Posts Tagged ‘conf’

Thoughts on BD2K AHM

December 6, 2016

TWEETS

https://storify.com/markgerstein/favorite-tweets-from-bd2k-all-hands-meeting-16-bd2

TAGGED ITEMS

https://linkstream2.gerstein.info/tag/i0bd2k16

PRIVATE SLIDE PICS

http://archive.gersteinlab.org/meetings/s/2016/12.03/i0bd2k16–bd2k_ahm-posters/

My notes from #BioData16 with a collection of links related to education in biomedical data science

November 7, 2016

# The meeting
https://meetings.cshl.edu/meetings.aspx?meet=DATA&year=16

# The panel

My lecture
http://lectures.gersteinlab.org/summary/Education-in-Bio-DataScience–20161028-i0bds16/

List of Curricular Topics for Bioinformatics http://goo.gl/303KXr An invitation for crowd-sourced comments to the talk

Panel Slides
https://docs.google.com/presentation/d/1mhcXpr_BhxvCx4Ki4jR4hLRNzm524JMW76H8zL31Yt4/edit?usp=sharing

Cached copy of above gdocs
http://archive.gersteinlab.org/public-docs/2016/11.01/cached-copy-of-biodata16-i0bds16-gdocs/

Earlier versions of the crowd-source edit:
http://cbb752b16.gersteinlab.org/assignments/homework0
Also:
http://blog.gerstein.info/2015/11/list-of-study-topics-prerequisites-for.html

# Related educational resources (unfortunately, Yale-centric):

The Yale CBB program & its focus on Data Science
http://cbb.yale.edu
http://cbb.yale.edu/graduate-program/optional-focus-biomedical-data-science

CBB752 – Biomedical Data Science: Mining & Modeling
http://www.gersteinlab.org/courses/452/

My ’14 list of US Bioinformatics Programs:
http://blog.gerstein.info/2015/05/updated-again-listing-of-us-programs-in.html https://twitter.com/markgerstein/status/600763647095341056

Hackathon slides:
https://docs.google.com/presentation/d/123NLmlYAUrJf2M709kPyDJl3N5wIcOO8W-EGJVxZKN4/edit?usp=sharing

Article on online curriculum:
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003662

Masters of Data Science
http://www.slideshare.net/ttimbers/ubc-mds-education-slides

Favorite Tweets
https://storify.com/markgerstein/favorite-tweets-from-biological-data-science-16-bi

Tagged from meeting
https://linkstream2.gerstein.info/tag/i0bds16/

Notes from recent nextgen seq. meeting in Boston & Genome workshop in DC

October 4, 2016

TWEETS

https://storify.com/markgerstein/tweets-from-plos-comp-bio-editors-meeting-i0plos16.html (includes NextGen meeting too)

TAGGED ITEMS

https://linkstream2.gerstein.info/tag/i0ng16
https://linkstream2.gerstein.info/tag/i0cgds

TOP LINK

http://www.nextgenerationsequencingusa-congress.com/venue/2016-venue/

MY LECTURES

http://lectures.gersteinlab.org/summary/Evaluating-exome-variants-using-structures-n-allelic-activity–20161004-i0ng16/
http://lectures.gersteinlab.org/summary/Bullets-for-NHGRI-workshop-M-Gerstein–20160929-i0cgds/

=###=> LAST WEEK NOTES (bundled with this) <=###=

https://linkstream2.gerstein.info/2016/09/24/notes-from-meetings-last-week-the-plos-comp-bio-summit-the-icgcpcawg-meeting-i0pcawg16i0plos16/

Notes from meetings last week: the PLOS Comp. Bio. Summit & the ICGC/PCAWG meeting (i0pcawg16,i0plos16)

September 24, 2016

TWEETS

https://storify.com/markgerstein/tweets-from-plos-comp-bio-editors-meeting-i0plos16.html

TAGGED ITEMS

https://linkstream2.gerstein.info/tag/i0plos16
https://linkstream2.gerstein.info/tag/i0pcawg16

