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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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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 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
Galaxy For Proteogenomics !
PAB 104
Timothy 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 320
Bérénice Batut
Tuesday
, June 26
9:00am PDT
Conda and Containers
PAB 320
John Chilton • Bjorn Gruning • Martin Čech
11:30am PDT
Lunch
Reed Commons Cafe
12:30pm PDT
Introduction to Common Workflow Language
PAB 320
Michael 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 Lounge
Johannes Köster • Paolo Di Tommaso
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
10:50am PDT
BOSC: Session 2: Translational & Medical Informatics
Vollum Lecture Hall
Hilmar Lapp
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
11:20am PDT
Open Humans - connecting, sharing and analyzing personal data that enables community-driven research
Vollum Lecture Hall
Bastian Greshake Tzovaras
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
Building a community menagerie of automated variant validations
Vollum Lecture Hall
Brad Chapman
11:55am PDT
Variant Transforms: Loading VCF files into BigQuery for large scale data analysis
Vollum Lecture Hall
Asha 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 Hall
Lorena Pantano Rubino
2:00pm PDT
Reproducible big data science: A case study in continuous FAIRness
Vollum Lecture Hall
Ravi K. Madduri
2:20pm PDT
InterMine 2.0: More than fifteen years of open biological data integration
Vollum Lecture Hall
Yo Yehudi
2:40pm PDT
GRADitude: A computational tool for the analysis of Grad-seq data
Vollum Lecture Hall
Silvia Di Giorgio
2:45pm PDT
NIH Data Commons Pilot Phase leverages the cloud to access, analyze, and share FAIR biomedical data
Vollum Lecture Hall
David Siedzik
3:01pm PDT
G13: Bacterial genomics in Galaxy
PAB Atrium
Delphine Lariviere
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
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
9:20am 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
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
10:10am 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 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
11:50am PDT
One Week to 1,000 Whole Genomes with Open Source: Arvados, CWL, and bcbio
Vollum Lecture Hall
Peter 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 130
Bérénice Batut
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
Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things)
Eliot Chapel
Hans-Rudolf Hotz
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
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
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
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GCC BOSC 2018
America/Los Angeles
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