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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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Thursday, June 28
 

8:00am

Conference desk open PAB Atrium

9:00am

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

9:01am

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

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

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

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

9:50am

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

9:55am

The Arachne Graph Database Server Vollum Lecture HallKyle Ellrott

10:00am

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

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

10:10am

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

10:20am

Break PAB Atrium Sponsors PAB Atrium

10:50am

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

10:51am

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

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

The GA4GH/DREAM Workflow Execution Challenge Vollum Lecture HallJames Eddy Galaxy HiCExplorer: HiCExplorer, deepTools3 and pyGenomeTracks Eliot ChapelJoachim Wolff

11:35am

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

11:40am

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

11:45am

Scaling bioinformatics analysis using Nextflow and AWS Vollum Lecture HallFrancesco Strozzi

11:50am

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

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

11:56am

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

12:02pm

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

12:10pm

Lunch PAB Atrium Sponsors PAB Atrium

12:30pm

Birds-of-a-Feather (BoFs), with Lunch! Performing Arts Building BoF: Common Workflow Language community chat Performing Arts BuildingJohn Chilton • Michael R. Crusoe • Hervé Ménager • Jeff Gentry • Peter Amstutz BoF: Galaxy Training Material: Let's improve the contributions! Performing Arts BuildingBérénice Batut BoF: Preparing for the next steps in AI Performing Arts BuildingKathy Wilson BoF: Standardizing Galaxy deployments Performing Arts BuildingEnis Afgan • Nuwan Goonasekera

1:40pm

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

1:41pm

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

1:50pm

GSOC update Vollum Lecture HallMichael R. Crusoe

2:00pm

Biopython Project Update 2018 Vollum Lecture HallPeter Cock

2:07pm

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

2:10pm

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

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

2:22pm

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

2:27pm

Late-Breaking Lightning Talks ⚡ Vollum Lecture Hall

2:28pm

Making Immune Repertoire Sequence Analysis Accessible to Anyone via Galaxy Eliot ChapelBradley W. Langhorst

2:34pm

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

2:40pm

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

2:46pm

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

2:52pm

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

Posters & Demos: Even Numbered PAB Atrium Sponsors PAB Atrium

3:01pm

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: Open Humans - connecting, sharing and analyzing personal data that enables community-driven research PAB AtriumBastian Greshake Tzovaras 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

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

4:01pm

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

5:00pm

Conference Closing Vollum Lecture HallBjörn Grüning • Nomi Harris • Nicole Vasilevsky • Heather Wiencko

5:40pm

Birds-of-a-Feather (BoFs), the Final Flight! Performing Arts Building BoF: GA4GH/DREAM group writing session Performing Arts BuildingBrian O'Connor • James Eddy

7:00pm

Conference Dinner Sponsored by Google Cloud TBA