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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.

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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 104Bérénice Batut • Joachim Wolff Intro to Galaxy Administration 1 PAB 320The 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 320The 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 104Anton Nekrutenko

3:00pm PDT

Break Reed Commons Cafe

3:30pm PDT

Galaxy For Proteogenomics ! PAB 104Timothy J. Griffin • Pratik Jagtap • James Johnson • Praveen Kumar • Subina Mehta Intro to Galaxy Administration 3 PAB 320The Other Enis Afgan • Marius van den Beek • John Chilton • Nate Coraor • Carrie Ganote • Simon Gladman • Nuwan Goonesekera • Martin Čech

6:00pm PDT

Dinner on your own TBA

7:30pm PDT

Bioinformatics Training and Education with the Galaxy Training Network PAB 320Bérénice Batut
 
Tuesday, June 26
 

8:00am PDT

Training Day 2 - All topics Reed College Campus Conference desk open PAB Atrium

9:00am PDT

Community built analyses that run everywhere with bcbio PAB 332Brad Chapman • Radhika S. Khetani • Lorena Pantano Rubino Conda and Containers PAB 320John Chilton • Bjorn Gruning • Martin Čech Data Carpentry Genomics Workshop: Data Organization and Automation with Shell I PAB 131Tracy K. Teal Handling integrated biological data using Python (or R) and InterMine PAB 104Daniela Butano • Leyla Ruzicka • Yo Yehudi WDL: the Workflow Description Language Vollum LoungeGeraldine Van der Auwera • Jeff Gentry • Chris Llanwarne

11:30am PDT

Lunch Reed Commons Cafe

12:30pm PDT

Data Carpentry Genomics Workshop: Data Organization and Automation with Shell II PAB 131Tracy K. Teal Galaxy Interactive Environments PAB 332Bjorn Gruning Introduction to Common Workflow Language PAB 320Michael R. Crusoe • Kenzo-Hugo Hillion • Hervé Ménager Practical use of the Galaxy API command line tools Vollum LoungeDannon Baker • Marius van den Beek • Nicola Soranzo Setting up for success: Everything you need to know when planning for an RNA-seq analysis I PAB 104Radhika S. Khetani • Meeta Mistry • Mary Piper

3:00pm PDT

Break PAB Atrium

3:30pm PDT

Command line workflow management systems: Snakemake and Nextflow Vollum LoungeJohannes Köster • Paolo Di Tommaso Data Carpentry Genomics Workshop: Data Organization and Automation with Shell III PAB 131Tracy K. Teal Galaxy Architecture PAB 320John Chilton • Nate Coraor GATK4: What's new and how to run it PAB 332Geraldine Van der Auwera • Kate Noblett Setting up for success: Everything you need to know when planning for an RNA-seq analysis II PAB 104Radhika S. Khetani • Meeta Mistry • Mary Piper

6:00pm PDT

BoF: Genome Browsers and visualization in Galaxy Gigantic BrewingAnthony Bretaudeau • Nathan Dunn • Rob Buels

6:20pm PDT

Birds-of-a-Feather (BoFs), With Your Dinner! TBA BoF: Galaxy for proteomics interest group Reed Commons CafeTimothy J. Griffin • Pratik Jagtap

8:00pm PDT

Opening & Welcome Vollum Lecture HallDave Clements • Nomi Harris Joint BOSC & GCC: Opening Session Vollum Lecture HallNicole Vasilevsky • Heather Wiencko

8:10pm PDT

Opening Keynote: Tracy K. Teal--"Democratizing Data" Vollum Lecture HallTracy K. Teal
 
Wednesday, June 27
 

8:00am PDT

Conference desk open PAB Atrium

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

10:20am PDT

Break PAB Atrium Sponsors PAB Atrium

10:50am PDT

BOSC: Session 2: Translational & Medical Informatics Vollum Lecture HallHilmar Lapp GCC Session 2: Galaxy Infrastructure Eliot ChapelSimon Gladman

