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.

Simple
Expanded
Grid
By Venue
B.g Conference - GCC [clear filter]
Wednesday, June 27
 

10:50am PDT

GCC Session 2: Galaxy Infrastructure
The first Galaxy Community Conference session of GCCBOSC 2018.  The session will include accepted oral presentations from the Galaxy community. 
Speakers
avatar for Simon Gladman

Simon Gladman

University of Melbourne

Wednesday June 27, 2018 10:50am - 12:10pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Session

10:51am PDT

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

GCC 2018 2 1 storage media federation pdf
S2 T1 FederatedStorageGCC2018 pdf
Wednesday June 27, 2018 10:51am - 11:10am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

11:10am PDT

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 Goonesekera

Nuwan Goonesekera

University of Melbourne

GCC 2018 2 2 laptop to supercomputer pdf
Wednesday June 27, 2018 11:10am - 11:30am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

11:30am PDT

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

GCC 2018 2 3 testing wide area lustre pdf
S2 T3 bridges pdf
Wednesday June 27, 2018 11:30am - 11:50am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

11:50am PDT

Galaxy for AnswerALS on Microsoft Azure and Kubernetes
→ Slides
→ Video 

Authors:
RC Carter, Microsoft; Abhik Ghosh, Applied Information Systems; Alex Lenail, MIT; Enis Afgan, Johns Hopkins University; Gaurav Hind, Microsoft; Nuwan Goonasekera, University of Melbourne
Speakers
RC

RC Carter

Microsoft

GCC 2018 2 4 answerals pdf
S2 T4 galaxy azure kubernetes pdf
Wednesday June 27, 2018 11:50am - 11:56am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

11:50am PDT

Lightning Talks ⚡
Lightning talks are short talks that concisely communicate resources, work in progress and other topics that lend themselves to just a few minutes coverage and a few slides.
Wednesday June 27, 2018 11:50am - 12:10pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

11:56am PDT

Adding Python 3 support to Galaxy: a status report
→ Slides @ F1000
→ Video

Authors:
Nicola Soranzo1, Marius van den Beek2, John Chilton3

  1. Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK. 
  2. Institut Curie, Paris, France.
  3. The Pennsylvania State University, University Park, PA, USA.
Speakers
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute

GCC 2018 2 L1 python3 pdf
S2 T5 Adding Python 3 support to Galaxy pdf
Wednesday June 27, 2018 11:56am - 12:02pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

12:02pm PDT

Aurora Galaxy Tools: Using R Markdown as a framework to build interactive Galaxy tool output reports
→ Slides
→ Video

Authors:
Ming Chen 1, Bradford Condon 1, Abdullah Almsaeed 1, Connor Wytko 2, Stephen Ficklin 2, MargaretStaton 1

  1. University of Tennessee, Knoxville, Tennessee (USA)
  2. Washington State University, Pullman, Washington (USA)
Speakers
MC

GCC 2018 2 L2 aurora pdf
S2 T6 AURORA pdf
Wednesday June 27, 2018 12:02pm - 12:08pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

1:40pm PDT

GCC Session 3: Challenges & Opportunities
The session will include accepted oral presentations from the Galaxy community. 
Moderators
avatar for Jeremy Goecks

Jeremy Goecks

Associate Professor of Biomedical Engineering and Computational Biology, Oregon Health & Science University

Wednesday June 27, 2018 1:40pm - 3:00pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Session

1:41pm PDT

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.

GCC 2018 3 1 galaksio pdf
S3 T1 2018 06 27 WP4 GCC Portland pdf
Wednesday June 27, 2018 1:41pm - 2:00pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

2:00pm PDT

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

Penn State University

GCC 2018 3 2 collections pdf
Wednesday June 27, 2018 2:00pm - 2:20pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

2:20pm PDT

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

GCC 2018 3 3 gtn pdf
S3 T3 GCCBOSC Berenice Batut pdf
Wednesday June 27, 2018 2:20pm - 2:40pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

2:40pm PDT

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

University of Melbourne

GCC 2018 3 4 usegalaxy pdf
S3 T4 usegalaxy architecture concepts GCCBOSC pdf
Wednesday June 27, 2018 2:40pm - 3:00pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk
 
Thursday, June 28
 

9:00am PDT

GCC Session 5: Galaxy in situ
Talks and lightning of interest to the Galaxy community.
Moderators
LQ

Thursday June 28, 2018 9:00am - 10:20am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Session

9:01am PDT

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
NH

GCC 2018 4 1 cartogratree pdf
S5 T1 Herndon GCC BOSC 2018 presentation pdf
Thursday June 28, 2018 9:01am - 9:20am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

