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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.

avatar for Delphine Lariviere

Delphine Lariviere

Penn State University
lariviere.delphine
Post-doc in the Galaxy Team (Nekrutenko Lab). Works on bacterial genomics, assembly, RNA Seq, TnSeq. Also interested in evolution, metagenomics, epigenetics and visualisation.
Monday, June 25
 

8:00am PDT

Conference desk open PAB Atrium

9:00am PDT

Intro to Galaxy Administration 1 PAB 320The Other Enis Afgan • Marius van den Beek • John Chilton • Nate Coraor • Carrie Ganote • Simon Gladman • Nuwan Goonesekera • Martin Čech

11:30am PDT

Lunch Reed Commons Cafe

12:30pm PDT

Intro to Galaxy Administration 2 PAB 320The Other Enis Afgan • Marius van den Beek • John Chilton • Nate Coraor • Carrie Ganote • Simon Gladman • Nuwan Goonesekera • Martin Čech

3:00pm PDT

Break Reed Commons Cafe

3:30pm PDT

Galaxy For Proteogenomics ! PAB 104Timothy J. Griffin • Pratik Jagtap • James Johnson • Praveen Kumar • Subina Mehta

6:00pm PDT

Dinner on your own TBA

7:30pm PDT

Bioinformatics Training and Education with the Galaxy Training Network PAB 320Bérénice Batut
 
Tuesday, June 26
 

9:00am PDT

Conda and Containers PAB 320John Chilton • Bjorn Gruning • Martin Čech

11:30am PDT

Lunch Reed Commons Cafe

12:30pm PDT

Introduction to Common Workflow Language PAB 320Michael R. Crusoe • Kenzo-Hugo Hillion • Hervé Ménager

3:00pm PDT

Break PAB Atrium

3:30pm PDT

Command line workflow management systems: Snakemake and Nextflow Vollum LoungeJohannes Köster • Paolo Di Tommaso

8:00pm PDT

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

8:10pm PDT

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

9:00am PDT

Joint BOSC & GCC Session 1 Vollum Lecture Hall

9:01am PDT

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

10:00am PDT

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

10:50am PDT

BOSC: Session 2: Translational & Medical Informatics Vollum Lecture HallHilmar Lapp

10:51am PDT

Cloud-based data ingest for the Human Cell Atlas Vollum Lecture HallDaniel Vaughan

11:05am PDT

The Human Cell Atlas Data Coordination Platform: an open source, cloud-based system for ingesting, storing, analyzing, discovering, and exploring single-cell data Vollum Lecture HallBrian O'Connor

11:20am PDT

Open Humans - connecting, sharing and analyzing personal data that enables community-driven research Vollum Lecture HallBastian Greshake Tzovaras

11:40am PDT

Enabling Machine Learning at Scale with “Tiled” Human Genomes Vollum Lecture HallSarah Wait Zaranek

11:45am PDT

JASS: a free and open source software for the joint analysis and interactive analysis of GWAS results Vollum Lecture HallHervé Ménager

11:50am PDT

Building a community menagerie of automated variant validations Vollum Lecture HallBrad Chapman

11:55am PDT

Variant Transforms: Loading VCF files into BigQuery for large scale data analysis Vollum Lecture HallAsha Rostamianfar

12:10pm PDT

Lunch, sponsored by Lenovo + Intel PAB Atrium

1:41pm PDT

miRTop: An open source community project for the development of a unified format file for miRNA data Vollum Lecture HallLorena Pantano Rubino

2:00pm PDT

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

2:20pm PDT

InterMine 2.0: More than fifteen years of open biological data integration Vollum Lecture HallYo Yehudi

2:40pm PDT

GRADitude: A computational tool for the analysis of Grad-seq data Vollum Lecture HallSilvia Di Giorgio

2:45pm PDT

NIH Data Commons Pilot Phase leverages the cloud to access, analyze, and share FAIR biomedical data Vollum Lecture HallDavid Siedzik

3:01pm PDT

G13: Bacterial genomics in Galaxy PAB AtriumDelphine Lariviere

4:00pm PDT

Session 4 - Joint BOSC & GCC Vollum Lecture HallBrad Chapman

4:01pm PDT

Improving the Bioinformatics Curriculum Vollum Lecture HallJason Williams

4:20pm PDT

Panel: Training and Documentation in Bioinformatics Vollum Lecture HallBrad Chapman • Bérénice Batut • Fernando Pérez • Tracy K. Teal • Jason Williams
 
Thursday, June 28
 

9:01am PDT

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

9:20am PDT

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

9:40am PDT

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

10:00am PDT

Owlery: An easily deployable web service for making reasoning queries over OWL ontologies web-native Vollum Lecture HallHilmar Lapp

10:05am PDT

taxa: taxonomic data standards and methods for R and Python Vollum Lecture HallScott Chamberlain

10:10am PDT

Q&A for lightning talks in this session⚡ Vollum Lecture Hall

10:20am PDT

Break PAB Atrium

10:51am PDT

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 PDT

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

11:30am PDT

Galaxy HiCExplorer: HiCExplorer, deepTools3 and pyGenomeTracks Eliot ChapelJoachim Wolff

11:50am PDT

One Week to 1,000 Whole Genomes with Open Source: Arvados, CWL, and bcbio Vollum Lecture HallPeter Amstutz

11:55am PDT

Q&A for lightning talks in this session⚡ Vollum Lecture Hall

12:30pm PDT

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

2:10pm PDT

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

2:16pm PDT

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

2:22pm PDT

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

2:28pm PDT

Making Immune Repertoire Sequence Analysis Accessible to Anyone via Galaxy Eliot ChapelBrad Langhorst

2:34pm PDT

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

2:40pm PDT

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

2:46pm PDT

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

2:52pm PDT

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

4:00pm PDT

Session 8 - Joint BOSC & GCC Closing Vollum Lecture HallPratik Jagtap

4:01pm PDT

Closing Keynote: Confound it! Reproducible biology from "omics" data analysis Vollum Lecture HallLucia Peixoto

5:00pm PDT

Conference Closing Vollum Lecture HallBjorn Gruning • Nomi Harris • Nicole Vasilevsky • Heather Wiencko

7:00pm PDT

Conference Dinner Sponsored by Google Cloud TBA
 
Friday, June 29
 

9:00am PDT

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

9:00am PDT

GCC OBF CollaborationFest: Core Performing Arts Building
 
Sunday, July 1
 

9:00am PDT

GCC OBF CollaborationFest: Encore Performing Arts Building
 
Monday, July 2
 

9:00am PDT

GCC OBF CollaborationFest: Encore Performing Arts Building