PPT-Tools for Scalable Genome

Haplotying in the Windows Azure Cloud Girish Subramanian subramagumailiuedu Yogesh Simmhan yogesmicrosoftcom Genome Haplotyping Goal Separating out the two haplotype. Blake Caldwell. National Center for . Computation Sciences. April 25, 2012. LUG . 2012 – Austin, TX. What’s different at scale?. What we expect:. O. verhead in administering more nodes. More frequent failures and new failure modes. Commutativity. Rule: Designing Scalable Software for Multicore Processors. Austin T. Clements, M. . Frans. . Kaashoek. , . Nickolai. . Zeldovich. , Robert T. Morris, and Eddie Kohler. MIT CSAIL and Harvard University. February 29, 2016. 1. 888-844-9904. passcode . 2590235# . Outline. Introductions. Recent accomplishment highlights. 5-Year Plan for USDA-ARS. Charge Questions. Executive Session (WG-only). Summary from WG to MaizeGDB Team. … synteny. sensu. . stricto. - no gene order information. collinearity. – recognizable (imperfect). synteny . <->. conserved synteny. s. yntenic chromosomes, syntenic blocks, perfect ~ imperfect synteny, thresholds???. Nikos. . Kyrpides. Genome . Biology . Program (GBP). DOE Joint Genome institute. IMG. Genes. Genomes. Functions. Metadata. Clusters. SNPs. Proteomics. Regulons. Transcriptomes. IMG Systems Data Types. Larry Peterson. In collaboration with . Arizona. , Akamai. ,. . Internet2. , NSF. , North Carolina, . Open Networking Lab, Princeton. (and several pilot sites). S3. DropBox. GenBank. iPlant. Data Management Challenge. A second step is determining the sequence of the gene, or genes, determining the phenotype and understanding how the expression of the genes is regulated at the transcriptional level  . Subsequent steps involve analysis of post-transcriptional events, understanding how the genes fit into metabolic pathways and how these pathways interact with the environment . Bioinformatics. GCBA815/MCGB815/BMI815, Fall 2017. Week-6: Genomics Browsers . (UCSC, IGV and . ExAC. ). Babu . Guda, Ph.D. .. Professor, Genetics, Cell Biology & Anatomy. Director, Bioinformatics and Systems Biology Core. Alex Rodriguez * Dinanath Sulakhe Elizabeth Marland arodri7@mcs.anl.gov sulakhe@mcs.anl.gov marland@mcs.anl. Veronika Nefedova Gong Xin Yu Natalia Maltsev * nefedova@mcs.anl.gov gxyu@mcs.anl.g Motivations. W. ho’s going to build large ARM systems and run HPC problems on them. . W. hat do people care about . wrt. binary instrumentation? Want to prioritize. . Collect feedback for colleagues on interest and how to use ARM tools and clusters. . and Accurate Assembly Polishing Algorithm. Can Firtina. 1. , Jeremie S. Kim. 1,2. , Mohammed Alser. 1. , . Damla. . Senol. Cali. 2. , A. . Ercument. Cicek. 3. ,. Can Alkan. 3. , and . Onur. Mutlu. G-OnRamp Beta Users Workshop. Wilson Leung. 07/2016. Outline. Obtain genome assemblies from NCBI. Transfer . large genomics datasets to Galaxy. Common bioinformatics file formats . D. atatypes in Galaxy. Jason Gill. Department of Animal Science. Center for Phage Technology. Texas A&M University. Why phages?. Phages are the . most abundant. . organisms on Earth, about 10. 31. in total. Recent interest as therapeutics and for their role in natural environments. Large scale computing systems. Scalability . issues. Low level and high level communication abstractions in scalable systems. Network interface . Common techniques for high performance communication.