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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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,
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and
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information
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Luciane Sussuchi Da Silva
Barretos Cancer Hospital
Postdoc
Brazil
Monday
, June 25
8:00am PDT
Conference desk open
PAB Atrium
Training Day 1 - Galaxy
Performing Arts Building
9:00am PDT
Intro to Galaxy Administration 1
PAB 320
The 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 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
Conference desk open
PAB Atrium
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
Galaxy Architecture
PAB 320
John Chilton • Nate Coraor
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
Wednesday
, June 27
8:00am PDT
Conference desk open
PAB Atrium
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
Sponsors
PAB Atrium
10:50am PDT
GCC Session 2: Galaxy Infrastructure
Eliot Chapel
Simon Gladman
10:51am PDT
Cloud-based data ingest for the Human Cell Atlas
Vollum Lecture Hall
Daniel 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 Hall
Brian O'Connor
11:10am PDT
From laptop to super-computer: standardizing installation and management of Galaxy
Eliot Chapel
Nuwan Goonesekera
11:20am PDT
Open Humans - connecting, sharing and analyzing personal data that enables community-driven research
Vollum Lecture Hall
Bastian Greshake Tzovaras
11:30am PDT
Testing Wide-Area Lustre File Systems for Sharing load in Galaxy
Eliot Chapel
Carrie Ganote
11:40am PDT
Enabling Machine Learning at Scale with “Tiled” Human Genomes
Vollum Lecture Hall
Sarah Wait Zaranek
11:45am PDT
JASS: a free and open source software for the joint analysis and interactive analysis of GWAS results
Vollum Lecture Hall
Hervé Ménager
11:50am PDT
Lightning Talks ⚡
Eliot Chapel
11:55am PDT
Variant Transforms: Loading VCF files into BigQuery for large scale data analysis
Vollum Lecture Hall
Asha Rostamianfar
11:56am PDT
Adding Python 3 support to Galaxy: a status report
Eliot Chapel
Nicola Soranzo
12:00pm PDT
Q&A for lightning talks in this session ⚡
Vollum Lecture Hall
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
Sponsors
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
2:40pm PDT
The usegalaxy.* servers: democratizing computational resources for life sciences at a new level
Eliot Chapel
Simon Gladman
2:45pm PDT
NIH Data Commons Pilot Phase leverages the cloud to access, analyze, and share FAIR biomedical data
Vollum Lecture Hall
David Siedzik
2:55pm PDT
Q&A for lightning talks in this session⚡
Vollum Lecture Hall
3:00pm PDT
Posters & Demos: Odd Numbered
PAB Atrium
Sponsors
PAB Atrium
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
Birds-of-a-Feather (BoFs), With Your Dinner!
TBA
8:00pm PDT
Birds-of-a-Feather (BoFs), wherever you want!
TBA
Thursday
, June 28
8:00am PDT
Conference desk open
PAB Atrium
9:00am PDT
GCC Session 5: Galaxy in situ
Eliot Chapel
Laure Quintric
9:01am PDT
Galaxy Enables Integrated Analysis of Phenotypic, Genotypic, and Environmental Data for Geo-referenced Trees in CartograTree
Eliot Chapel
Nic Herndon
9:20am PDT
G-OnRamp: Create UCSC Assembly Hubs and JBrowse/Apollo Archives for Collaborative Eukaryotic Genome Annotations
Eliot Chapel
Luke Sargent
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
9:50am PDT
Plugging Docker-based visualizations into Django with django_docker_engine
Vollum Lecture Hall
Chuck McCallum
9:55am PDT
The Arachne Graph Database Server
Vollum Lecture Hall
Kyle Ellrott
10:00am PDT
Galaxy in a proteomics core facility
Eliot Chapel
