PPT-Using SWARM service to run a Grid based EST Sequence Assembly

Karthik Narayan Primary Advisor Dr Geoffrey Fox 1 Outline 2 Objective EST Sequence Assembly The Problem SWARM Tools Results Future Work Objective Use the SWARM service and leverage the High Performance clusters for EST Sequence Assembly. lecture. . by. Veli Mäkinen. Thu. 10-12 C222 . study. . group. . by. VM. . Mon. 10-12 C222 . exercises. . by. Anna Kuosmanen. Algorithms. in . Molecular. . Biology. , . 5 . cr. , . Spring. SWARM service to run a Grid based EST Sequence Assembly. Karthik. . Narayan. Primary Advisor : Dr. Geoffrey Fox. 1. Outline. 2. Objective. EST Sequence Assembly. The Problem. SWARM. Tools. Results. V.A. Schneider, P. Flicek, T. Graves, T. Hubbard & D.M. Church for. the Genome Reference Consortium. http://genomereference.org. @GenomeRef. GRCh37.p13 Assembly Statistics. The GRCh38 human . reference assembly . C. onifer . G. enome, Loblolly Pine. Jill Wegrzyn. Pieter . de Jong, . Chuck Langley, Dorrie Main, Keithanne Mockaitis, . Steven Salzberg, . Kristian. . Stevens. , Nick . Wheeler, Jim . Yorke, . Aleksey . GIS . Prof. Yuji Murayama - Instructor. Hao. . HOU . – Teaching Assistant. Division of Spatial Information Science. University of Tsukuba. TA Tutorial in Spring Semester 2015. In cartography, any network of parallel and perpendicular lines superimposed on a map and used for reference. These grids are usually referred to by the map projection or coordinate system they . Swarm Intelligence: Develop systems where sets of agents of agents solve problems without centralized control intelligently. . Agent-based Modeling and Simulation (Develop models of agent-based systems in nature, business, society…). genome . assembly. Sorin. . Istrail. CSCI1820 Short-read genome assembly algorithms. 3/6/2014. 1. Genomathica Assembler. Mathematica. notebook for genome assembly simulation. Assembler can be found at: . Summary Slides. Marlon Pierce, Geoffrey Fox, . Sashikiran. . Challa. IU’s ORE-CHEM Pipeline. Harvest NIH . PubChem. for 3D Structures. Convert . PubChem. XML to CML. Convert . PubChem. XML to CML. Jacob Katz. , . Swati. Mohan, and David W. Miler. MIT Space Systems Laboratory. AIAA . Infotech@Aerospace. 2010. April 22, 2010. 1. Autonomous On-Orbit Assembly. Enabling technology for. Large telescopes. germslab.org. @. teeniedeenie. Today’s Schedule. Morning. Mapping and assembly basics lecture. Tutorial – BASH for genomics. Afternoon:. Tutorial – Variant Calling. FUN IN THE SUN!. Evening:. Lecture – Teach me scripting. Analysis. Jessica Holmes. High Performance Biological Computing (HPCBio). Roy J. Carver Biotechnology Center. General Outline. Getting the RNA-Seq data: from RNA -> Sequence data. Experimental and practical considerations. . Synthetic Biology &. . iGEM. MADE. . BY. . AISSU-Union . THE. . TRUTH. . ABOUT. . DNA. ：. . A. . REALLY. . YOUNG. . DISCOVERY. ！！！. The full name of DNA is . D. eoxyribonucleic Acid (. Silly Quiz. Who are these people, and what is the occasion?. Genome Sequencing and Assembly. Sequencing. A break at T is shown here.. Measuring the lengths using electrophoresis allows us to get the position of each T. Outline. Reference Assembly Basics. GRC: Assembly management and dataflow. GRCh38. Accessing the assembly and data. http://genomereference.org. What. is the . Reference. Assembly?. Reference Assembly Basics.