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GCC BOSC 2018
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
.
Videos:
BOSC
,
GCC
; and
Program PDF
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,
lodging
and
childcare
information
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,
BoFs
,
Frequently Asked Questions (FAQ)
,
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Philip Mabon
Public Health Agency of Canada
Senior Bioinformatician
Monday
, June 25
8:00am PDT
Conference desk open
PAB Atrium
12:30pm PDT
Intro to Galaxy Administration 2
PAB 320
The 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
Intro to Galaxy Administration 3
PAB 320
The Other Enis Afgan • Marius van den Beek • John Chilton • Nate Coraor • Carrie Ganote • Simon Gladman • Nuwan Goonesekera • Martin Čech
6:00pm PDT
Dinner on your own
TBA
7:30pm PDT
Bioinformatics Training and Education with the Galaxy Training Network
PAB 320
Bérénice Batut
Tuesday
, June 26
8:00am PDT
Training Day 2 - All topics
Reed College Campus
9:00am PDT
Conda and Containers
PAB 320
John Chilton • Bjorn Gruning • Martin Čech
11:30am PDT
Lunch
Reed Commons Cafe
12:30pm PDT
Galaxy Interactive Environments
PAB 332
Bjorn Gruning
3:00pm PDT
Break
PAB Atrium
3:30pm PDT
Command line workflow management systems: Snakemake and Nextflow
Vollum Lounge
Johannes Köster • Paolo Di Tommaso
6:20pm PDT
Birds-of-a-Feather (BoFs), With Your Dinner!
TBA
8:00pm PDT
Joint BOSC & GCC: Opening Session
Vollum Lecture Hall
Nicole Vasilevsky • Heather Wiencko
Opening & Welcome
Vollum Lecture Hall
Dave Clements • Nomi Harris
8:10pm PDT
Opening Keynote: Tracy K. Teal--"Democratizing Data"
Vollum Lecture Hall
Tracy 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 Hall
Fernando Pérez
10:00am PDT
The journey of a team of engineers in learning packaging technology
Vollum Lecture Hall
Patrick Durand • Valentin Marcon • Laure Quintric
10:20am PDT
Break
PAB Atrium
10:50am PDT
GCC Session 2: Galaxy Infrastructure
Eliot Chapel
Simon Gladman
10:51am PDT
Storage Media Federation for Galaxy
Eliot Chapel
Vahid Jalili
11:10am PDT
From laptop to super-computer: standardizing installation and management of Galaxy
Eliot Chapel
Nuwan Goonesekera
11:30am PDT
Testing Wide-Area Lustre File Systems for Sharing load in Galaxy
Eliot Chapel
Carrie Ganote
11:50am PDT
Galaxy for AnswerALS on Microsoft Azure and Kubernetes
Eliot Chapel
RC Carter
Lightning Talks ⚡
Eliot Chapel
11:56am PDT
Adding Python 3 support to Galaxy: a status report
Eliot Chapel
Nicola Soranzo
12:02pm PDT
Aurora Galaxy Tools: Using R Markdown as a framework to build interactive Galaxy tool output reports
Eliot Chapel
Ming Chen
12:10pm PDT
Lunch, sponsored by Lenovo + Intel
PAB Atrium
12:30pm PDT
Birds-of-a-Feather (BoFs), with Lunch!