Jeremy Volkening
10:05am PDT
taxa: taxonomic data standards and methods for R and Python
Vollum Lecture Hall
Scott Chamberlain
10:10am PDT
Q&A for lightning talks in this session⚡
Vollum Lecture Hall
10:20am PDT
Break
PAB Atrium
Sponsors
PAB Atrium
10:50am PDT
GCC Session 6: Galaxy in situ
Eliot Chapel
Maria Doyle
10:51am PDT
Quantifying Functional Microbiomes: An integrated, quantitative metaproteomics approach reveals connections between taxa, function and protein expression in complex microbiomes
Eliot Chapel
Caleb Easterly • Pratik Jagtap
11:10am PDT
GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline
Eliot Chapel
Nicola Soranzo
11:30am PDT
Galaxy HiCExplorer: HiCExplorer, deepTools3 and pyGenomeTracks
Eliot Chapel
Joachim Wolff
11:35am PDT
Bespin: An open source system to run reproducible computational workflows on cloud infrastructure
Vollum Lecture Hall
John Bradley
11:40am PDT
CWL-Airflow pipeline manager as a backend for BioWardrobe data analysis platform
Vollum Lecture Hall
Andrey Kartashov
11:45am PDT
Scaling bioinformatics analysis using Nextflow and AWS
Vollum Lecture Hall
Francesco Strozzi
11:50am PDT
Lightning Talks ⚡
Eliot Chapel
11:55am PDT
Q&A for lightning talks in this session⚡
Vollum Lecture Hall
11:56am PDT
ImmPort Galaxy, facilitating analysis and meta-analysis of flow cytometry data
Eliot Chapel
Cristel Thomas
12:02pm PDT
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
Eliot Chapel
Sveinung Gundersen
12:10pm PDT
Lunch
PAB Atrium
Sponsors
PAB Atrium
12:30pm PDT
Birds-of-a-Feather (BoFs), with Lunch!
Performing Arts Building
BoF: Preparing for the next steps in AI
PAB 131
Kathy Wilson
1:40pm PDT
GCC Session 7: Community Update(s)
Eliot Chapel
Frederik Coppens
1:41pm PDT
Galaxy Community Update
Eliot Chapel
Daniel Blankenberg • Jeremy Goecks • Anton Nekrutenko • James Taylor
1:50pm PDT
GSOC update
Vollum Lecture Hall
Michael R. Crusoe
2:00pm PDT
Biopython Project Update 2018
Vollum Lecture Hall
Peter Cock
2:07pm PDT
Community Annotation with Apollo: Engaging the Collective in a Genome Annotation Workflow
Vollum Lecture Hall
Nathan Dunn
2:10pm PDT
Integrative proteo-transcriptomics workflows within the Galaxy framework to explore the correlation between the expression of RNA and proteins
Eliot Chapel
Praveen 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 Chapel
Bob Brown
2:22pm PDT
Candidate Gene Methylation quantification (CandiMeth) Within the Galaxy Bioinformatics Interface
Eliot Chapel
Sara-Jayne Thursby
2:28pm PDT
Making Immune Repertoire Sequence Analysis Accessible to Anyone via Galaxy
Eliot Chapel
Brad Langhorst
2:34pm PDT
Galaxy Genome Annotation project: integrating Galaxy and GMOD for genome annotation
Eliot Chapel
Anthony Bretaudeau
2:40pm PDT
OrthoQuery: A Tripal Module to Assess Gene Family Evolution in Sequenced Gymnosperms
Eliot Chapel
Sumaira Zaman
2:46pm PDT
Galaxy-E, a first step towards collaborative data analysis by citizens
Eliot Chapel
Yvan Le Bras
2:52pm PDT
Q&A for lightning talks in this session⚡
Vollum Lecture Hall
Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things)
Eliot Chapel
Hans-Rudolf Hotz
3:00pm PDT
Posters & Demos: Even Numbered
PAB Atrium
Sponsors
PAB Atrium
4:00pm PDT
Session 8 - Joint BOSC & GCC Closing
Vollum Lecture Hall
Pratik Jagtap
4:01pm PDT
Closing Keynote: Confound it! Reproducible biology from "omics" data analysis
Vollum Lecture Hall
Lucia Peixoto
5:00pm PDT
Conference Closing
Vollum Lecture Hall
Bjorn Gruning • Nomi Harris • Nicole Vasilevsky • Heather Wiencko
5:40pm PDT
Birds-of-a-Feather (BoFs), the Final Flight!
Performing Arts Building
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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