Loading…
GCC BOSC 2018 has ended
The 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) are meeting together in Portland, Oregon, United States, June 25-30, 2018.  There will be two days of training, a two+ day meeting, and four days of intense collaboration.  The meeting features joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events.  GCCBOSC is organized by Oregon Health & Science University and will be at Reed College.

Sign up or log in to bookmark your favorites and sync them to your phone or calendar.

B.g Conference - GCC [clear filter]
Wednesday, June 27
 

10:51am

Storage Media Federation for Galaxy
→ Slides @ F1000 (and @ Slideshare)
Video

Authors
Vahid Jalili 1, Enis Afgan 2, Nuwan Goonasekera 3, Dannon Baker 2, Jeremy Goecks 1

  1. Oregon Health and Science University, Portland, OR, USA, 
  2. Johns Hopkins University, Baltimore, MD, USA
  3. University of Melbourne, Melbourne, Australia.


A GCC Talk

Speakers
VJ

Vahid Jalili

Galaxy Project, Oregon Health & Science University



Wednesday June 27, 2018 10:51am - 11:10am
Eliot Chapel Eliot Hall, Reed Campus

11:10am

From laptop to super-computer: standardizing installation and management of Galaxy
Slides
Video

Authors
Nuwan Goonasekera 1, Enis Afgan 2, Vahid Jalili 3

  1. University of Melbourne, Melbourne, Australia
  2. Johns Hopkins University, Baltimore, MD, USA
  3. Oregon Health and Science University, Portland, OR, USA

Speakers
avatar for Nuwan Goonasekera

Nuwan Goonasekera

University of Melbourne



Wednesday June 27, 2018 11:10am - 11:30am
Eliot Chapel Eliot Hall, Reed Campus

11:30am

Testing Wide-Area Lustre File Systems for Sharing load in Galaxy
Slides
Video

Authors
CarrieGanote 1, Philip Blood 2, Bhavya NP 1, Sheri Sanders 1, Thomas Doak 1

  1. Indiana University Bloomington.
  2. PittsburghSupercomputingCenter.


Speakers
avatar for Carrie Ganote

Carrie Ganote

Indiana University Bloomington



Wednesday June 27, 2018 11:30am - 11:50am
Eliot Chapel Eliot Hall, Reed Campus

1:41pm

Galaksio, a more user friendly interface for Galaxy using workflows
→ Slides @ F1000
Video

Authors
Tomas Klingström, Oskar Danielsson, Rafael Hernández-de-Diego and Erik Bongcam-Rudloff

Speakers
avatar for Tomas Klingström

Tomas Klingström

Project manager, SLU-Global Bioinformatics Centre, Swedish University of Agricultural Sciences
Biobanking, data management from sampling to publication, support infrastructures, and Africa.



Wednesday June 27, 2018 1:41pm - 2:00pm
Eliot Chapel Eliot Hall, Reed Campus

2:00pm

Large scale analyses with improved dataset collections
Video

Authors
Marius van den Beek 1, John Chilton 2, Nicola Soranzo 3, Anil S. Thanki 3, Martin Čech 2, and the Galaxy Team

  1. Institut Curie, 26 rue d’Ulm, F-75248 Paris, France.
  2. Department of Biochemistry and Molecular Biology, Penn State University, University Park PA USA .
  3. Earlham Institute (EI), Norwich Research Park, Norwich NR4 7UZ, UK.

Speakers
avatar for Marius van den Beek

Marius van den Beek

Institut Curie, Paris



Wednesday June 27, 2018 2:00pm - 2:20pm
Eliot Chapel Eliot Hall, Reed Campus

2:20pm

A fruitful year for the Galaxy Training materials
Slides
Video

Authors
Bérénice Batut, Saskia Hiltemann, Björn Grüning and the Galaxy Training Network

Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy.Bérénice is also passionate about training. She regularly gives workshops on data... Read More →



Wednesday June 27, 2018 2:20pm - 2:40pm
Eliot Chapel Eliot Hall, Reed Campus

2:40pm

The usegalaxy.* servers: democratizing computational resources for life sciences at a new level
→ Slides @ F1000
Video

Authors
Simon Gladman 1, Eric Rasche 2, Björn Grüning 2, Nate Coraor 3, Derek Benson 4, Andrew Lonie 1 and James Taylor5
  1. Melbourne Bioinformatics, The University of Melbourne, Australia.
  2. University of Freiburg, Freiburg, Germany.
  3. Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
  4. Research Computing Centre, The University of Queensland, Brisbane, Australia
  5. Department of Biology, Johns Hopkins University, Baltimore, MD, USA

Speakers
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne



Wednesday June 27, 2018 2:40pm - 3:00pm
Eliot Chapel Eliot Hall, Reed Campus
 
Thursday, June 28
 

9:01am

Galaxy Enables Integrated Analysis of Phenotypic, Genotypic, and Environmental Data for Geo-referenced Trees in CartograTree
→ Slides @ F1000
Video

Authors
Nic Herndon∗, Peter Richter†, Taylor Falk†, Sean Buehler†, Emily Grau†, Dorrie Main‡,Sook Jung‡, Stephen Ficklin‡, Margaret Staton§, Alex Feltus¶, Jill Wegrzyn†

∗ Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA. Email: nic.herndon@uconn.edu
† Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
‡ Department of Horticulture, Washington State University, Pullman, WA, USA
§ Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
¶ Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA

Speakers


Thursday June 28, 2018 9:01am - 9:20am
Eliot Chapel Eliot Hall, Reed Campus

9:20am

G-OnRamp: Create UCSC Assembly Hubs and JBrowse/Apollo Archives for Collaborative Eukaryotic Genome Annotations
→ Slides @ F1000
Video

Authors
Luke Sargent 1, Yating Liu 2, Wilson Leung 2, Sarah C.R. Elgin 2,Jeremy Goecks 1

1 Oregon Health & Science University
2 Washington University in St. Louis

Speakers
avatar for Luke Sargent

Luke Sargent

Oregon Health and Science University (OHSU)
Hello, I am a developer on the G-OnRamp project (g-onramp.org). I am happy to talk about all manifestations of the logical majesty of the Machine Spirit.



