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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
childcare
information
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,
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,
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Thursday
, June 28
Eliot Chapel
9:00am •
GCC Session 5: Galaxy in situ
9:01am •
Galaxy Enables Integrated Analysis of Phenotypic, Genotypic, and Environmental Data for Geo-referenced Trees in CartograTree
9:20am •
G-OnRamp: Create UCSC Assembly Hubs and JBrowse/Apollo Archives for Collaborative Eukaryotic Genome Annotations
9:40am •
Canada's Integrated Rapid Infectious Disease Analysis Platform (IRIDA)
10:00am •
Galaxy in a proteomics core facility
10:50am •
GCC Session 6: Galaxy in situ
10:51am •
Quantifying Functional Microbiomes: An integrated, quantitative metaproteomics approach reveals connections between taxa, function and protein expression in complex microbiomes
11:10am •
GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline
11:30am •
Galaxy HiCExplorer: HiCExplorer, deepTools3 and pyGenomeTracks
11:50am •
Using Galaxy to analyze TCGA data: the experience of a Brazilian center
11:50am •
Lightning Talks ⚡
11:56am •
ImmPort Galaxy, facilitating analysis and meta-analysis of flow cytometry data
12:02pm •
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
1:40pm •
GCC Session 7: Community Update(s)
1:41pm •
Galaxy Community Update
2:10pm •
Integrative proteo-transcriptomics workflows within the Galaxy framework to explore the correlation between the expression of RNA and proteins
2:10pm •
Lightning Talks ⚡
2:16pm •
A Galaxy Implementation of Next-Generation Clustered Heat Maps for Interactive Exploration of Large-Scale Molecular Profiling Data
2:22pm •
Candidate Gene Methylation quantification (CandiMeth) Within the Galaxy Bioinformatics Interface
2:28pm •
Making Immune Repertoire Sequence Analysis Accessible to Anyone via Galaxy
2:34pm •
Galaxy Genome Annotation project: integrating Galaxy and GMOD for genome annotation
2:40pm •
OrthoQuery: A Tripal Module to Assess Gene Family Evolution in Sequenced Gymnosperms
2:46pm •
Galaxy-E, a first step towards collaborative data analysis by citizens
2:52pm •
Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things)
Gigantic Brewing
5:40pm •
BoF: Galaxy Dataset Collection: Defining Priorities
PAB 104
12:30pm •
BoF: Standardizing Galaxy deployments
5:40pm •
BoF: Bioconda gathering
PAB 130
12:30pm •
BoF: Galaxy Training Material: Let's improve the contributions!
PAB 131
12:30pm •
BoF: Preparing for the next steps in AI
5:40pm •
BoF: GalaxyAdmins
PAB 332
12:30pm •
BoF: Common Workflow Language community chat
5:40pm •
BoF: GA4GH/DREAM group writing session
PAB Atrium
8:00am •
Conference desk open
10:20am •
Break
10:20am •
Sponsors
12:10pm •
Sponsors
12:10pm •
Lunch
3:00pm •
Sponsors
3:00pm •
Posters & Demos: Even Numbered
3:01pm •
B32: iMADS: A sustainable software collaboration for predicting transcription factor binding specificity
3:01pm •
B42: The GA4GH/DREAM Workflow Execution Challenge
3:01pm •
G26: ISAcreate: a Galaxy tool for Prospective Data Management with ISA format support - Application to Metabolomics Datasets
3:01pm •
B02: Tripal Sequence Similarity Search provides efficient protein sequence similarity search for Tripal sites
3:01pm •
G02: Testing Wide-Area Lustre File Systems for Sharing load in Galaxy
3:01pm •
B44: A composable container system for genomic analysis pipelines
3:01pm •
B40: Running portable workflow and container specifications at production scale in the cloud: strategy & best practices
3:01pm •
D08: Owlery: An easily deployable web service for making reasoning queries over OWL ontologies web-native
3:01pm •
B06: Bioinformatics in the age of AI and personalized medicine: an open source example
3:01pm •
B04: TreeGenes: enabling visualization and analysis in forest tree genomics
3:01pm •
G28: EDAM: the ontology of bioinformatics operations, types of data, topics, and data formats (2018 update)
3:01pm •
G08: Collecting data for association genetics: Tripal Plant PopGen Submit pipeline
3:01pm •
G14: HIV transmission clustering in Galaxy
3:01pm •
G20: Using Galaxy to analyze TCGA data: the experience of a Brazilian center
3:01pm •
G10: Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
3:01pm •
B38: You can't spell Cromwell without CWL
3:01pm •
G06: Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things)
3:01pm •
B36: Understanding reproducibility of bioinformatics workflows
3:01pm •
G30: Compliance? We don’t need no stinking compliance!