PRIVATE SLIDE PICS

http://archive.gersteinlab.org/meetings/s/2016/09.24/slide-pics-from-i0pcawg16/ http://archive.gersteinlab.org/meetings/s/2016/09.24/i0pcawg16-extra/

TOP LINK

http://blogs.plos.org/biologue/2016/08/31/plos-computational-biology-symposium-2016/

Notes from the ENCODE Consortium meeting

June 21, 2016

TAGGED ITEMS

https://linkstream2.gerstein.info/tag/i0enc16

PICS

https://twitter.com/markgerstein/status/744628388078493696

LECTURES

http://lectures.gersteinlab.org/summary/Mining-an-ENCODE-Data-Exhaust–20160616-i0enc16/

Some public notes from #modSTI & #BoG16

May 23, 2016

TWEETS

https://storify.com/markgerstein/favorite-tweets-from-biology-of-genomes-modelling-/preview

TAGGED ITEMS

https://linkstream2.gerstein.info/tag/i0scisipc/
https://linkstream2.gerstein.info/tag/i0bog16/

PICS

https://www.flickr.com/photos/tags/seriesBeingFeltbytheSentientChamber

LECTURES

http://lectures.gersteinlab.org/summary/Mapping-Diffusion-Ideas-n-Data–20160518-i0scisipc/
http://lectures.gersteinlab.org/summary/SV-callsets-n-PersonalGenomes–20160514-i0bog16+sv2/

TAGGED EMAIL (private)

https://mail.google.com/mail/u/0/#search/i0bog16
https://mail.google.com/mail/u/0/#search/i0scisipc

Thoughts on Meetings at End of Oct (Genome Informatics ’15 & NextGen Congress in Boston)

November 3, 2015

TWEETS

https://storify.com/markgerstein/favorite-tweets-from-genome-informatics-nextgen-co

TAGGED ITEMS

https://linkstream2.gerstein.info/tag/i0gi2015
https://linkstream2.gerstein.info/tag/i0ngs15

PICS

https://www.flickr.com/photos/mbgmbg/tags/seriesi0gi2015upload https://www.flickr.com/photos/mbgmbg/tags/cshl
(ALL CSHL)

LECTURES

http://lectures.gersteinlab.org/summary/Transcriptome-Mining-Building-Models-while-Protecting-Privacy–20151030-i0gi2015/
http://lectures.gersteinlab.org/summary/Transcriptome-Mining-Building-Models-while-Protecting-Privacy–20151027-i0ngs15/

TAGGED EMAIL (private)

https://mail.google.com/mail/u/0/#search/i0gi2015
https://mail.google.com/mail/u/0/#search/i0ngs15

INTERNAL LAB LINKS (private)

http://archive.gersteinlab.org/meetings/s/2015/10.27/Genome-Informatics/i0gi2015–Info_AbstractBook.pdf http://archive.gersteinlab.org/meetings/s/2015/11.03/LH-poster

Thoughts on ASHG ’15 & Associated Satellite Meetings

October 17, 2015

Favorite tweets
https://storify.com/markgerstein/favorite-tweets-from-ashg-15-its-satellites-ashg15

My lectures:
http://lectures.gersteinlab.org/summary/LARVA–20151010-i0ashg15
http://lectures.gersteinlab.org/summary/Genomic-Privacy-Soc-n-Tech–20151006-i0pgx

Related tagged items:
https://linkstream2.gerstein.info/tag/i0ashg15
https://linkstream2.gerstein.info/tag/i0pgx

Day of Data 2015 | Yale Day of Data & Yale RNA Center Retreat

September 23, 2015

TAG
https://linkstream2.gerstein.info/tag/ydod2015

http://elischolar.library.yale.edu/dayofdata/2015/
http://rnacenter.yale.edu/retreat/RNA%20retreat%20schedule%20Sept%202015-final%20(2)_209184_284_25366.pdf

Tweets:
https://storify.com/markgerstein/favorite-tweets-from-the-yale-day-of-data-ydod2015

