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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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,
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Brad Langhorst
NEB
Developmenet Group Leader
Massachusetts, USA
Tuesday
, June 26
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
10:50am PDT
GCC Session 2: Galaxy Infrastructure
Eliot Chapel
Simon Gladman
10:51am PDT
Storage Media Federation for Galaxy
Eliot Chapel
Vahid Jalili
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
11:30am 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
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
12:30pm PDT
BoF: JBrowse
PAB 104
Rob Buels
1:41pm PDT
miRTop: An open source community project for the development of a unified format file for miRNA data
Vollum Lecture Hall
Lorena Pantano Rubino
2:00pm PDT
Large scale analyses with improved dataset collections
Eliot Chapel
Marius van den Beek
2:40pm PDT
GRADitude: A computational tool for the analysis of Grad-seq data
Vollum Lecture Hall
Silvia Di Giorgio
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
B13: READemption - from reads to knowledge
PAB Atrium
Till Sauerwein
B23: Oxidizing Python: writing extensions in Rust
PAB Atrium
Luiz Carlos Irber Junior
B39: CWL-Airflow pipeline manager as a backend for BioWardrobe data analysis platform
PAB Atrium
Andrey Kartashov
B41: Scaling bioinformatics analysis using Nextflow and AWS
PAB Atrium
Francesco Strozzi
D03: Aurora Galaxy Tools: Using R Markdown as a framework to build interactive Galaxy tool output reports
PAB Atrium
Ming Chen
D09: taxa: taxonomic data standards and methods for R and Python
PAB Atrium
Scott Chamberlain
G01: Galaxy-E, a first stage towards collaborative data analysis by citizens
PAB Atrium
Yvan Le Bras
G05: Galaksio, a more user friendly interface for Galaxy using workflows
PAB Atrium
Tomas Klingström
G07: Identifying suitable spliced mapper and genomic assembly for variant detection
PAB Atrium
Akila Parvathy Dharshini
G11: Candidate Gene Methylation quantification (CandiMeth) Within the Galaxy Bioinformatics Interface
PAB Atrium
Sara-Jayne Thursby
G15: Galaxy in a proteomics core facility
PAB Atrium
Jeremy Volkening
G33: Refinery: a data management, analysis, and visualization platform utilizing the Galaxy workbench
PAB Atrium
Scott Ouellette
4:01pm PDT
Improving the Bioinformatics Curriculum
Vollum Lecture Hall
Jason Williams
5:40pm PDT
Birds-of-a-Feather (BoFs), With Your Dinner!
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
9:20am PDT
G-OnRamp: Create UCSC Assembly Hubs and JBrowse/Apollo Archives for Collaborative Eukaryotic Genome Annotations
Eliot Chapel
Luke Sargent
9:40am PDT
Distributed execution of bioinformatics tools on Apache Spark with ADAM and Cannoli
Vollum Lecture Hall
Michael Heuer
9:55am PDT
The Arachne Graph Database Server
Vollum Lecture Hall
Kyle Ellrott
10:00am PDT
Owlery: An easily deployable web service for making reasoning queries over OWL ontologies web-native
Vollum Lecture Hall
Hilmar Lapp
10:05am PDT
taxa: taxonomic data standards and methods for R and Python
Vollum Lecture Hall
Scott Chamberlain
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
11:30am 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
11:50am PDT
One Week to 1,000 Whole Genomes with Open Source: Arvados, CWL, and bcbio
Vollum Lecture Hall
Peter Amstutz
12:02pm PDT
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
Eliot Chapel
Sveinung Gundersen
2:07pm PDT
Community Annotation with Apollo: Engaging the Collective in a Genome Annotation Workflow
Vollum Lecture Hall
Nathan Dunn
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
2:46pm 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
3:01pm PDT
B08: GRADitude: A computational tool for the analysis of Grad-seq data
PAB Atrium
Silvia Di Giorgio
B10: Debarcer2, De-Barcoding and Error Correction of sequencing data containing molecular barcodes designed to handle different library designs.
PAB Atrium
Lawrence Heisler
B20: Reproducible data analysis with Snakemake
PAB Atrium
Johannes Köster
B22: Code is Science: a manifesto for open source code in science
PAB Atrium
Yo Yehudi
B26: Fast, sustainable, and secure bioinformatics with Rust-Bio and Rust-Htslib
PAB Atrium
Johannes Köster
B34: Implementation of Nextflow for the automated processing of NovaSeq data sets
PAB Atrium
Netsanet (Net) Gebremedhin
B38: You can't spell Cromwell without CWL
PAB Atrium
Jeff Gentry
D02: Adding R shiny apps as Galaxy interactive environment. A Galaxy-E demo
PAB Atrium
Valintin Chambon
D04: A Galaxy Implementation of Next-Generation Clustered Heat Maps for Interactive Exploration of Large-Scale Molecular Profiling Data
PAB Atrium
Bob Brown
D06: Distributed execution of bioinformatics tools on Apache Spark with ADAM and Cannoli
PAB Atrium
Michael Heuer
D08: Owlery: An easily deployable web service for making reasoning queries over OWL ontologies web-native
PAB Atrium
Hilmar Lapp
G02: Testing Wide-Area Lustre File Systems for Sharing load in Galaxy
PAB Atrium
Carrie Ganote
G06: Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things)
PAB Atrium
Hans-Rudolf Hotz
G32: Results of an Extended Developer Support consultation with the CloudLaunch project
PAB Atrium
Marcus Christie
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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