9:20am PDT

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)

GCC BOSC GOnRamp abstract pdf
S5 T2 gonramp gcc bosc 2018 pdf
Thursday June 28, 2018 9:20am - 9:40am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

9:40am PDT

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

GCC 2018 4 2 irida pdf
S5 T3 IRIDA Galaxy portland pdf
Thursday June 28, 2018 9:40am - 10:00am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

10:00am PDT

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
JV

GCC 2018 4 3 protomics core pdf
S5 T4 Volkening GCC pdf
Thursday June 28, 2018 10:00am - 10:20am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

10:50am PDT

GCC Session 6: Galaxy in situ
Galaxy Community Conference continues on Thursday.
Moderators
MD

Maria Doyle

Application and Training Specialist, Peter MacCallum Cancer Centre

Thursday June 28, 2018 10:50am - 12:10pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Session

10:51am PDT

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
Metaproteomics . DIA . Proteogenomics

GCC 2018 6 1 functional microbiomes pdf
S6 T1 metaQuant GCCBOSC 2018 pdf
Thursday June 28, 2018 10:51am - 11:10am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

11:10am PDT

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

GCC 2018 6 2 geneseqtofamily pdf
S6 T2 GeneSeqToFamily a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline GCCBOSC 2018 pdf
Thursday June 28, 2018 11:10am - 11:30am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

11:30am PDT

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

GCC 2018 6 3 hicexplorer pdf
f1000research 211133 (1) pdf
Thursday June 28, 2018 11:30am - 11:50am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

11:50am PDT

Using Galaxy to analyze TCGA data: the experience of a Brazilian center
→ Slides @ F1000
→ Video

Thais Talarico1, Murilo Machado1, Luciane Sussuchi da Silva1, José Humberto Tavares Guerreiro Fregnani1, Rui Manuel Reis1, Adriane Feijó Evangelista1

  1. Barretos Cancer Hospital
Speakers
avatar for Thais Talarico

Thais Talarico

Project assistant/Student, Barretos Cancer Hospital
I'm a Pharmacist who works with project design, development, and management. I'm also a master candidate in Oncology focused on Bioinformatics and a Systems analysis and development student.

GCC 2018 6 4 tcga pdf
S6 T4 Lightning talk Thais Talarico Hosokawa 1.4 pdf
Thursday June 28, 2018 11:50am - 11:56am PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

11:50am PDT

Lightning Talks ⚡
Lightning talks are short talks that concisely communicate resources, work in progress and other topics that lend themselves to just a few minutes coverage and a few slides.
Thursday June 28, 2018 11:50am - 12:10pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

11:56am PDT

ImmPort Galaxy, facilitating analysis and meta-analysis of flow cytometry data
→ Slides @ F1000
→ Video

Authors:
Cristel G Thomas1, Elizabeth Thomson1, Henry Schaefer2, Patrick Dunn1, John C Campbell1

  1. Northrop Grumman TS, Rockville, MD USA
  2. ESAC, Inc, Rockville, MD, USA
Speakers
CT

GCC 2018 6 5 immport galaxy pdf
S6 T5 IG gcc2018 pdf
Thursday June 28, 2018 11:56am - 12:02pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

12:02pm PDT

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
→ Slides @ Prezi
→ Video

Authors:
Boris Simovski 1, Chakravarthi Kanduri 1,2, Sveinung Gundersen 1,3, Dmytro Titov 1,3, Diana Domanska 1, Christoph Bock 4,5,6, Lara Bossini-Castillo 7, Maria Chikina 8, Alexander Favorov 9,10, Ryan M. Layer 11,12, Andrey A. Mironov 13,14,15, Aaron R. Quinlan 11,12,16, Nathan C. Sheffield 17, Gosia Trynka 7 and Geir K. Sandve 1,2

  1. Department of Informatics, University of Oslo, Gaustadalleen 23 B, N-0373 Oslo, Norway
  2. K. G. Jebsen Centre for Coeliac Disease Research, Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway
  3. Elixir Norway - Oslo node, Department of Informatics, University of Oslo, Gaustadalleen 23 B, N-0373 Oslo, Norway
  4. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
  5. Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
  6. Max Planck Institute for Informatics, 66123 Saarbrucken, Germany
  7. 7Cellular Genetics Programme, Wellcome Sanger Institute, CB10 1SA Hinxton, UK
  8. University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15213, USA, 
  9. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, 550 N Broadway, Baltimore, MD 21205, USA
  10. Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Gubkina Street 3, Moscow 119333, Russia
  11. Department of Human Genetics, University of Utah, 15 N 2030 E, Salt Lake City, UT 84112, USA 
  12. USTAR Center for Genetic Discovery, University of Utah, 15 N 2030 E, Salt Lake City, UT 84112, USA
  13. Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Lab. Bldg B, Vorobiovy Gory 1-73, Moscow 119992, Russia
  14. Skolkovo Institute of Science and Technology, Nobelya ul. 3, Moscow 121205, Russia
  15. Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karenty per. 19, Moscow 127994, Russia
  16. Department of Biomedical Informatics, University of Utah, 421 Wakara Way, Salt Lake City, UT 84108, USA and 
  17. Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903 USA


