\, she also acts as users' advocate and works w
 ith software developers to improve user experience of ArrayExpress and Exp
 ression Atlas websites.\nBefore joining EMBL-EBI\, Amy was a senior bioinf
 ormatician in the Ensembl GeneBuild team\, curating gene models for key 
 model organisms such as mouse and rat.\n          Affiliation: EMBL-E
 BI\, UK\n \n\nAdelino V. M. Canário is a full professor at University of
  Algarve (Portugal) is a specialist in fish physiology. He is the Director
  of the Centre of Marine Sciences (ccmar.ualg.pt) since 1994 and leads the
  Comparative and Molecular Endocrinology research group. He teaches Cell B
 iology to undergraduate students and Reproductive Biology to graduate stud
 ents. He coordinates courses for graduate students on Molecular and Cellul
 ar Biology Techniques and marine Genomics. He is the promoter of 2 ongoing
  PhDs and has supervised to completion 12 PhDs (8 in the last 5 years). He
  is internationaly recognized expert in his field with over 140 published 
 articles (H=26) in regulation of calcium homeostasis\, fish reproductive p
 hysiology\, hormone-behavour relationships\, chemical communication and ge
 nomics. He has coordinated and participated in European Commission funded 
 research including recently Marine Genomics Europe\, Assemble and EMBRC (E
 SFRI infrastructure).\n          Affiliation: Fundação para a Ciên
 cia (FCT) / CCMAR\, Faro\, PT\n \n\nGrace Mugumbate Scientific Training 
 Officer - Training\n          Affiliation: EMBL-EBI\, UK\n \nCourse 
 Lecturers:​\n\nSteven Jupe is a Knowledge Database Curator/Developer fo
 r the Hermjakob team at the EML-EBI.\n           Affiliation: EMBL-
 EBI\, UK\n \n\nAmy Tang (Bio above)\n          Affiliation: EMBL-EB
 I\, UK\n \nAudience:\nThis course is aimed at wet-lab researchers who hav
 e minimum or no prior experience in bioinformatics\, who want to explore\,
  and use EMBL-EBI resources for their research. No knowledge of programmin
 g is required\, but the trainer expects an undergraduate level knowledge o
 f biology and/or biochemistry.\n \nModules and resources:\nDuring this co
 urse\, you will learn about:\nEMBL-EBI data services: an overview of the 
 free databases and data services covering a wide range of subject areas ac
 ross biological sciences.\nArrayExpress: a public archive of functional ge
 nomics data (e.g. expression microarrays\, RNA-seq\, ChIP-seq)\, often dep
 osited as a pre-requisite of journal publication\nExpression Atlas: a publ
 ic resource of systematically analysed gene and protein expression data fr
 om manually curated studies across many species (not limited to model orga
 nisms)\nData management: the problems we face in poor reproducibility of p
 ublished research results\, and how to alleviate them with some simple dat
 a management techniques\n \nLearning Outcomes:\nAfter this course\, you s
 hould be able to:\nDefine some of the public data services EMBL-EBI provid
 es\nExplore functional genomics data in ArrayExpress effectively\, and sub
 mit your own data with ease.\nSearch for and interpret expression informat
 ion using Expression Atlas\nDiscuss the value of biocuration in safeguardi
 ng reproducibility of research data\n \nProgram:\nTime\nTopic\nLecturer\n
 Day 1 - 2nd October 2017\n09:00 - 09:30\nWelcome and Introduction to EBI r
 esources\nAmy Tang\n09:30 - 10:30\nArrayExpress\nAmy Tang\n10:30 - 11:00\n
 Tea/coffee break\n \n11:00 - 12:30\nArrayExpress\nAmy Tang\n12:30 - 13:30
 \nLunch\n \n13:30 - 14:30\nArrayExpress and data submission\nAmy Tang\n14
 :30 - 15:00\nTea/coffee break\n \n15:00 - 16:00\nAn introduction to EBI M
 etagenomics\nAmy Tang\n16:00 - 17:00\nData management for reproducible res
 earch\nAmy Tang\n17:00\nEnd of Day 1\n \nDay 2 - 3rd October 2017\n09:00 
 - 10:30\nExpression Atlas\nAmy Tang\n10:30 - 11:00\nTea/coffee break\n \n
 11:00 - 12:30\nExpression Atlas\nAmy Tang\n12:30 - 13:30\nLunch\n \n13:30
  - 15:00\nExpression Atlas &amp\; RNAseq-er API\nAmy Tang\n15:00 - 15:30\n
 Tea/coffee break\n \n15:30 - 16:30\nReactome (webinar)\nSteve Jupe (TBC)\
 n16:30 - 17:00\nWrap up and feedback\nAmy Tang\n17:00\nEnd of course\n \n
  \n \nParticipation:\nParticipation has a 50€ registration fee.\nRegis
 tration for this course is done at the Centre for Marine Sciences (CCMAR) 
 \, until September the 28th!\nA maximum of 20 participants will be accep
 ted.\nIf you require assistance in finding accommodation\, please contact 
 Cymon J. Cox (e-mail bellow).
LOCATION:Centre for Marine Sciences (CCMAR)
SUMMARY:EMBL-EBI Bioinformatics Workshop
URL;VALUE=URI:http://elixir-portugal.org/event/embl-ebi-bioinformatics-work
 shop
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