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
 

11:50am

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



Wednesday June 27, 2018 11:50am - 11:56am
Eliot Chapel Eliot Hall, Reed Campus

11:50am

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
Eliot Chapel Eliot Hall, Reed Campus

11:56am

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



Wednesday June 27, 2018 11:56am - 12:02pm
Eliot Chapel Eliot Hall, Reed Campus

12:02pm

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


Wednesday June 27, 2018 12:02pm - 12:08pm
Eliot Chapel Eliot Hall, Reed Campus
 
Thursday, June 28
 

11:50am

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.



Thursday June 28, 2018 11:50am - 11:56am
Eliot Chapel Eliot Hall, Reed Campus

11:50am

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
Eliot Chapel Eliot Hall, Reed Campus

11:56am

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


Thursday June 28, 2018 11:56am - 12:02pm
Eliot Chapel Eliot Hall, Reed Campus

12:02pm

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





Thursday June 28, 2018 12:02pm - 12:08pm
Eliot Chapel Eliot Hall, Reed Campus

2:10pm

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



Thursday June 28, 2018 2:10pm - 2:16pm
Eliot Chapel Eliot Hall, Reed Campus

2:10pm

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
Eliot Chapel Eliot Hall, Reed Campus

2:16pm

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.



Thursday June 28, 2018 2:16pm - 2:22pm
Eliot Chapel Eliot Hall, Reed Campus

2:22pm

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



Thursday June 28, 2018 2:22pm - 2:28pm
Eliot Chapel Eliot Hall, Reed Campus

2:28pm

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 Bradley W. Langhorst

Bradley W. Langhorst

New England Biolabs



Thursday June 28, 2018 2:28pm - 2:34pm
Eliot Chapel Eliot Hall, Reed Campus

2:34pm

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



Thursday June 28, 2018 2:34pm - 2:40pm
Eliot Chapel Eliot Hall, Reed Campus

2:40pm

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



Thursday June 28, 2018 2:40pm - 2:46pm
Eliot Chapel Eliot Hall, Reed Campus

2:46pm

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



Thursday June 28, 2018 2:46pm - 2:52pm
Eliot Chapel Eliot Hall, Reed Campus

2:52pm

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



Thursday June 28, 2018 2:52pm - 2:58pm
Eliot Chapel Eliot Hall, Reed Campus