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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.


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Yvan Le Bras

French National Museum of Natural History
Concarneau, FRANCE
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Tuesday, June 26
 

6:20pm

BoF: Galaxy for proteomics interest group Reed Commons CafeTim Griffin • Pratik Jagtap

8:00pm

Joint BOSC & GCC: Opening Session Vollum Lecture HallNicole Vasilevsky • Heather Wiencko Opening & Welcome Vollum Lecture HallDave Clements • Nomi Harris

8:10pm

Opening Keynote: Tracy K. Teal--"Democratizing Data" Vollum Lecture HallTracy K. Teal
 
Wednesday, June 27
 

9:00am

Joint BOSC & GCC Session 1 Vollum Lecture Hall

9:01am

Keynote: Fernando Pérez--"Sustainable development of scientific open source tools: a view from Jupyter" Vollum Lecture HallFernando Pérez

10:00am

The journey of a team of engineers in learning packaging technology Vollum Lecture HallPatrick Durand • Valentin Marcon • Laure Quintric

10:20am

Break PAB Atrium

10:50am

GCC Session 2: Galaxy Infrastructure Eliot ChapelSimon Gladman

10:51am

Storage Media Federation for Galaxy Eliot ChapelVahid Jalili

11:10am

From laptop to super-computer: standardizing installation and management of Galaxy Eliot ChapelNuwan Goonasekera

11:30am

Testing Wide-Area Lustre File Systems for Sharing load in Galaxy Eliot ChapelCarrie Ganote

11:50am

Galaxy for AnswerALS on Microsoft Azure and Kubernetes Eliot ChapelRC Carter

11:56am

Adding Python 3 support to Galaxy: a status report Eliot ChapelNicola Soranzo

12:02pm

Aurora Galaxy Tools: Using R Markdown as a framework to build interactive Galaxy tool output reports Eliot ChapelMing Chen

1:40pm

GCC Session 3: Challenges & Opportunities Eliot ChapelJeremy Goecks

1:41pm

Galaksio, a more user friendly interface for Galaxy using workflows Eliot ChapelTomas Klingström

2:00pm

Reproducible big data science: A case study in continuous FAIRness Vollum Lecture HallRavi K. Madduri

2:20pm

A fruitful year for the Galaxy Training materials Eliot ChapelBérénice Batut

2:40pm

The usegalaxy.* servers: democratizing computational resources for life sciences at a new level Eliot ChapelSimon Gladman

3:01pm

B01: Association Mapping and Landscape Genomics of Georeferenced Forest Trees via CartograTree and TreeGenes PAB AtriumTaylor Falk B05: One Week to 1,000 Whole Genomes with Open Source: Arvados, CWL, and bcbio PAB AtriumPeter Amstutz B11: flowDashboard: An Interactive Dashboard for Comparative Flow Analysis PAB AtriumTed Laderas B13: READemption - from reads to knowledge PAB AtriumTill Sauerwein B19: Reproducible big data science: A case study in continuous FAIRness PAB AtriumRavi K. Madduri B21: FAIRsharing: Working with the community to map the landscape of standards, databases and data policies PAB AtriumMassimiliano Izzo B25: The GTrack ecosystem: expressive file formats for genomic track data and metadata - through compilation, exchange, storage and analysis PAB AtriumSveinung Gundersen B27: JASS: a free and open source software for the joint analysis and interactive analysis of GWAS results PAB AtriumHervé Ménager B33: BioThings Hub: An API Gateway for Biomedical Knowledge PAB AtriumSébastien Lelong B43: CWLProv - Interoperable retrospective provenance capture and its challenges PAB AtriumFarah Zaib Khan D01: From laptop to super-computer: standardizing installation and management of Galaxy PAB AtriumNuwan Goonasekera D03: Aurora Galaxy Tools: Using R Markdown as a framework to build interactive Galaxy tool output reports PAB AtriumMing Chen G01: Galaxy-E, a first stage towards collaborative data analysis by citizens PAB AtriumYvan Le Bras G03: Predicting Galaxy Tool Runtimes with Random Forests PAB AtriumAnastasia Tyryshkina G05: Galaksio, a more user friendly interface for Galaxy using workflows PAB AtriumTomas Klingström G09: EWAS-Galaxy: a tool suite for population epigenetics integrated into the Galaxy PAB AtriumKrzysztof Poterlowicz G13: Bacterial genomics in Galaxy PAB AtriumDelphine Lariviére G15: Galaxy in a proteomics core facility PAB AtriumJeremy Volkening G17: Evaluation of moFF and FlashLFQ for label-free peptide quantification in proteomic workflows within the Galaxy-P framework PAB AtriumSubina Mehta G19: Implementation of machine learning algorithms for medulloblastoma classification in a local galaxy server PAB AtriumLuciane Sussuchi Da Silva G23: SECIMTools: A suite of Metabolomics Data Analysis Tools PAB AtriumOleksandr Moskalenko G25: VKMZ: Visualizing Metabolomics on a van Krevelen Diagram through Galaxy PAB AtriumMark Esler G33: Refinery: a data management, analysis, and visualization platform utilizing the Galaxy workbench PAB AtriumScott Ouellette