Speakers
avatar for Sveinung Gundersen

GCC 2018 6 6 coloc stats pdf
Thursday June 28, 2018 12:02pm - 12:08pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

1:40pm PDT

GCC Session 7: Community Update(s)
The session includes the Galaxy Project update talk, and lightning talks from the Galaxy community. 
Moderators
avatar for Frederik Coppens

Frederik Coppens

VIB-UGent Center for Plant Systems Biology

Thursday June 28, 2018 1:40pm - 3:00pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Session

1:41pm PDT

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, Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute
avatar for Jeremy Goecks

Jeremy Goecks

Associate Professor of Biomedical Engineering and Computational Biology, Oregon Health & Science University
avatar for Anton Nekrutenko

Anton Nekrutenko

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 →

S7 T1 Community Update pdf
Thursday June 28, 2018 1:41pm - 2:10pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Talk

2:10pm PDT

Integrative proteo-transcriptomics workflows within the Galaxy framework to explore the correlation between the expression of RNA and proteins
→ Slides @ F1000
→ Video
→ Poster @ F1000

Authors:
Praveen Kumar 1,2, Priyabrata Panigrahi 3, James Johnson 4, Caleb Easterly 2, Subina Mehta 2, Andrew Rajczewski 2, RaySajulga 2, Mohammad Heydarian 5, Krishanpal Anamika 3, Timothy Griffin 2, Pratik Jagtap 2

  1. Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, USA
  2. Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA
  3. LABS, Persistent Systems, Pingala-Aryabhata, Erandwane, Pune 411004, India
  4. Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, USA
  5. Department of Biology, Johns Hopkins University, Baltimore, USA
Speakers
avatar for Praveen Kumar

Praveen Kumar

Graduate Student, University of Minnesota

GCC 2018 7 2 Integrative proteo transcriptomics pdf
S7 T2 Praveen GCC 2018 LightningTalk FINAL pdf
Thursday June 28, 2018 2:10pm - 2:16pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

2:10pm PDT

Lightning Talks ⚡
Lightning talks are short talks that concisely communicate resources, work in progress and other topics that lend themselves to just a few minutes coverage and a few slides.
Thursday June 28, 2018 2:10pm - 3:00pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

2:16pm PDT

A Galaxy Implementation of Next-Generation Clustered Heat Maps for Interactive Exploration of Large-Scale Molecular Profiling Data
→ Slides @ F1000
→ Video

Authors:
Bradley M. Broom 1, Michael Ryan 2, Robert Brown 2 ,Chris Wakefield 1, Rehan Akbani 1, and John N. Weinstein 1,3

  1. Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
  2. In Silico Solutions, Falls Church, Virginia.
  3. Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
Speakers
avatar for Bob Brown

Bob Brown

Scientist, In Silico Solutions
Viewing and analyzing complex datasets with our Next Generation Clustered Heat Map (NG-CHM) tool in Partnership with MD Anderson.Solving difficult biological problems with our bioinformatic expertise.Addressing significance in very large multivariate studies.

GCC 2018 7 3 clustered heatmaps pdf
S7 T3 GCC NGCHM Allign Analyze pdf
Thursday June 28, 2018 2:16pm - 2:22pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

2:22pm PDT

Candidate Gene Methylation quantification (CandiMeth) Within the Galaxy Bioinformatics Interface
→ Slides @ F1000
→ Video

Authors:
Sara-Jayne Thursby, Sarah-Jayne Mackin, Rachelle Irwin and Colum P Walsh.

