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GCC BOSC 2018 has ended
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.

avatar for Brad Langhorst

Brad Langhorst

NEB
Developmenet Group Leader
Massachusetts, USA
Tuesday, June 26
 

8:10pm PDT

Opening Keynote: Tracy K. Teal--"Democratizing Data" Vollum Lecture HallTracy 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 HallFernando Pérez

10:00am PDT

The journey of a team of engineers in learning packaging technology Vollum Lecture HallPatrick Durand • Valentin Marcon • Laure Quintric

10:50am PDT

GCC Session 2: Galaxy Infrastructure Eliot ChapelSimon Gladman

10:51am PDT

Storage Media Federation for Galaxy Eliot ChapelVahid 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 HallBrian O'Connor

11:10am PDT

From laptop to super-computer: standardizing installation and management of Galaxy Eliot ChapelNuwan Goonesekera

11:30am PDT

Testing Wide-Area Lustre File Systems for Sharing load in Galaxy Eliot ChapelCarrie Ganote

11:50am PDT

Galaxy for AnswerALS on Microsoft Azure and Kubernetes Eliot ChapelRC Carter

11:56am PDT

Adding Python 3 support to Galaxy: a status report Eliot ChapelNicola Soranzo

12:02pm PDT

Aurora Galaxy Tools: Using R Markdown as a framework to build interactive Galaxy tool output reports Eliot ChapelMing Chen

12:30pm PDT

BoF: JBrowse PAB 104Rob Buels

1:41pm PDT

miRTop: An open source community project for the development of a unified format file for miRNA data Vollum Lecture HallLorena Pantano Rubino

2:00pm PDT

Large scale analyses with improved dataset collections Eliot ChapelMarius van den Beek

2:40pm PDT

GRADitude: A computational tool for the analysis of Grad-seq data Vollum Lecture HallSilvia Di Giorgio

2:50pm PDT

Reproducible data analysis with Snakemake Vollum Lecture HallJohannes Köster

3:01pm PDT

B11: flowDashboard: An Interactive Dashboard for Comparative Flow Analysis PAB AtriumTed Laderas B13: READemption - from reads to knowledge PAB AtriumTill Sauerwein B23: Oxidizing Python: writing extensions in Rust PAB AtriumLuiz Carlos Irber Junior B39: CWL-Airflow pipeline manager as a backend for BioWardrobe data analysis platform PAB AtriumAndrey Kartashov B41: Scaling bioinformatics analysis using Nextflow and AWS PAB AtriumFrancesco Strozzi D03: Aurora Galaxy Tools: Using R Markdown as a framework to build interactive Galaxy tool output reports PAB AtriumMing Chen D09: taxa: taxonomic data standards and methods for R and Python PAB AtriumScott Chamberlain G01: Galaxy-E, a first stage towards collaborative data analysis by citizens PAB AtriumYvan Le Bras G05: Galaksio, a more user friendly interface for Galaxy using workflows PAB AtriumTomas Klingström G07: Identifying suitable spliced mapper and genomic assembly for variant detection PAB AtriumAkila Parvathy Dharshini G11: Candidate Gene Methylation quantification (CandiMeth) Within the Galaxy Bioinformatics Interface PAB AtriumSara-Jayne Thursby G15: Galaxy in a proteomics core facility PAB AtriumJeremy Volkening G33: Refinery: a data management, analysis, and visualization platform utilizing the Galaxy workbench PAB AtriumScott Ouellette

4:01pm PDT

Improving the Bioinformatics Curriculum Vollum Lecture HallJason Williams

5:40pm PDT

Birds-of-a-Feather (BoFs), With Your Dinner! TBA

6:00pm PDT

BOSC & GCC Social Mixer | by Lifebit Woodstock NeighborhoodLifebit

8:00pm PDT

BoF: Nextflow Gathering Sitka Dorm, Ground FloorEvan Floden
 
Thursday, June 28
 

9:20am PDT

G-OnRamp: Create UCSC Assembly Hubs and JBrowse/Apollo Archives for Collaborative Eukaryotic Genome Annotations Eliot ChapelLuke Sargent

9:40am PDT

Distributed execution of bioinformatics tools on Apache Spark with ADAM and Cannoli Vollum Lecture HallMichael Heuer

