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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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,
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VIJAY
Genomic Medicine Institute/ Lerner Research Institute CLEVELAND CLINIC FOUNDATION
Postdoctoral fellow
CLEVELAND
Sunday
, June 24
3:00pm PDT
Conference desk open
PAB Atrium
Monday
, June 25
8:00am PDT
Conference desk open
PAB Atrium
Training Day 1 - Galaxy
Performing Arts Building
9:00am PDT
Galaxy 101 - A gentle introduction to using Galaxy
PAB 104
Bérénice Batut • Joachim Wolff
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
RNA-Seq Analysis with Galaxy
PAB 104
Anton Nekrutenko
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
8:00am PDT
Training Day 2 - All topics
Reed College Campus
9:00am PDT
Community built analyses that run everywhere with bcbio
PAB 332
Brad Chapman • Radhika S. Khetani • Lorena Pantano Rubino
Conda and Containers
PAB 320
John Chilton • Bjorn Gruning • Martin Čech
Data Carpentry Genomics Workshop: Data Organization and Automation with Shell I
PAB 131
Tracy K. Teal
Handling integrated biological data using Python (or R) and InterMine
PAB 104
Daniela Butano • Leyla Ruzicka • Yo Yehudi
12:30pm PDT
Data Carpentry Genomics Workshop: Data Organization and Automation with Shell II
PAB 131
Tracy K. Teal
Practical use of the Galaxy API command line tools
Vollum Lounge
Dannon Baker • Marius van den Beek • Nicola Soranzo
3:30pm PDT
Data Carpentry Genomics Workshop: Data Organization and Automation with Shell III
PAB 131
Tracy K. Teal
GATK4: What's new and how to run it
PAB 332
Geraldine Van der Auwera • Kate Noblett
Setting up for success: Everything you need to know when planning for an RNA-seq analysis II
PAB 104
Radhika S. Khetani • Meeta Mistry • Mary Piper
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
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
Sponsors
PAB Atrium
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
11:45am PDT
JASS: a free and open source software for the joint analysis and interactive analysis of GWAS results
Vollum Lecture Hall
Hervé Ménager
11:55am PDT
Variant Transforms: Loading VCF files into BigQuery for large scale data analysis
Vollum Lecture Hall
Asha Rostamianfar
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
1:41pm PDT
Galaksio, a more user friendly interface for Galaxy using workflows
Eliot Chapel
Tomas Klingström
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
2:50pm PDT
Reproducible data analysis with Snakemake
Vollum Lecture Hall
Johannes Köster
3:00pm PDT
Posters & Demos: Odd Numbered
PAB Atrium
Sponsors
PAB Atrium
3:01pm PDT
B15: RyuGoo-Saba: a CWL-based execution engine utilizing cloud resources for big data analysis in life science
PAB Atrium
Hirotaka Suetake
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
G23: SECIMTools: A suite of Metabolomics Data Analysis Tools
PAB Atrium
Oleksandr Moskalenko
4:00pm PDT
Session 4 - Joint BOSC & GCC
Vollum Lecture Hall
Brad Chapman
5:40pm PDT
Birds-of-a-Feather (BoFs), With Your Dinner!
TBA
BoF: Educating Funders/PIs on Open Science
TBA
Tracy K. Teal • Jason Williams
Dinner on your own (or join a BoF)
TBA
6:00pm PDT
BOSC & GCC Social Mixer | by Lifebit
Woodstock Neighborhood
Lifebit
8:00pm PDT
Birds-of-a-Feather (BoFs), wherever you want!
TBA
Thursday
, June 28
9:00am PDT
BOSC Session 5: Developer Tools and Libraries
Vollum Lecture Hall
Peter Cock
9:01am PDT
iMADS: A sustainable software collaboration for predicting transcription factor binding specificity
Vollum Lecture Hall
Dan Leehr
10:00am PDT
Galaxy in a proteomics core facility
Eliot Chapel
Jeremy Volkening
10:20am PDT
Break
PAB Atrium
Sponsors
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
12:10pm PDT
Lunch
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
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
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
3:01pm PDT
B04: TreeGenes: enabling visualization and analysis in forest tree genomics
PAB Atrium
Emily Grau
B08: GRADitude: A computational tool for the analysis of Grad-seq data
PAB Atrium
Silvia Di Giorgio
B20: Reproducible data analysis with Snakemake
PAB Atrium
Johannes Köster
D04: A Galaxy Implementation of Next-Generation Clustered Heat Maps for Interactive Exploration of Large-Scale Molecular Profiling Data
PAB Atrium
Bob Brown
G08: Collecting data for association genetics: Tripal Plant PopGen Submit pipeline
PAB Atrium
Peter Richter
G10: Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
PAB Atrium
Sveinung Gundersen
G24: New tools to enhance the Galaxy-based metabolomics workbench
PAB Atrium
Arthur Eschenlauer
G28: EDAM: the ontology of bioinformatics operations, types of data, topics, and data formats (2018 update)
PAB Atrium
Hervé Ménager
4:01pm PDT
Closing Keynote: Confound it! Reproducible biology from "omics" data analysis
Vollum Lecture Hall
Lucia Peixoto
5:40pm PDT
Birds-of-a-Feather (BoFs), the Final Flight!
Performing Arts Building
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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