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.

2018

• 15 Nov 2018 Kate Rosenbloom, Program in Bioinformatics and Integrative Biology, U Mass Medical Center Worcester, MA: UCSC Genome Browser: New Features and Hidden Features (Nov 2018) PDF PPT
• 14 Nov 2018, Jorge Garcia, The Genome Browser - Under The Hood 2018 review Browsermap2018.pdf (See 2010 and 2017 entry for earlier machine maps).
• 05 Nov 2018 Kate Rosenbloom, Genome Browser team meeting: "Interact (and bigInteract) tracks in the UCSC browser". PDF PPT
• 30 Oct. 2018 Angie Hinrichs, Genome Browser team meeting: "Patchwork": adding new alternate haplotype and fix patch sequences to an existing db
• 16-17 May 2018 Kate Rosenbloom, Tel Aviv Medical Center, Genetics Institute and Weizmann Institute, Life Sciences Core Tel Aviv and Rehovot, Israel: UCSC Genome Browser: New Features and Hidden Features (May 2018)
• 09 May 2018 Kate Rosenbloom, Biology of Genomes 2018 Cold Spring Harbor, NY. Poster: GTEx resources and new ‘barChart’ and ‘interaction’ track displays inspired by GTEx. PDF PPT
• 01 March 2018 Jairo Navarro, 3rd Annual Postdoc Symposium Santa Cruz, CA: Visualizing RNA-seq data in the UCSC Genome Browser; A Discussion of Tools for Visualizing RNA-seq Data. PDF PPT
• 17 January 2018 Brian Lee, PAG (Plant and Animal Genomes) XXVI in San Diego, CA: Assembly Hubs at UCSC; A Discussion of Assembly Track Hubs at UCSC. PDF
• 15 January 2018 Brian Lee, PAG (Plant and Animal Genomes) XXVI in San Diego, CA: Viewing Data Hosted at CyVerse on the UCSC Genome Browser; A Discussion of hosting Assembly Track Hubs at CyVerse). PDF
• 13 January 2018 Brian Lee, PAG (Plant and Animal Genomes) XXVI in San Diego, CA: Benefits of Track Hubs and Byte-Range Requests; A Discussion of Assembly Track Hubs and the benefits of binary indexed data formats in that only portions of the file needed to display in a particular genomic region are transferred over the Internet and cached as a sparse file). PDF

2017

• 6 December 2017, Jorge Garcia, The Genome Browser - Under The Hood 2017 review (recording available) File:Browsermap2017.pdf (See 2010 entry for earlier machine maps).
• 27 Nov 2017 Angie, Slides: Genome Informatics 2017 - Angie's summary of conference, for staff meeting
• 2 Nov 2017 Angie, Genome Informatics, CSHL: "HGVS variant nomenclature in the UCSC Genome Browser" poster PDF Pages(Mac)
• 12 Sep 2017 Angie: Building upon Personalis’s “Ground Truth Set” slides presented in GA4GH Variant Annotation Task Team conference call
• 16 Aug 2017 Angie: HGVS for QA slides presented to QA group
• 15 May 2017 Chris E, Kate R and Chris L: Bar charts in the browser Slides by Chris E presented in GB mtg
• 26 January 2017 Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection PPT
• 18 January 2017 Brian Lee, PAG (Plant and Animal Genomes) XXV in San Diego, CA: UCSC Genome Browser -- Assembly Hubs: Display Any Organism A Discussion of Custom Annotations, Building an Assembly Hub, GenBank Assembly Hubs, Assembly Hub BLAT, and Hosting Assembly Hubs on GBiB and CyVerse (Here is an associated page with quick links from the talk). PDF