9:55am PDT

The Arachne Graph Database Server Vollum Lecture HallKyle Ellrott

10:00am PDT

Owlery: An easily deployable web service for making reasoning queries over OWL ontologies web-native Vollum Lecture HallHilmar Lapp

10:05am PDT

taxa: taxonomic data standards and methods for R and Python Vollum Lecture HallScott Chamberlain

10:51am PDT

Quantifying Functional Microbiomes: An integrated, quantitative metaproteomics approach reveals connections between taxa, function and protein expression in complex microbiomes Eliot ChapelCaleb Easterly • Pratik Jagtap

11:30am PDT

Galaxy HiCExplorer: HiCExplorer, deepTools3 and pyGenomeTracks Eliot ChapelJoachim Wolff

11:35am PDT

Bespin: An open source system to run reproducible computational workflows on cloud infrastructure Vollum Lecture HallJohn Bradley

11:50am PDT

One Week to 1,000 Whole Genomes with Open Source: Arvados, CWL, and bcbio Vollum Lecture HallPeter Amstutz

12:02pm PDT

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features Eliot ChapelSveinung Gundersen

2:07pm PDT

Community Annotation with Apollo: Engaging the Collective in a Genome Annotation Workflow Vollum Lecture HallNathan Dunn

2:16pm PDT

A Galaxy Implementation of Next-Generation Clustered Heat Maps for Interactive Exploration of Large-Scale Molecular Profiling Data Eliot ChapelBob Brown

2:22pm PDT

Candidate Gene Methylation quantification (CandiMeth) Within the Galaxy Bioinformatics Interface Eliot ChapelSara-Jayne Thursby

2:28pm PDT

Making Immune Repertoire Sequence Analysis Accessible to Anyone via Galaxy Eliot ChapelBrad Langhorst

2:34pm PDT

Galaxy Genome Annotation project: integrating Galaxy and GMOD for genome annotation Eliot ChapelAnthony Bretaudeau

2:46pm PDT

Galaxy-E, a first step towards collaborative data analysis by citizens Eliot ChapelYvan 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 ChapelHans-Rudolf Hotz

3:01pm PDT

B08: GRADitude: A computational tool for the analysis of Grad-seq data PAB AtriumSilvia Di Giorgio B10: Debarcer2, De-Barcoding and Error Correction of sequencing data containing molecular barcodes designed to handle different library designs. PAB AtriumLawrence Heisler B20: Reproducible data analysis with Snakemake PAB AtriumJohannes Köster B22: Code is Science: a manifesto for open source code in science PAB AtriumYo Yehudi B26: Fast, sustainable, and secure bioinformatics with Rust-Bio and Rust-Htslib PAB AtriumJohannes Köster B34: Implementation of Nextflow for the automated processing of NovaSeq data sets PAB AtriumNetsanet (Net) Gebremedhin B38: You can't spell Cromwell without CWL PAB AtriumJeff Gentry D02: Adding R shiny apps as Galaxy interactive environment. A Galaxy-E demo PAB AtriumValintin Chambon D04: A Galaxy Implementation of Next-Generation Clustered Heat Maps for Interactive Exploration of Large-Scale Molecular Profiling Data PAB AtriumBob Brown D06: Distributed execution of bioinformatics tools on Apache Spark with ADAM and Cannoli PAB AtriumMichael Heuer D08: Owlery: An easily deployable web service for making reasoning queries over OWL ontologies web-native PAB AtriumHilmar Lapp G02: Testing Wide-Area Lustre File Systems for Sharing load in Galaxy PAB AtriumCarrie Ganote G06: Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things) PAB AtriumHans-Rudolf Hotz G32: Results of an Extended Developer Support consultation with the CloudLaunch project PAB AtriumMarcus Christie

4:00pm PDT

Session 8 - Joint BOSC & GCC Closing Vollum Lecture HallPratik Jagtap

4:01pm PDT

Closing Keynote: Confound it! Reproducible biology from "omics" data analysis Vollum Lecture HallLucia Peixoto

5:00pm PDT

Conference Closing Vollum Lecture HallBjorn 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 BuildingBjorn Gruning • Dannon Baker • Jennifer Hillman-Jackson • Frederik Coppens • Brad Chapman
 
Saturday, June 30
 

9:00am PDT

GCC OBF CollaborationFest: Core Performing Arts Building