10:51am PDT

Cloud-based data ingest for the Human Cell Atlas Vollum Lecture HallDaniel Vaughan 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

11:20am PDT

Open Humans - connecting, sharing and analyzing personal data that enables community-driven research Vollum Lecture HallBastian Greshake Tzovaras

11:30am PDT

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

11:40am PDT

Enabling Machine Learning at Scale with “Tiled” Human Genomes Vollum Lecture HallSarah Wait Zaranek

11:45am PDT

JASS: a free and open source software for the joint analysis and interactive analysis of GWAS results Vollum Lecture HallHervé Ménager

11:50am PDT

Building a community menagerie of automated variant validations Vollum Lecture HallBrad Chapman Galaxy for AnswerALS on Microsoft Azure and Kubernetes Eliot ChapelRC Carter Lightning Talks ⚡ Eliot Chapel

11:55am PDT

Variant Transforms: Loading VCF files into BigQuery for large scale data analysis Vollum Lecture HallAsha Rostamianfar

11:56am PDT

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

12:00pm PDT

Q&A for lightning talks in this session ⚡ Vollum Lecture Hall

12:02pm PDT

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

12:10pm PDT

Lunch, sponsored by Lenovo + Intel PAB Atrium Sponsors PAB Atrium

12:30pm PDT

Birds-of-a-Feather (BoFs), with Lunch! Performing Arts Building BoF: Getting contributors to your open project PAB 130Yo Yehudi BoF: JBrowse PAB 104Rob Buels BoF: Let's talk about WDL PAB 332Geraldine Van der Auwera • Chris Llanwarne • Jeff Gentry BoF: Stable and persistent URIs in biological data integration systems PAB 131Daniela Butano

1:40pm PDT

BOSC Session 3: All About Data Vollum Lecture HallBastian Greshake Tzovaras GCC Session 3: Challenges & Opportunities Eliot ChapelJeremy Goecks

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 Galaksio, a more user friendly interface for Galaxy using workflows Eliot ChapelTomas Klingström

2:00pm PDT

Reproducible big data science: A case study in continuous FAIRness Vollum Lecture HallRavi K. Madduri Large scale analyses with improved dataset collections Eliot ChapelMarius van den Beek

2:20pm PDT

InterMine 2.0: More than fifteen years of open biological data integration Vollum Lecture HallYo Yehudi A fruitful year for the Galaxy Training materials Eliot ChapelBérénice Batut

2:40pm PDT

GRADitude: A computational tool for the analysis of Grad-seq data Vollum Lecture HallSilvia Di Giorgio The usegalaxy.* servers: democratizing computational resources for life sciences at a new level Eliot ChapelSimon Gladman

2:45pm PDT

NIH Data Commons Pilot Phase leverages the cloud to access, analyze, and share FAIR biomedical data Vollum Lecture HallDavid Siedzik

