Presentations

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.

2011

• 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

• 10 November 2010, Xin Zhou, Human Epigenomics Browser File:2010-11-10 - Genecats.pdf
• 4 Novermber 2010, Kate Rosenbloom, Genome-wide ENCODE Data at UCSC (poster for ASHG2010) Media:ENCODE_ASHG2010.ppt
• 29 September 2010, Andy Pohl, Investigation of the Nucleosome Linker File:2010-09-29 - Genecats.pdf
• 25 August 2010, Ann Zweig, Redmine Task-Tracking Tool File:Genecats08252010.ppt File:Genecats082510.mp3
• 18 August 2010, Kate Rosenbloom, Genome-wide ENCODE Data at UCSC (poster for CSB2010) Media:ENCODE_CSB2010.ppt
• 18 August 2010, Melissa Cline, Genome-wide Mouse ENCODE Data at UCSC (presented at CSB2010) File:Cline.MouseEncode.CSB2010.ppt
• 11 August, 2010, Mary Goldman, Working with git Media:Genecats_08_11_10.mp3
• 23 June, 2010, Ed Green, Detecting positive selection in humans using the Neandertal genome Media:Genecats062310.mp3
• 17 June, 2010, Kate Rosenbloom, ENCODE Data at UCSC (presented at CSHL Integrated Analysis of Genome-Scale Data short course) Media:Rosenbloom.ENCODE_CSHL_Jun2010.ppt
• 16 June, 2010, Larry Meyer, Bringing Web 2.0 to the UCSC Genome Browser File:Genecats061610.pdf audio: File:Genecats061610.mp3
• 15 June, 2010, Steve Benz, Thesis Advancement File:Sbenz thesis advancement.pdf audio: File:BenzAdvancement061510.mp3
• 09 June, 2010, Ann Zweig & Galt Barber, git Source Code Management File:GitSourceCodeMgmt.pdf partial audio: Media:Genecats060910.mp3
• 05 May 2010, Hiram Clawson, Unix environment
• 21 April 2010, Mitchell Skinner, JBrowse - An AJAX Genome Browser File:UCSC-4-21-10.pdf
• 10 February 2010, Jorge Garcia, The Genome Browser - Under The Hood File:Browsermap.pdf
• 03 February 2010, Melissa Cline, Coordinated Alternative Splicing File:CoordinatedSplicing.ppt
• 05,07 January 2010 BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. File:BME230 Winter 2010.ppt Browser [Session] for example intersection.

2009

• 14 October Genecats meeting, File:MonsatoIntroduction Oct2009.pdf Brad Fabbri
• 14 October Genecats meeting, Hiram Clawson - building the kent source tree and a UCSC genome browser assembly, File:Genecats 2009 10 14.pptx or older style File:Genecats 2009 10 14.ppt
• 24 August Genecats meeting, Larry and Tim present 3 new hgTracks features coming down the shute: image20ui.pdf.
• 29 July Genecats meeting, Mark's presentation on SVS/subversion proposal to replace CVS File:SvnForGb.pdf.
• 08 April Genecats meeting, Fan Hsu: "Some thoughts from Fan" File:SomeThoughtsFromFan0408B.pdf.
• 08 January 2009 BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. File:BME230 Winter 2009.ppt Browser [Session] for example intersection.

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.

• 11 December 2008, Paul Flicek, EBI, presenting 1,000 genomes project status File:Flicek 11 DEC 2008.pdf

• Genecats - 10 December 2008 - Ed Green from Max Planck Institute for Evolutionary Anthropology discusses the [Neandertal mtDNA] project

• Genecats - 15 October 2008 - File:Metcalf.Richardson.2008-10-15.pdf Jake Metcalf, Sarah Richardson discussion of ethics controversy concerning Bruce T. Lahn of U. Chicago publications.

• 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

• Genecats - 06 August 2008 - File:ISMB2008 genecats summary.ppt summary of ISMB 2008, Toronto, Hiram Clawson

• Genecats - July 30, 2008 - Biased Clustered Subsitutions in the Human Genome: Sex, Gambling and Non-Darwinian Evolution. Tim Dreszer's presentation of his master's thesis work.

• 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

• Genecats - 16 April 2008 - Rachel Harte trip report from Mouse Genome Annotation Summit Meeting and RefSeq/CCDS visit, NIH, Bethesda MD 12-14 March 2008 File:MouseAnnotAndCCDSVisitReport041608.ppt

• Genecats - 06 April 2008 - Jim Kent reviewing the Parasol super computer job management system File:Kent parasolArchitecture.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

• Genecats - 16 April 2008 - File:ISMB2007TripReportGenecats.ppt Rachel Harte summary from ISMB 2007 meeting in Vienna, Austria

2006

• Genecats - September 12, 2006 - File:Automation 2006 09 12 v2.ppt Overview of the automation scripts that are now in kent/src/hg/utils/automation/ (Angie).

2005

• Chicken Genome Meeting - May, 2005 - File:Browsers CSHL Chicken 2005 05.ppt An intro to the Genome Browser and Table Browser (Angie).

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

• Charles Sugnet's talk January 2002 - "Adding tracks to the Human Genome Browser" File:HowToAddTrack Sugnet.pdf and examples used in the talk - File:SampTracksChr22.tab

• Genecats October 2002 - "Software Sermon" File:SoftwareSermon2002 Jim Kent.ppt - software development philosophy and guidelines, Jim Kent.

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