Performing Arts Building
1:40pm PDT
GCC Session 3: Challenges & Opportunities
Eliot Chapel
Jeremy Goecks
1:41pm PDT
Galaksio, a more user friendly interface for Galaxy using workflows
Eliot Chapel
Tomas Klingström
2:00pm PDT
Large scale analyses with improved dataset collections
Eliot Chapel
Marius van den Beek
2:20pm PDT
A fruitful year for the Galaxy Training materials
Eliot Chapel
Bérénice Batut
2:45pm PDT
NIH Data Commons Pilot Phase leverages the cloud to access, analyze, and share FAIR biomedical data
Vollum Lecture Hall
David Siedzik
2:50pm PDT
Reproducible data analysis with Snakemake
Vollum Lecture Hall
Johannes Köster
3:01pm PDT
B11: flowDashboard: An Interactive Dashboard for Comparative Flow Analysis
PAB Atrium
Ted Laderas
B19: Reproducible big data science: A case study in continuous FAIRness
PAB Atrium
Ravi K. Madduri
B21: FAIRsharing: Working with the community to map the landscape of standards, databases and data policies
PAB Atrium
Massimiliano Izzo
B23: Oxidizing Python: writing extensions in Rust
PAB Atrium
Luiz Carlos Irber Junior
D01: From laptop to super-computer: standardizing installation and management of Galaxy
PAB Atrium
Nuwan Goonesekera
D03: Aurora Galaxy Tools: Using R Markdown as a framework to build interactive Galaxy tool output reports
PAB Atrium
Ming Chen
G01: Galaxy-E, a first stage towards collaborative data analysis by citizens
PAB Atrium
Yvan Le Bras
G03: Predicting Galaxy Tool Runtimes with Random Forests
PAB Atrium
Anastasia Tyryshkina
G05: Galaksio, a more user friendly interface for Galaxy using workflows
PAB Atrium
Tomas Klingström
G09: EWAS-Galaxy: a tool suite for population epigenetics integrated into the Galaxy
PAB Atrium
Krzysztof Poterlowicz
G13: Bacterial genomics in Galaxy
PAB Atrium
Delphine Lariviere
G31: A fruitful year for the Galaxy Training materials
PAB Atrium
Bérénice Batut
G33: Refinery: a data management, analysis, and visualization platform utilizing the Galaxy workbench
PAB Atrium
Scott Ouellette
4:00pm PDT
Session 4 - Joint BOSC & GCC
Vollum Lecture Hall
Brad Chapman
4:01pm PDT
Improving the Bioinformatics Curriculum
Vollum Lecture Hall
Jason Williams
4:20pm PDT
Panel: Training and Documentation in Bioinformatics
Vollum Lecture Hall
Brad Chapman • Bérénice Batut • Fernando Pérez • Tracy K. Teal • Jason Williams
5:40pm PDT
BoF: Sharing and Leveraging Galaxy Tool Execution Data
TBA
Martin Čech • Anastasia Tyryshkina
BoF: Using Galaxy in bioinformatics support infrastructures
Reed Commons Cafe
Tomas Klingström
Dinner on your own (or join a BoF)
TBA
6:00pm PDT
BOSC & GCC Social Mixer | by Lifebit
Woodstock Neighborhood
Lifebit
8:00pm PDT
BoF: Nextflow Gathering
Sitka Dorm, Ground Floor
Evan Floden
Thursday
, June 28
9:01am PDT
Galaxy Enables Integrated Analysis of Phenotypic, Genotypic, and Environmental Data for Geo-referenced Trees in CartograTree
Eliot Chapel
Nic Herndon
9:40am PDT
Canada's Integrated Rapid Infectious Disease Analysis Platform (IRIDA)
Eliot Chapel
Thomas Matthews
9:45am PDT
Extended Extraction Transform Load: A novel framework for batch jobs on cloud computing resources
Vollum Lecture Hall
Hiromu Ochiai
10:20am PDT
Break
PAB Atrium
11:10am PDT
Running portable workflow and container specifications at production scale in the cloud: strategy & best practices
Vollum Lecture Hall
Geet Duggal
11:35am PDT
Bespin: An open source system to run reproducible computational workflows on cloud infrastructure
Vollum Lecture Hall
John Bradley
11:45am PDT
Scaling bioinformatics analysis using Nextflow and AWS
Vollum Lecture Hall
Francesco Strozzi
11:50am PDT
One Week to 1,000 Whole Genomes with Open Source: Arvados, CWL, and bcbio
Vollum Lecture Hall
Peter Amstutz
12:10pm PDT
Lunch
PAB Atrium
12:30pm PDT
BoF: Common Workflow Language community chat
PAB 332
John Chilton • Michael R. Crusoe • Hervé Ménager • Jeff Gentry • Peter Amstutz
BoF: Standardizing Galaxy deployments
PAB 104
The Other Enis Afgan • Nuwan Goonesekera
1:40pm PDT
GCC Session 7: Community Update(s)
Eliot Chapel
Frederik Coppens
1:50pm PDT
GSOC update
Vollum Lecture Hall
Michael R. Crusoe
2:00pm PDT
Biopython Project Update 2018
Vollum Lecture Hall
Peter Cock
3:01pm PDT
D02: Adding R shiny apps as Galaxy interactive environment. A Galaxy-E demo
PAB Atrium
Valintin Chambon
G12: Canada's Integrated Rapid Infectious Disease Analysis Platform (IRIDA)
PAB Atrium
Thomas Matthews
5:00pm PDT
Conference Closing
Vollum Lecture Hall
Bjorn 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 Building
Bjorn Gruning • Dannon Baker • Jennifer Hillman-Jackson • Frederik Coppens • Brad Chapman
Saturday
, June 30
9:00am PDT
GCC OBF CollaborationFest: Core
Performing Arts Building
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GCC BOSC 2018
America/Los Angeles
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