2:50pm PDT

Reproducible data analysis with Snakemake Vollum Lecture HallJohannes Köster

2:55pm PDT

Q&A for lightning talks in this session⚡ Vollum Lecture Hall

3:00pm PDT

Posters & Demos: Odd Numbered PAB Atrium Sponsors PAB Atrium

3:01pm PDT

B01: Association Mapping and Landscape Genomics of Georeferenced Forest Trees via CartograTree and TreeGenes PAB AtriumTaylor Falk B03: CRI iAtlas: an interactive portal for immuno-oncology research PAB AtriumJames Eddy B05: One Week to 1,000 Whole Genomes with Open Source: Arvados, CWL, and bcbio PAB AtriumPeter Amstutz B07: Classification of short read alignments from xenograft samples PAB AtriumLawrence Heisler B09: Enabling Machine Learning at Scale with “Tiled” Human Genomes PAB AtriumSarah Wait Zaranek B11: flowDashboard: An Interactive Dashboard for Comparative Flow Analysis PAB AtriumTed Laderas B13: READemption - from reads to knowledge PAB AtriumTill Sauerwein B15: RyuGoo-Saba: a CWL-based execution engine utilizing cloud resources for big data analysis in life science PAB AtriumHirotaka Suetake B17: High-performance computing service in the Health Science and Human Services Library at University of Maryland Baltimore PAB AtriumJean-Paul Courneya B19: Reproducible big data science: A case study in continuous FAIRness PAB AtriumRavi K. Madduri B21: FAIRsharing: Working with the community to map the landscape of standards, databases and data policies PAB AtriumMassimiliano Izzo B23: Oxidizing Python: writing extensions in Rust PAB AtriumLuiz Carlos Irber Junior B25: The GTrack ecosystem: expressive file formats for genomic track data and metadata - through compilation, exchange, storage and analysis PAB AtriumSveinung Gundersen B27: JASS: a free and open source software for the joint analysis and interactive analysis of GWAS results PAB AtriumHervé Ménager B29: Extended Extraction Transform Load: A novel framework for batch jobs on cloud computing resources PAB AtriumHiromu Ochiai B31: The Arachne Graph Database Server PAB AtriumKyle Ellrott B33: BioThings Hub: An API Gateway for Biomedical Knowledge PAB AtriumSébastien Lelong B35: Modernising somatic mutation calling pipelines with Open Source tools and Containers. PAB AtriumMr Keiran M Raine B37: Accumulating computational resource usage of data analysis workflow to select suitable cloud instance PAB AtriumTazro Ohta 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 B43: CWLProv - Interoperable retrospective provenance capture and its challenges PAB AtriumFarah Zaib Khan B45: CWL Community Update PAB AtriumMichael R. Crusoe D01: From laptop to super-computer: standardizing installation and management of Galaxy PAB AtriumNuwan Goonesekera D03: Aurora Galaxy Tools: Using R Markdown as a framework to build interactive Galaxy tool output reports PAB AtriumMing Chen D05: Open Humans - connecting, sharing and analyzing personal data that enables community-driven research PAB AtriumBastian Greshake Tzovaras D07: Building a community menagerie of automated variant validations PAB AtriumBrad Chapman 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 G03: Predicting Galaxy Tool Runtimes with Random Forests PAB AtriumAnastasia Tyryshkina 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 G09: EWAS-Galaxy: a tool suite for population epigenetics integrated into the Galaxy PAB AtriumKrzysztof Poterlowicz G11: Candidate Gene Methylation quantification (CandiMeth) Within the Galaxy Bioinformatics Interface PAB AtriumSara-Jayne Thursby G13: Bacterial genomics in Galaxy PAB AtriumDelphine Lariviere G15: Galaxy in a proteomics core facility PAB AtriumJeremy Volkening G17: Evaluation of moFF and FlashLFQ for label-free peptide quantification in proteomic workflows within the Galaxy-P framework PAB AtriumSubina Mehta G19: Implementation of machine learning algorithms for medulloblastoma classification in a local galaxy server PAB AtriumLuciane Sussuchi Da Silva G21: The Mammalian Ortholog and Annotation Database: enhanced ortholog information with an accurate identifier mapping between NCBI and Ensembl accessible from a Galaxy-server PAB AtriumJochen Bick G23: SECIMTools: A suite of Metabolomics Data Analysis Tools PAB AtriumOleksandr Moskalenko G25: VKMZ: Visualizing Metabolomics on a van Krevelen Diagram through Galaxy PAB AtriumMark Esler G27: BioXSD | BioJSON | BioYAML – towards unified formats for sequences, alignments, features, and annotations PAB AtriumMatúš Kalas G29: ELIXIR contributions to the FAIRness of Bioinformatics resources, with bio.tools, Galaxy and CWL PAB AtriumKenzo-Hugo Hillion G31: A fruitful year for the Galaxy Training materials PAB AtriumBérénice Batut G33: Refinery: a data management, analysis, and visualization platform utilizing the Galaxy workbench PAB AtriumScott Ouellette

