Presentations

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An archive of presentations by staff and researchers of the UCSC Genome Browser group and the Center for Biomolecular Science and Engineering (CBSE). Please keep the list in order by date, newest ones at the top.

2013

  • 10 May 2013, Brooke Rhead, New variation resources at the UCSC Genome Browser. Poster presented at Biology of Genomes at CSHL. wiki, PPTX, PDF.
  • 20 Mar 2013, Brian Raney, UCSC Genes Genecats talk PPT PDF

2012

  • 06 Sep 2012, Brian Raney, Remote Data Track Storage for Viewing on the UCSC Genome Browser wiki,
  • 09 May 2012, Angie Hinrichs, Using the UCSC Genome Browser to evaluate putative genetic variants wiki, PPTX, PDF
  • 11 April 2012, Ted Pak, JavaScript/Ruby version of the UCSC Yeast Genome Browser PDF
  • 21 March 2012, Larry Meyer, Genome Browser API. (Genecats) PPT
  • 15 February 2012, Greg Roe & Venkat Malladi, Selenium Testing PPTX
  • 26 January 2012, Hiram Clawson, BME230 browser introduction, table browser intersection PPT
  • 18 January 2012, Jim Kent, Software Engineering and Testing. (Genecats) PPTX
  • 11 January 2012, Brooke Rhead, The QA Release Process: what gets pushed and when. (Genecats) PPTX or PDF

2011

  • 18-19 October 2011, XLDB presentations including from UCSC, the 5th lightning talk on the 18th of October. Note additional interesting genomics presentations, for example the NCBI sequence read archive architecture on the morning of the 19th.
  • 09 September 2011, Angie Hinrichs, Visually integrating genomic data in the UCSC Genome Browser. Poster presented at HGV2011. .pptx PDF
  • 24 August 2011, Sol Katzman, Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hotspots File:Sol GCBias GeneCats 2011-08-24.pdf
  • 27 July 2011, Larry Meyer, Browser Performance and Architecture
  • May 2011, Ann Zweig, UCSC Genome Browser Track Data Hubs. Poster given at Biology of Genomes conference at CSHL. File:BoG2011.pdf
  • May 2011, Gabor Marth, Toward a unified view of human genetic variation. Talk given at Biology of Genomes conference at CSHL. File:Marth-1000G-CSHL2011.pptx
  • 27 April 2011, Jim Kent, Accelerating Biomedical Research for 10 Years and Counting. File:AcceleratingBiomedicine2011.pptx
  • 06 April 2011, Angie Hinrichs, Recent work on human variation tracks. .pptx PDF (PDF has squashed animations)
  • 09 March 2011, Josh Stuart, Ph.D., Integrated Pathway Modeling. File:Jstuart.pptx
  • 03 March 2011, Andreas Sundquist, Ph.D., DNAnexus -- Data Management for the First 1,000,000 Human Genomes. File:DNAnexus.pptx
  • 02 March 2011, MDB and CV in the shadow of the shadow of greatness. File:MdbAndCvPresentation.pdf or File:MdbAndCvPresentation.ppt Brian Raney and Tim Dreszer.
  • 02 February 2011, Benedict Paten, JobTree. File:JobtreeSlides.pdf
  • 06 January 2011, BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. File:BME230 Winter 2011.ppt

2010

2009

2008

  • 18 December 2008 File:FrankJacobs181208.ppt - Frank Jacobs, Developmental Neurobiology, Rudolf Magnus Institute of Neuroscience, University of Utrecht, The Netherlands, "Pitx3 outSMRTs Nurr1 in dopamine neuron terminal differentiation"
  • Genecats - 17 December 2008 - Composite sketch: Nifty tricks for composite tracks (multi-view, dimensions, sorting, drag and drop, etc.). Tim Dreszer.
  • Genecats - 10 December 2008 - Ed Green from Max Planck Institute for Evolutionary Anthropology discusses the [Neandertal mtDNA] project
  • Sep. 2008 - Angie's "UCSC Genome Browser Tool Suite" poster presented at Genomics of Common Disease PPT PDF
  • 27 August 2008 - Jim Kent at the Computational Systems Bioinformatics Conference, Stanford CA, File:Kent decodingEncode.ppt a wide-ranging discussion of Encode research, using the Gene Sorter, using the Table browser, source code design issues
  • ISMB Toronto - July 2008 - Intelligent Systems for Molecular Biology File:ISMB2008 UCSC.ppt presentation by Hiram Clawson. A brief tutorial on browser usage with special emphasis on how to perform intersections with the table browser. Task demonstrated: finding highly conserved non-coding regions of the genome.
  • Genecats - 05 July 2008 - Jim Kent describing the all.joiner file used by the UCSC genome browser to specify database table relationships - the database "schema" behind the browser File:Kent allJoiner.ppt
  • Bejerano Lab (Stanford) - March 31, 2008 - File:Bejerano Lab 2008 03 31.ppt Angie's crash course on using the kent/src tools and libraries. Did a brief live demo (TB intersection -> custom track) first. Group was already very familiar with browser and had their own mirror.
  • BME 230 Winter 2008, 10 January 2008, Robert Baertsch File:Baertsch-code-talk.ppt genome browser introduction and kent src code preview

2007

2006

2005

2003

  • CSHL June 2003 "Evolution and the Santa Cruz Genome Browser" File:CSHL 2003 Jim Kent.ppt presentation by Jim Kent. Recent new functions in the genome browser, using the chain and net process to highlight evolutionary processes, a new rat genome assembly with 3-way human-mouse-rat multiple alignment.

2002

2000

  • October 2000 - "Details of the Genome Browser" File:CompBioOct2000 Jim Kent.ppt - Description of the genome browser software architecture, the early days. Jim Kent
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