RNA Center Lecture
http://lectures.gersteinlab.org/summary/Expression-Clustering-across-Distant-Organisms–20150918-i0rnacent/

My notes from 2015 CSHL Conference on THE EVOLUTION OF SEQUENCING TECHNOLOGY

July 21, 2015

Tweets:
https://storify.com/markgerstein/favorite-tweets-from-evolseq-i0biohist15

TAG
https://linkstream2.gerstein.info/tag/i0biohist15/

http://meetings.cshl.edu/meetings.aspx?meet=biohist&year=15

CSHL Genentech Center Conferences
on the History of Molecular Biology and Biotechnology
THE EVOLUTION OF SEQUENCING TECHNOLOGY:
A HALF-CENTURY OF PROGRESS

July 16 – 19, 2015

SCHEDULE BELOW

Cold Spring Harbor Laboratory Genentech Center Conferences on the History of Molecular Biology and Biotechnology

THE EVOLUTION OF SEQUENCING TECHNOLOGY: A HALF-CENTURY OF PROGRESS July 16 – 19, 2015

Grace Auditorium

Thursday, July 16
7:00 pm – Session I—Early Days

Friday, July 17
9:00 am – Session II – Capturing Sequences/Survey
2:00 pm – Session III – Access to Sequence—From Past to the

Future
4:30 pm – Poster Session – Wine & Cheese Reception

7:00 pm – Session IV – Scaling to Genomes Saturday, July 18

9:00 am – Session V – Sequences to Genomes
1:45 pm – Session VI – All Roads Lead to DNA: Beyond Genomes 5:00 pm – Panel Discussion – Steps and mis-steps during the

development of sequencing technologies 6:00 pm – Cocktails and Banquet

Sunday, July 19
9:00 am – Session VII – Human Variation & Disease 12:00 Noon – Lunch and Departures

Mealtimes at Blackford Hall are as follows:

Breakfast 7:30 am-9:00 am Lunch 11:30 am-1:30 pm Dinner 5:30 pm-7:00 pm Bar is open from 5:00 pm until late

Cover Art: Fred Sanger at the LMB

Thursday, 7:00 pm: Session I – Early Days moderated by Bob Waterston

James Watson, Cold Spring Harbor Laboratory “Early Days with DNA” George Brownlee, University of Oxford, UK
“The early days of RNA sequencing at the LMB” Gillian Air, University of Oklahoma
“Integration of protein & DNA sequencing for PhiX174” Clyde Hutchison, J. Craig Venter Institute “Sequencing of PhiX174”

COFFEE BREAK
Wally Gilbert, Harvard University
“Origin of DNA Sequencing”
Tom Maniatis, Columbia University Medical Center

“The transition from RNA to DNA sequencing in the Sanger lab: The DNA sequence of the phage lambda operator/promoter regions””

Joachim Messing, Waksman Institute, Rutgers University “Development of M13 cloning systems for sequencing”

Friday 9:00 am: Session II—Capturing Sequences moderated by Mila Pollock

Lee Hood, Institute of Systems Biology “Automation of Sanger Sequencing” Lloyd Smith, University of Wisconsin, Madison “Fluorescence-based automated DNA Sequencing” Norman Dovichi, University of Notre Dame “Development of capillary electrophoresis” Mostafa Ronaghi, Illumina, Inc.
“Development of pyrosequencing”

COFFEE BREAK

Session II—Capturing Sequences moderated by Miguel Garcia-Sancho (continued) Shankar Balasubramanian, University of Cambridge, UK
“Early development of Solexa technology-key insights & technical breakthroughs” Jonas Korlach, Pacific Biosciences

“Technical innovations of SMRT Sequencing and applications of long-read sequencing”

Hagan Bayley, University of Oxford, UK “Nanopore Sequencing”

Friday, 2:00 pm: Session III—Access to Sequence from the past to the future moderated by Miguel Garcia-Sancho