4:00pm PDT

Session 4 - Joint BOSC & GCC Vollum Lecture HallBrad Chapman

4:01pm PDT

Improving the Bioinformatics Curriculum Vollum Lecture HallJason Williams

4:20pm PDT

Panel: Training and Documentation in Bioinformatics Vollum Lecture HallBrad Chapman • Bérénice Batut • Fernando Pérez • Tracy K. Teal • Jason Williams

5:40pm PDT

Birds-of-a-Feather (BoFs), With Your Dinner! TBA BoF: Educating Funders/PIs on Open Science TBATracy K. Teal • Jason Williams BoF: Open Bioinformatics Foundation Community (OBF) Reed Commons CafeYo Yehudi BoF: Sharing and Leveraging Galaxy Tool Execution Data TBAMartin Čech • Anastasia Tyryshkina BoF: Using Galaxy in bioinformatics support infrastructures Reed Commons CafeTomas Klingström Dinner on your own (or join a BoF) TBA

6:00pm PDT

BOSC & GCC Social Mixer | by Lifebit Woodstock NeighborhoodLifebit

8:00pm PDT

Birds-of-a-Feather (BoFs), wherever you want! TBA BoF: Nextflow Gathering Sitka Dorm, Ground FloorEvan Floden BoF: Snakemake get together Woodstock NeighborhoodJohannes Köster
 
Thursday, June 28
 

8:00am PDT

Conference desk open PAB Atrium

9:00am PDT

BOSC Session 5: Developer Tools and Libraries Vollum Lecture HallPeter Cock GCC Session 5: Galaxy in situ Eliot ChapelLaure Quintric

9:01am PDT

iMADS: A sustainable software collaboration for predicting transcription factor binding specificity Vollum Lecture HallDan Leehr Galaxy Enables Integrated Analysis of Phenotypic, Genotypic, and Environmental Data for Geo-referenced Trees in CartograTree Eliot ChapelNic Herndon

9:20am PDT

The Funnel Task Execution Server Vollum Lecture HallAlexander Buchanan 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 Canada's Integrated Rapid Infectious Disease Analysis Platform (IRIDA) Eliot ChapelThomas Matthews

9:45am PDT

Extended Extraction Transform Load: A novel framework for batch jobs on cloud computing resources Vollum Lecture HallHiromu Ochiai

9:50am PDT

Plugging Docker-based visualizations into Django with django_docker_engine Vollum Lecture HallChuck McCallum

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 Galaxy in a proteomics core facility Eliot ChapelJeremy Volkening

10:05am PDT

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

10:10am PDT

Q&A for lightning talks in this session⚡ Vollum Lecture Hall

10:20am PDT

Break PAB Atrium Sponsors PAB Atrium

10:50am PDT

BOSC Session 6: Workflows Vollum Lecture HallKarsten Hokamp GCC Session 6: Galaxy in situ Eliot ChapelMaria Doyle

10:51am PDT

CWLProv - Interoperable retrospective provenance capture and its challenges Vollum Lecture HallFarah Zaib Khan Quantifying Functional Microbiomes: An integrated, quantitative metaproteomics approach reveals connections between taxa, function and protein expression in complex microbiomes Eliot ChapelCaleb Easterly • Pratik Jagtap

11:10am PDT

Running portable workflow and container specifications at production scale in the cloud: strategy & best practices Vollum Lecture HallGeet Duggal GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline Eliot ChapelNicola Soranzo

11:30am PDT

The GA4GH/DREAM Workflow Execution Challenge Vollum Lecture HallJames Eddy 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

11:40am PDT

CWL-Airflow pipeline manager as a backend for BioWardrobe data analysis platform Vollum Lecture HallAndrey Kartashov

11:45am PDT

Scaling bioinformatics analysis using Nextflow and AWS Vollum Lecture HallFrancesco Strozzi