Centre for Molecular Biosciences, School of Biomedical Sciences, University of Ulster,Cromore Road, Coleraine BT52 1SA, UK.
Speakers
ST

Sara-Jayne Thursby

University of Ulster

GCC 2018 7 4 candimeth pdf
S7 T4 Candimeth pdf
Thursday June 28, 2018 2:22pm - 2:28pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

2:28pm PDT

Making Immune Repertoire Sequence Analysis Accessible to Anyone via Galaxy
→ Slides
→ Video

Authors:
Timothy Fennel 1, Chen Song 2, Pingfang Liu 2, Timur Shtatland 2, Eileen T. Dimalanta 2, Bradley W. Langhorst 2

  1. Fulcrum Genomics
  2. New England Biolabs
Speakers
avatar for Brad Langhorst

Brad Langhorst

Developmenet Group Leader, NEB

GCC 2018 7 5 immune repertoire pdf
S7 T5 langhorst analysis of immune sequence data in galaxy zip
Thursday June 28, 2018 2:28pm - 2:34pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

2:34pm PDT

Galaxy Genome Annotation project: integrating Galaxy and GMOD for genome annotation
→ Slides @ F1000
→ Video

Authors:
Anthony Bretaudeau 1, Nathan Dunn 2, Simon Gladman 3, Björn Grüning 4, Eric Rasche 4, Torsten Seemann 3

  1. INRA, UMR IGEPP, BIPAA/GenOuest, Campus Beaulieu, Rennes, France
  2. Lawrence Berkeley National Lab, Berkeley, CA, USA
  3. Melbourne Bioinformatics, University of Melbourne, Australia
  4. de.NBI, Albert Ludwigs Universität, Freiburg, Baden-Württemberg, Germany.
Speakers
avatar for Anthony Bretaudeau

Anthony Bretaudeau

BIPAA/GenOuest

GCC 2018 7 6 gga pdf
S7 T6 20180628 gga gcc pdf
Thursday June 28, 2018 2:34pm - 2:40pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

2:40pm PDT

OrthoQuery: A Tripal Module to Assess Gene Family Evolution in Sequenced Gymnosperms
→ Slides @ F1000
→ Video

Authors: 
Sumaira Zaman 1, Emily Grau 2, Sean Buehler 2, Stephen Ficklin 3, Jill Wegrzyn 2

  1. Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.
  2. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
  3. Department of Horticulture, Washington State University, Pullman, WA, USA
Speakers
SZ

Sumaira Zaman

University of Connecticut

GCC 2018 7 7 orthoquery pdf
S7 T7 Zaman Galaxy2018 pdf
Thursday June 28, 2018 2:40pm - 2:46pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

2:46pm PDT

Galaxy-E, a first step towards collaborative data analysis by citizens
→ Slides
→ Video

Authors:
Yvan Le Bras 1, Valentin Chambon 1, Alan Amossé 1, Julien Sananikone 2, Elise Brax 2, Marianne Linares 2, Marie Delannoy 2, Grégoire Loïs 2, Romain Julliard 2

  1. French National Museum of Natural History, Station de Biologie marine BP 225, 29182 Concarneau CEDEX - CESCO UMR 7204 43 rue Buffon 75005 PARIS.
  2. French National Museum of Natural History, CESCO UMR 7204 43 rue Buffon 75005 PARIS.
Speakers
avatar for Yvan Le Bras

Yvan Le Bras

Research engineer, French National Museum of Natural History

GCCBOSC 2018 7 8 galaxy e pdf
S7 T8 LightningTalkGCC2018 Galaxy E pdf
Thursday June 28, 2018 2:46pm - 2:52pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning

2:52pm PDT

Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things)
→ Slides @ F1000
→ Video

Authors:
Hans-Rudolf Hotz, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
Speakers
avatar for Hans-Rudolf Hotz

Hans-Rudolf Hotz

Friedrich Miescher Institute for Biomedical Research, Basel

GCC 2018 7 9 shiny pdf
S7 T9 GCC2018 Galaxy2Shiny2Galaxy GCC final talk pdf
Thursday June 28, 2018 2:52pm - 2:58pm PDT
Eliot Chapel Eliot Hall, Reed Campus
  B.g Conference - GCC, Lightning
 
Filter sessions
Apply filters to sessions.
Sunday, June 24
Monday, June 25
Tuesday, June 26
Wednesday, June 27
Thursday, June 28
Friday, June 29
Saturday, June 30
Sunday, July 1
Monday, July 2
Eliot Chapel
Gigantic Brewing
PAB 104
PAB 130
PAB 131
PAB 320
PAB 332
PAB Atrium
Performing Arts Building
Reed College Campus
Reed Commons Cafe
Sitka Dorm, Ground Floor
TBA
Vollum Lecture Hall
Vollum Lounge
Woodstock Neighborhood
  • A. Training
  • B. Conference
  • B.b Conference - BOSC
  • B.g Conference - GCC
  • C. CollaborationFest