4:01pm

Improving the Bioinformatics Curriculum Vollum Lecture HallJason Williams

4:20pm

Panel: Training and Documentation in Bioinformatics Vollum Lecture HallBrad Chapman • Bérénice Batut • Fernando Pérez • Tracy K. Teal • Jason Williams

5:40pm

BoF: Using Galaxy in bioinformatics support infrastructures Reed Commons CafeTomas Klingström

6:00pm

BOSC & GCC Social Mixer | by Lifebit Woodstock NeighborhoodLifebit
 
Thursday, June 28
 

9:00am

GCC Session 5: Galaxy in situ Eliot ChapelLaure Quintric

9:01am

Galaxy Enables Integrated Analysis of Phenotypic, Genotypic, and Environmental Data for Geo-referenced Trees in CartograTree Eliot ChapelNic Herndon

9:20am

G-OnRamp: Create UCSC Assembly Hubs and JBrowse/Apollo Archives for Collaborative Eukaryotic Genome Annotations Eliot ChapelLuke Sargent

9:40am

Canada's Integrated Rapid Infectious Disease Analysis Platform (IRIDA) Eliot ChapelThomas Matthews

10:00am

Galaxy in a proteomics core facility Eliot ChapelJeremy Volkening

10:20am

Break PAB Atrium

10:51am

Quantifying Functional Microbiomes: An integrated, quantitative metaproteomics approach reveals connections between taxa, function and protein expression in complex microbiomes Eliot ChapelCaleb Easterly • Pratik Jagtap

11:10am

GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline Eliot ChapelNicola Soranzo

11:30am

The GA4GH/DREAM Workflow Execution Challenge Vollum Lecture HallJames Eddy Galaxy HiCExplorer: HiCExplorer, deepTools3 and pyGenomeTracks Eliot ChapelJoachim Wolff

11:50am

Using Galaxy to analyze TCGA data: the experience of a Brazilian center Eliot ChapelThais Talarico

11:56am

ImmPort Galaxy, facilitating analysis and meta-analysis of flow cytometry data Eliot ChapelCristel Thomas

12:02pm

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features Eliot ChapelSveinung Gundersen

12:10pm

Lunch PAB Atrium

12:30pm

BoF: Galaxy Training Material: Let's improve the contributions! PAB 130Bérénice Batut

1:40pm

GCC Session 7: Community Update(s) Eliot ChapelFrederik Coppens

1:41pm

Galaxy Community Update Eliot ChapelDan Blankenberg • Jeremy Goecks • Anton Nekrutenko • James Taylor

2:10pm

Integrative proteo-transcriptomics workflows within the Galaxy framework to explore the correlation between the expression of RNA and proteins Eliot ChapelPraveen Kumar

2:16pm

A Galaxy Implementation of Next-Generation Clustered Heat Maps for Interactive Exploration of Large-Scale Molecular Profiling Data Eliot ChapelBob Brown

2:22pm

Candidate Gene Methylation quantification (CandiMeth) Within the Galaxy Bioinformatics Interface Eliot ChapelSara-Jayne Thursby

2:28pm

Making Immune Repertoire Sequence Analysis Accessible to Anyone via Galaxy Eliot ChapelBradley W. Langhorst

2:34pm

Galaxy Genome Annotation project: integrating Galaxy and GMOD for genome annotation Eliot ChapelAnthony Bretaudeau

2:40pm

OrthoQuery: A Tripal Module to Assess Gene Family Evolution in Sequenced Gymnosperms Eliot ChapelSumaira Zaman

2:46pm

Galaxy-E, a first step towards collaborative data analysis by citizens Eliot ChapelYvan Le Bras

2:52pm

Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things) Eliot ChapelHans-Rudolf Hotz

3:01pm

D02: Adding R shiny apps as Galaxy interactive environment. A Galaxy-E demo PAB AtriumValintin Chambon
 
Friday, June 29
 

9:00am

GCC OBF CollaborationFest: Core Performing Arts BuildingBjörn Grüning • Dannon Baker • Jennifer Hillman-Jackson • Frederik Coppens • Brad Chapman
 
Saturday, June 30
 

9:00am

GCC OBF CollaborationFest: Core Performing Arts Building