11:50am PDT

One Week to 1,000 Whole Genomes with Open Source: Arvados, CWL, and bcbio Vollum Lecture HallPeter Amstutz Using Galaxy to analyze TCGA data: the experience of a Brazilian center Eliot ChapelThais Talarico Lightning Talks ⚡ Eliot Chapel

11:55am PDT

Q&A for lightning talks in this session⚡ Vollum Lecture Hall

11:56am PDT

ImmPort Galaxy, facilitating analysis and meta-analysis of flow cytometry data Eliot ChapelCristel Thomas

12:02pm PDT

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

12:10pm PDT

Lunch PAB Atrium Sponsors PAB Atrium

12:30pm PDT

Birds-of-a-Feather (BoFs), with Lunch! Performing Arts Building BoF: Common Workflow Language community chat PAB 332John Chilton • Michael R. Crusoe • Hervé Ménager • Jeff Gentry • Peter Amstutz BoF: Galaxy Training Material: Let's improve the contributions! PAB 130Bérénice Batut BoF: Preparing for the next steps in AI PAB 131Kathy Wilson BoF: Standardizing Galaxy deployments PAB 104The Other Enis Afgan • Nuwan Goonesekera

1:40pm PDT

BOSC Session 7: Project Updates and Late-Breaking Research Vollum Lecture HallChris Fields GCC Session 7: Community Update(s) Eliot ChapelFrederik Coppens

1:41pm PDT

OBF update Vollum Lecture HallHilmar Lapp Galaxy Community Update Eliot ChapelDaniel Blankenberg • Jeremy Goecks • Anton Nekrutenko • James Taylor

1:50pm PDT

GSOC update Vollum Lecture HallMichael R. Crusoe

2:00pm PDT

Biopython Project Update 2018 Vollum Lecture HallPeter Cock

2:07pm PDT

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

2:10pm PDT

Integrative proteo-transcriptomics workflows within the Galaxy framework to explore the correlation between the expression of RNA and proteins Eliot ChapelPraveen 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 ChapelBob Brown

2:22pm PDT

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

2:27pm PDT

Late-Breaking Lightning Talks ⚡ Vollum Lecture Hall

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

2:40pm PDT

OrthoQuery: A Tripal Module to Assess Gene Family Evolution in Sequenced Gymnosperms Eliot ChapelSumaira Zaman

2:46pm PDT

Galaxy-E, a first step towards collaborative data analysis by citizens Eliot ChapelYvan Le Bras

2:52pm PDT

Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things) Eliot ChapelHans-Rudolf Hotz Q&A for lightning talks in this session⚡ Vollum Lecture Hall

