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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
Sponsorships
,
BoFs
,
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,
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Lorena Pantano Rubino
Harvard Chan School
Research Scientist
Boston
lpantano.github.io
I work with small RNAs, mainly detected through sequencing technology. I like visualization and multi-omic integration methods. :)
Tuesday
, June 26
9:00am PDT
Community built analyses that run everywhere with bcbio
PAB 332
Brad Chapman • Radhika S. Khetani • Lorena Pantano Rubino
12:30pm PDT
Introduction to Common Workflow Language
PAB 320
Michael R. Crusoe • Kenzo-Hugo Hillion • Hervé Ménager
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
9:01am 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
11:20am PDT
Open Humans - connecting, sharing and analyzing personal data that enables community-driven research
Vollum Lecture Hall
Bastian Greshake Tzovaras
11:50am PDT
Lightning Talks ⚡
Eliot Chapel
12:30pm PDT
BoF: JBrowse
PAB 104
Rob Buels
1:40pm PDT
BOSC Session 3: All About Data
Vollum Lecture Hall
Bastian Greshake Tzovaras
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
3:00pm PDT
Posters & Demos: Odd Numbered
PAB Atrium
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
BoF: Open Bioinformatics Foundation Community (OBF)
Reed Commons Cafe
Yo Yehudi
6:00pm PDT
BOSC & GCC Social Mixer | by Lifebit
Woodstock Neighborhood
Lifebit
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
9:20am PDT
The Funnel Task Execution Server
Vollum Lecture Hall
Alexander Buchanan
9:40am PDT
Distributed execution of bioinformatics tools on Apache Spark with ADAM and Cannoli
Vollum Lecture Hall
Michael Heuer
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
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
10:50am PDT
BOSC Session 6: Workflows
Vollum Lecture Hall
Karsten Hokamp
10:51am PDT
CWLProv - Interoperable retrospective provenance capture and its challenges
Vollum Lecture Hall
Farah Zaib Khan
11:10am PDT
Running portable workflow and container specifications at production scale in the cloud: strategy & best practices
Vollum Lecture Hall
Geet Duggal
11:30am PDT
The GA4GH/DREAM Workflow Execution Challenge
Vollum Lecture Hall
James Eddy
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
One Week to 1,000 Whole Genomes with Open Source: Arvados, CWL, and bcbio
Vollum Lecture Hall
Peter Amstutz
Lightning Talks ⚡
Eliot Chapel
11:55am PDT
Q&A for lightning talks in this session⚡
Vollum Lecture Hall
12:30pm PDT
BoF: Preparing for the next steps in AI
PAB 131
Kathy Wilson
1:40pm PDT
BOSC Session 7: Project Updates and Late-Breaking Research
Vollum Lecture Hall
Chris Fields
1:41pm PDT
OBF update
Vollum Lecture Hall
Hilmar Lapp
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
2:27pm PDT
Late-Breaking Lightning Talks ⚡
Vollum Lecture Hall
2:52pm PDT
Q&A for lightning talks in this session⚡
Vollum Lecture Hall
3:00pm PDT
Posters & Demos: Even Numbered
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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Southeast Reed College Place, Portland, Oregon, United States
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Gigantic Brewing
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Reed College Campus
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Sitka Dorm, Ground Floor
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Woodstock Neighborhood
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