2016

• 15 Nov 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser: December 2016 Update (presentation for the GTEx Steering Committee at Dec meeting in DC) PPTX
• 20 Aug 2016, Max Haeussler, Evaluation of scoring algorithms for Crispor and the UCSC Genome Browser, CSHL Crispr Meeting 2016, Poster File:CrisporCshl2016.pdf
• 12 July 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser: July 2016 Update (presentation to the GTEx Steering Committee, Stanford) PPTX
• 11 July 2016, Christopher Lee poster presented at the 2016 GTEx Community Meeting at Stanford PDF
• 09 June 2016, Hiram Clawson presentation to Bejerano Lab, Stanford, assembly nomenclature, assembly hubs, lastz/chain/net procedures PPTX
• 24 May 2016, Chris Eisenhart phone conference presentation, explaining the new data transfer to the CIRM CRP and CIP labs google doc
• 10 May 2016, Galt Barber, Multi-Region (Exon Mostly) at Biology of Genomes PDF‎
• 29 April 2016, Chris Eisenhart presentation at the 2nd Annual CIRM retreat, CDW, Stem cell hub, current lab status google doc
• 29 April 2016, Clay Fischer poster presented at the 2nd Annual CIRM retreat PDF
• 04 April 2016, Robert Kuhn. poster presented at International Congress of Human Genetics (ICHG) in Kyoto. Reformatted from Luvina's ACMG poster. Thanks, Luvina PDF
• 11 March 2016, Luvina Guruvado presented poster about about accessing variation data in the GBiB and Data Integrator at the American College of Medical Genetics (ACMG) annual meeting in Tampa PDF
• 17 February 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser (presentation at Genecats) PPTX PDF
• 12 January 2016 Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection PPT

2015

• 4 December 2015, Kate Rosenbloom, GTEx in the UCSC Genome Browser (presentation at the December 2015 GTEx Steering Committee meeting) PPTX PDF
• 28-30 September 2015, Kate Rosenbloom, Visualizing proteomics data in genomic context using the UCSC Genome Browser (poster presented by collaborator Eric Deutsch (PeptideAtlas Project, Institute for Systems Biology) at the HUPO2015 (Human Proteomics Organization) Congress in Vancouver) PPTX
• 29 June - 1 July 2015, Pauline Fujita, ENCODE Users Meeting Visualizing ENCODE Data in the UCSC Genome Browser. PPTX
• 23 June 2015, Kate Rosenbloom, GTEx Data in the UCSC Genome Browser (poster presented at the June 2015 GTEx Community Meeting in Chicago) PPTX PDF
• 22-24 June 2015, Matthew Speir, Use The UCSC Genome Browser To Visualize And Analyze Your Genomic Data (poster presented at UC-wide Bioengineering Symposium 2015 at UCSC) wiki PPTX PDF
• 9 May 2015, Angie Hinrichs, The Data Integrator: a new way to combine datasources underlying the UCSC Genome Browser (poster presented at Biology of Genomes 2015 at CSHL) wiki PPTX PDF
• 11 March 2015, Angie Hinrichs, Annotation Integrator PDF PPTX
• 5 March 2015, Brian Raney, Genome 10K, Poster on assembly hubs and GBiB. PDF
• 26 Feb 2015, Robert Kuhn, ACMG meeting, Salt Lake. UCSC Genome Browser and Variant Annotation Integrator PDF

2014

• 13 October 2014, Brian Raney, The American Society of Human Genetics, Poster on assembly hubs and GBiB. PDF
• 20 September 2014, Galt Barber, Genome Informatics 2014 Poster on hubs, security, and GBiB. PDF
• 19 Sept 2014 Jim Kent, Ebola Scramble PPTX
• 22 Aug 2014 Jim Kent, hg38, mapping sponge, and ENCODE PPTX
• 19 May 2014, Karen Miga, GRCh38 Centromere Reference Models PDF
• 11 February 2014, Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection PPT

2013

• 19 June 2013, Tracy Ballinger, Track Hubs and Assembly Hubs presentation for Epigenome Roadmap working group meeting. PPT PDF
• 10 May 2013, Brooke Rhead, New variation resources at the UCSC Genome Browser. Poster presented at Biology of Genomes 2013 at CSHL. wiki, PPTX, PDF.
• 08 May 2013, Hiram Clawson, Assembly Hubs poster presentation at Biology of Genomes 2013 at CSHL. wiki, PDF, PPTX
• 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)
• 24 March 2011, Robert Kuhn. poster presented at Genomic Disorders meeting, Hinxton. File:GenomicDisorders2011.pdf
• 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 and 2013 review File:Dependency-Review-20130826.pdf and 2016 review File:Browsermap2016.pdf and 2017 review File:Browsermap2017.pdf and 2018 review Browsermap2018.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.

• 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

• 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
• Jim's talk - 12 September 2007 - File:GeneSorter.ppt "Inside the Gene Sorter - A moderately complex CGI application" talk by Jim Kent

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