David Lipman, NCBL/NLM National Institutes of Health “Origins of GenBank” Graham Cameron, Founder, Ex-Director EMBL
“DNA database prehistory”

Jim Ostell, NCBL/ National Center for Biotechnology Information “Databases for the future”
Miguel Garcia-Sancho, University of Edinburgh
“Sequencing & computing technologies: a Historical Convergence” Mila Pollock, Cold Spring Harbor Laboratory

“Genome legacy (preserving the history)”
4:30 pm: Wine & Cheese Reception on Davenport Lawn

Friday, 7:00 pm: Session IV – Scaling to Genomes moderated by Mark Adams

Jean Weissenbach, Genoscope—CNRG, France “Genoscope early efforts at automation” Stanley Tabor, Harvard Medical School
“How enzymology enabled advances in DNA sequencing”

Session IV – Scaling to Genomes (continued)
Melvin Simon, CalTech
“Large insert cloning”
William Efcavitch, Molecular Assemblies, Inc. “Technology development in scaling up Sanger sequencing” COFFEE BREAK

Jane Rogers, The Genome Analysis Centre UK
“Scaling up Sanger sequencing in the genome era”
Richard Myers, HudsonAlpha Institute for Biotechnology
“A personal perspective on DNA sequencing from 1978 to 2015” Yoshuiyuki Sakaki, University of Tokyo, Japan

“From the proposal of automated DNA sequencing to the completion of the Human Genome: Japanese contribution to Human Genome sequencing”

Saturday, 9:00 am: Session V – Sequences to Genomes moderated by Richard Roberts

J. Craig Venter, J. Craig Venter Institute
“Whole genome shotgun sequencing”
Hamilton Smith, J. Craig Venter Institute “Haemophilus influenzae and the value of completeness” Philip Green, University of Washington

“Sequence quality & assembly”

COFFEE BREAK

James Kent, University of California, Santa Cruz “Integrating the Sequence & Map into a genome” Gene Meyers, Max Planck Institute, Germany “Shotgun assembly strategies”

Suzanna Lewis, Lawrence Berkeley National Laboratory “Making sense of genomes with visualization and collaboration”

Saturday, 1:45 pm: Session VI – All Roads Lead to DNA: Beyond Genomes moderated by Jane Rogers

Mark Adams, J Craig Venter Institute “Sequencing ESTs for gene discovery” Barbara Wold, CalTech
“Developments & Applications of RNA-seq” Jack Gilbert, University of Chicago “Metagenomic Sequencing”

COFFEE BREAK

Piero Carninci, RIKEN, Japan
“cDNA Sequencing for genome analysis & biological interpretation” Jay Shendure, University of Washington
“Novel applications of DNA sequencing
Victor Ling, BC Cancer Agency, Canada
“Fractionation & sequences of large pyrimidine oligonucleotides—1970-71”

BREAK

Saturday, 5:00 pm: Panel Discussion—Steps and mis-steps during the development of sequencing technologies

Richard McCombie Cold Spring Harbor Laboratory Richard Roberts, New England BioLabs
Cheryl Heiner, Pacific Biosciences

Saturday, 6:00 pm: Cocktails and Banquet in Blackford Hall

(Cocktails location TBA)

Sunday, 9:00 am: Session VII – Human Variation and Disease moderated by Barbara Wold

Robert Waterston, University of Washington
“C. elegans: How complete can we get?” Huanming Yang, Beijing Genomics Institute, China “China: a latecomer to the global sequencing effort” Debbie Nickerson, University of Washington “Sequencing in human genetics”

COFFEE BREAK

Mark Gerstein, Yale University “ENCODE”
David Bentley, Illumina, Inc., UK “Genomes for Medicine”

Jim Lupski, Baylor College of Medicine “Applications of sequencing in clinical genetics”

12:00 Noon: Lunch and Departures

Organizers:

Mark Adams, J. Craig Venter Institute Nigel Brown, University of Edinburgh, UK

Mila Pollock, Cold Spring Harbor Laboratory Robert Waterston, University of Washington

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