Thursday June 28, 2018 9:20am - 9:40am
Eliot Chapel Eliot Hall, Reed Campus

9:40am

Canada's Integrated Rapid Infectious Disease Analysis Platform (IRIDA)
Slides
Video

Authors
Thomas Matthews 1, Franklin Bristow 2, Aaron Petkau 1, Josh Adam 1, Peter Kruczkiewicz 1, Jen Cabral 1, Damion Dooley 4, Emma Griffiths 3, Dan Fornika 4, Geoff Winsor 3, Morag Graham 1, The IRIDA consortium, Eduardo Taboada 1, Robert Beiko 5, William Hsiao 4, Fiona Brinkman 3, Gary Van Domselaar 1,2

1. Public Health Agency of Canada, Canada
2. University of Manitoba, Winnipeg, Canada
3. Simon Fraser University, Burnaby, Canada
4. BC Public Health Microbiology and Reference Laboratory, Vancouver, Canada
5. Dalhousie University, Halifax, Canada

Speakers
avatar for Thomas Matthews

Thomas Matthews

Public Health Agency of Canada



Thursday June 28, 2018 9:40am - 10:00am
Eliot Chapel Eliot Hall, Reed Campus

10:00am

Galaxy in a proteomics core facility
→ Slides @ F1000
Video

Authors
Jeremy D Volkening 1, Grzegorz Sabat 1, Gregory A Barrett-Wilt 1, and Michael R Sussman 1

1. Biotechnology Center, University of Wisconsin-Madison

Speakers


Thursday June 28, 2018 10:00am - 10:20am
Eliot Chapel Eliot Hall, Reed Campus

10:51am

Quantifying Functional Microbiomes: An integrated, quantitative metaproteomics approach reveals connections between taxa, function and protein expression in complex microbiomes
→ Slides @ F1000
Video

Authors
Caleb W Easterly 1; Nadia Szeinbaum 2; Bjoern Gruening 3; Lee S Parsons 1; Shane L Hubler 4; Subina Mehta 1; Ray Sajulga 1; Bart Mesuere 5; James E Johnson 1; Alessandro Tanca6; Carolin Kolmeder 7; Praveen Kumar 1; Jennifer Glass 2; Joel Rudney 1; Brook L Nunn 8; Timothy J. Griffin 1; Pratik D. Jagtap 1

  1. University of Minnesota, Minneapolis, MN
  2. Georgia Institute of Technology, Atlanta,GA
  3. University of Freiburg, Freiburg, Germany
  4. Rhapsody Data LLC, Madison, WI
  5. Ghent University, Ghent, Belgium
  6. Porto Conte Ricerche Science & Technology Park of Sardinia, Alghero, Italy
  7. Universityof Helsinki, Helsinki, Finland
  8. University of Washington Department of Genome Sciences, Seattle, WA.

Speakers
CE

Caleb Easterly

University of Minnesota
avatar for Pratik Jagtap

Pratik Jagtap

Research assistant Professor, University of Minnesota
University of Minnesota



Thursday June 28, 2018 10:51am - 11:10am
Eliot Chapel Eliot Hall, Reed Campus

11:10am

GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline
→ Slides @ F1000
Video

Authors
Anil S. Thanki, Nicola Soranzo, Wilfried Haerty, Robert P. Davey

Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK

Speakers
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute



Thursday June 28, 2018 11:10am - 11:30am
Eliot Chapel Eliot Hall, Reed Campus

11:30am

Galaxy HiCExplorer: HiCExplorer, deepTools3 and pyGenomeTracks
→ Slides @ F1000
Video

Authors
Joachim Wolff 1, Devon Ryan 2, Fidel Ramirez 2, Bjoern Gruening 1
  1. Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
  2. Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg im Breisgau, Germany

Speakers
JW

Joachim Wolff

Albert-Ludwigs-University Freiburg



Thursday June 28, 2018 11:30am - 11:50am
Eliot Chapel Eliot Hall, Reed Campus

1:41pm

Galaxy Community Update
Slides
Video

What's happened, what's happening, and what's going to happen in the Galaxy Community - the annual project update.

Speakers
avatar for Daniel Blankenberg

Daniel Blankenberg

Assistant Professor, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University
avatar for Jeremy Goecks

Jeremy Goecks

Assistant Professor of Biomedical Engineering and Computational Biology, Oregon Health & Science University (OHSU)
avatar for Anton Nekrutenko

Anton Nekrutenko

Galaxy Project, Penn State University
Penn State University
avatar for James Taylor

James Taylor

Professor, Johns Hopkins University
James Taylor is the Ralph S. O'Connor Professor of Biology and professor of computer science at Johns Hopkins University. Until 2014, he was an associate professor in the departments of biology and mathematics and computer science at Emory University. He is one of the original developers... Read More →



Thursday June 28, 2018 1:41pm - 2:10pm
Eliot Chapel Eliot Hall, Reed Campus