Program and Abstract Book - 19th International C. elegans Meeting

PLENARY, PARALLEL AND WORKSHOP LISTINGSThursday, June 27 1:30 PM–2:30 PMStrategies for TransgenesisRoom:Ackerman Grand BallroomOrganizer: Peter Boag, Monash University, Melbourne, AustraliaA key technology for understanding gene function is the generation oftransgenic animals. The aim of this workshop is to highlight the recenttechnological advances that allow for rapid generation of expressionconstructs and transformation of C. elegans. The advantages anddisadvantages of various approaches will be discussed.Speakers:Recombineering: Mihail Sarov, MPI-CBGMosSCI: Christian Frøkjaer-Jensen, Jorgensen Lab, HHMI, UtahBombardment: Jenny Semple, Lehner lab, EMBL/CRGSingle/low-copy integration of transgenes: Shohei Mitani, TokyoWomen's Medical University School of MedicineThursday, June 27 1:30 PM–2:30 PMWormBase tutorial: Genomes, Comparative Genomics,Genomic Variation and modENCODERoom: Bradley International BallroomOrganizer: Kevin Howe, WormBase, European Bioinformatics InstituteOne of the core roles of WormBase is to act as a central repository forthe genome sequences and genomic annotations that form thefoundation of many nematode molecular biology studies. In thisworkshop, WormBase biologists will present an overview of thegenomic data served by the resource and how to access it. Theworkshop will be presented in five parts: (a) an introduction to the newfeatures of the WormBase web-site; (b) genomes, transcriptomes andproteomes in WormBase, including discourse on the curation andanalysis pipelines employed, nomenclature, and how to access thesecore data types; (c) the tools and views provided for comparativegenomics, with focus on gene orthology and paralogy, and genomicalignments; (d) genomic variation data - how it is collected, analysed,represented and displayed, including an overview of nomenclatureused; and (e) an update from modENCODE, with focus on data setsproduced by the project in the last two years.Thursday, June 27 1:30 PM–2:30 PMMapping and Cloning Mutants from Whole GenomeSequence Data Using a Free, Cloud-based PipelineRoom: Grand Horizon BallroomOrganizer: Gregory Minevich, Columbia UniversityWhole genome sequencing (WGS) allows researchers to pinpointgenetic differences between individuals and significantly shortcuts thecostly and time-consuming part of forward genetic analysis in modelorganism systems. Currently, the most effort-intensive part of WGS isthe bioinformatic analysis of the relatively short reads generated bysecond generation sequencing platforms. We will present a free cloudbasedpipeline, called CloudMap, which greatly simplifies the analysis ofmutant genome sequences. Available on the Galaxy web platform,CloudMap requires no software installation when run on the cloud, butit can also be run locally or via Amazon's Elastic Compute Cloud (EC2)service. CloudMap uses a series of predefined workflows to pinpointsequence variations in animal genomes, such as those of premutagenizedand mutagenized Caenorhabditis elegans strains. Incombination with a variant-based mapping procedure, CloudMapallows users to sharply define genetic map intervals graphically and toretrieve very short lists of candidate variants with a few simple clicks.Automated workflows and extensive video user guides are available todetail the individual analysis steps performed(http://usegalaxy.org/cloudmap).Topics covered:Choosing the correct type of mapping cross for a given genetic screen.Analyzing mapping cross data.Variant subtraction of previouslysequenced strains.In silico complementation analysis.Analyzing putative deletions.Using CloudMap for nematodes or organisms other than C.elegans.Running CloudMap on the Cloud, locally, or on Amazon's servers.Speakers:Gregory Minevich, Columbia UniversityRichard Poole, University College LondonSpeakers:Abigail Cabunoc, WormBase, Ontario Institute for Cancer Research(OICR), An introduction to WormBase 2.0Gareth Williams, WormBase, European Bioinformatics Institute (EBI),An overview of genomic data in WormBaseMichael Paulini, WormBase, European Bioinformatics Institute (EBI),Comparative genomics in WormBaseMary Ann Tuli, WormBase, European Bioinformatics Institute (EBI),Genomic variation data in WormBaseMarc Perry, Ontario Inst for Cancer Research, modENCODE - an update12