3:00pm PDT

Posters & Demos: Even Numbered PAB Atrium Sponsors PAB Atrium

3:01pm PDT

B02: Tripal Sequence Similarity Search provides efficient protein sequence similarity search for Tripal sites PAB AtriumSean Buehler B04: TreeGenes: enabling visualization and analysis in forest tree genomics PAB AtriumEmily Grau B06: Bioinformatics in the age of AI and personalized medicine: an open source example PAB AtriumMichael Duncan 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 B12: Plugging Docker-based visualizations into Django with django_docker_engine PAB AtriumChuck McCallum B14: Cirrus-NGS: Cloud-optimized compute infrastructure for next generation sequencing analysis PAB AtriumGuorong Xu B16: Infrastructure for coordinating multi-site clinical research projects via REDCap and Synapse PAB AtriumXindi Guo B18: NIH Data Commons Pilot Phase leverages the cloud to access, analyze, and share FAIR biomedical data PAB AtriumDavid Siedzik B20: Reproducible data analysis with Snakemake PAB AtriumJohannes Köster B22: Code is Science: a manifesto for open source code in science PAB AtriumYo Yehudi B24: The Hypergraph Algorithms Package PAB AtriumAnna Ritz B26: Fast, sustainable, and secure bioinformatics with Rust-Bio and Rust-Htslib PAB AtriumJohannes Köster B28: Community Annotation with Apollo: Engaging the Collective in a Genome Annotation Workflow PAB AtriumNathan Dunn B30: The Funnel Task Execution Server PAB AtriumAlexander Buchanan B32: iMADS: A sustainable software collaboration for predicting transcription factor binding specificity PAB AtriumDan Leehr B34: Implementation of Nextflow for the automated processing of NovaSeq data sets PAB AtriumNetsanet (Net) Gebremedhin B36: Understanding reproducibility of bioinformatics workflows PAB AtriumSehrish Kanwal B38: You can't spell Cromwell without CWL PAB AtriumJeff Gentry B40: Running portable workflow and container specifications at production scale in the cloud: strategy & best practices PAB AtriumGeet Duggal B42: The GA4GH/DREAM Workflow Execution Challenge PAB AtriumJames Eddy B44: A composable container system for genomic analysis pipelines PAB AtriumYu Xang B46: Bespin: An open source system to run reproducible computational workflows on cloud infrastructure PAB AtriumJohn Bradley 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 G04: Galaxy for AnswerALS on Microsoft Azure and Kubernetes PAB AtriumRC Carter G06: Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things) PAB AtriumHans-Rudolf Hotz G08: Collecting data for association genetics: Tripal Plant PopGen Submit pipeline PAB AtriumPeter Richter G10: Coloc-stats: a unified web interface to perform colocalization analysis of genomic features PAB AtriumSveinung Gundersen G12: Canada's Integrated Rapid Infectious Disease Analysis Platform (IRIDA) PAB AtriumThomas Matthews G14: HIV transmission clustering in Galaxy PAB AtriumDave Bouvier G16: Integrative proteo-transcriptomics workflows within the Galaxy framework to explore the correlation between the expression of RNA and proteins PAB AtriumPraveen Kumar G18: CRAVAT (Cancer-Related Analysis of Variants Toolkit) integration into Galaxy-P and extension towards proteogenomic studies PAB AtriumRay Sajulga G20: Using Galaxy to analyze TCGA data: the experience of a Brazilian center PAB AtriumThais Hosokawa G22: ARIAWeb: a structural bioinformatics web interface linked to galaxy PAB AtriumFabien Mareuil G24: New tools to enhance the Galaxy-based metabolomics workbench PAB AtriumArthur Eschenlauer G26: ISAcreate: a Galaxy tool for Prospective Data Management with ISA format support - Application to Metabolomics Datasets PAB AtriumPhilippe Rocca-Serra G28: EDAM: the ontology of bioinformatics operations, types of data, topics, and data formats (2018 update) PAB AtriumHervé Ménager G30: Compliance? We don’t need no stinking compliance! PAB AtriumJeffrey Miller 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 BoF: Bioconda gathering PAB 104Johannes Köster BoF: GA4GH/DREAM group writing session PAB 332Brian O'Connor • James Eddy BoF: Galaxy Dataset Collection: Defining Priorities Gigantic BrewingAnton Nekrutenko BoF: GalaxyAdmins PAB 131Nate Coraor

7:00pm PDT

Conference Dinner Sponsored by Google Cloud TBA
 
Friday, June 29
 

8:00am PDT

Conference desk open PAB Atrium

9:00am PDT

GCC OBF CollaborationFest: Core Performing Arts BuildingBjorn Gruning • Dannon Baker • Jennifer Hillman-Jackson • Frederik Coppens • Brad Chapman
 
Saturday, June 30
 

8:45am PDT

Conference desk open PAB Atrium

9:00am PDT

GCC OBF CollaborationFest: Core Performing Arts Building
 
Sunday, July 1
 

8:45am PDT

Conference desk open PAB Atrium

9:00am PDT

GCC OBF CollaborationFest: Encore Performing Arts Building
 
Monday, July 2
 

8:45am PDT

Conference desk open PAB Atrium

9:00am PDT

GCC OBF CollaborationFest: Encore Performing Arts Building
 
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