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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

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

Conference desk open PAB Atrium

9:00am

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

11:30am

Lunch Reed Commons Cafe

12:30pm

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

3:00pm

Break Reed Commons Cafe

3:30pm

Galaxy For Proteogenomics ! PAB 104Tim Griffin • Pratik Jagtap • JJ Johnson • Praveen Kumar • Subina Mehta

6:00pm

Dinner on your own TBA

7:30pm

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

9:00am

Conda and Containers PAB 320John Chilton • Björn Grüning • Martin Čech

11:30am

Lunch Reed Commons Cafe

12:30pm

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

3:00pm

Break PAB Atrium

3:30pm

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

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

10:50am

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

10:51am

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

11:05am

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

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

11:40am

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

11:45am

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

11:50am

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

11:55am

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

12:10pm

Lunch, sponsored by Lenovo + Intel PAB Atrium

1:41pm

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

2:00pm

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

2:20pm

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

2:40pm

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

2:45pm

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

3:01pm

G13: Bacterial genomics in Galaxy PAB AtriumDelphine Lariviere

4:00pm

Session 4 - Joint BOSC & GCC Vollum Lecture HallBrad Chapman

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
 
Thursday, June 28
 

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

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

10:05am

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

10:10am

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

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

Galaxy HiCExplorer: HiCExplorer, deepTools3 and pyGenomeTracks Eliot ChapelJoachim Wolff

11:50am

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

11:55am

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

12:30pm

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

2:10pm

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

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

4:00pm

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

4:01pm

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

5:00pm

Conference Closing Vollum Lecture HallBjörn Grüning • Nomi Harris • Nicole Vasilevsky • Heather Wiencko

7:00pm

Conference Dinner Sponsored by Google Cloud TBA
 
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
 
Sunday, July 1
 

9:00am

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

9:00am

GCC OBF CollaborationFest: Encore Performing Arts Building