3:01pm •
B22: Code is Science: a manifesto for open source code in science
3:01pm •
D04: A Galaxy Implementation of Next-Generation Clustered Heat Maps for Interactive Exploration of Large-Scale Molecular Profiling Data
3:01pm •
G32: Results of an Extended Developer Support consultation with the CloudLaunch project
3:01pm •
B14: Cirrus-NGS: Cloud-optimized compute infrastructure for next generation sequencing analysis
3:01pm •
B46: Bespin: An open source system to run reproducible computational workflows on cloud infrastructure
3:01pm •
B12: Plugging Docker-based visualizations into Django with django_docker_engine
3:01pm •
B30: The Funnel Task Execution Server
3:01pm •
B34: Implementation of Nextflow for the automated processing of NovaSeq data sets
3:01pm •
G22: ARIAWeb: a structural bioinformatics web interface linked to galaxy
3:01pm •
G24: New tools to enhance the Galaxy-based metabolomics workbench
3:01pm •
B16: Infrastructure for coordinating multi-site clinical research projects via REDCap and Synapse
3:01pm •
B26: Fast, sustainable, and secure bioinformatics with Rust-Bio and Rust-Htslib
3:01pm •
B10: Debarcer2, De-Barcoding and Error Correction of sequencing data containing molecular barcodes designed to handle different library designs.
3:01pm •
D06: Distributed execution of bioinformatics tools on Apache Spark with ADAM and Cannoli
3:01pm •
B08: GRADitude: A computational tool for the analysis of Grad-seq data
3:01pm •
G18: CRAVAT (Cancer-Related Analysis of Variants Toolkit) integration into Galaxy-P and extension towards proteogenomic studies
3:01pm •
B28: Community Annotation with Apollo: Engaging the Collective in a Genome Annotation Workflow
3:01pm •
G04: Galaxy for AnswerALS on Microsoft Azure and Kubernetes
3:01pm •
B20: Reproducible data analysis with Snakemake
3:01pm •
G16: Integrative proteo-transcriptomics workflows within the Galaxy framework to explore the correlation between the expression of RNA and proteins
3:01pm •
B18: NIH Data Commons Pilot Phase leverages the cloud to access, analyze, and share FAIR biomedical data
3:01pm •
B24: The Hypergraph Algorithms Package
3:01pm •
D02: Adding R shiny apps as Galaxy interactive environment. A Galaxy-E demo
3:01pm •
G12: Canada's Integrated Rapid Infectious Disease Analysis Platform (IRIDA)
Performing Arts Building
12:30pm •
Birds-of-a-Feather (BoFs), with Lunch!
5:40pm •
Birds-of-a-Feather (BoFs), the Final Flight!
TBA
7:00pm •
Conference Dinner Sponsored by Google Cloud
Vollum Lecture Hall
9:00am •
BOSC Session 5: Developer Tools and Libraries
9:01am •
iMADS: A sustainable software collaboration for predicting transcription factor binding specificity
9:20am •
The Funnel Task Execution Server
9:40am •
Distributed execution of bioinformatics tools on Apache Spark with ADAM and Cannoli
9:45am •
Extended Extraction Transform Load: A novel framework for batch jobs on cloud computing resources
9:50am •
Plugging Docker-based visualizations into Django with django_docker_engine
9:55am •
The Arachne Graph Database Server
10:00am •
Owlery: An easily deployable web service for making reasoning queries over OWL ontologies web-native
10:05am •
taxa: taxonomic data standards and methods for R and Python
10:10am •
Q&A for lightning talks in this session⚡
10:50am •
BOSC Session 6: Workflows
10:51am •
CWLProv - Interoperable retrospective provenance capture and its challenges
11:10am •
Running portable workflow and container specifications at production scale in the cloud: strategy & best practices
11:30am •
The GA4GH/DREAM Workflow Execution Challenge
11:35am •
Bespin: An open source system to run reproducible computational workflows on cloud infrastructure
11:40am •
CWL-Airflow pipeline manager as a backend for BioWardrobe data analysis platform
11:45am •
Scaling bioinformatics analysis using Nextflow and AWS
11:50am •
One Week to 1,000 Whole Genomes with Open Source: Arvados, CWL, and bcbio
11:55am •
Q&A for lightning talks in this session⚡
1:40pm •
BOSC Session 7: Project Updates and Late-Breaking Research
1:41pm •
OBF update
1:50pm •
GSOC update
2:00pm •
Biopython Project Update 2018
2:07pm •
Community Annotation with Apollo: Engaging the Collective in a Genome Annotation Workflow
2:27pm •
Late-Breaking Lightning Talks ⚡
2:52pm •
Q&A for lightning talks in this session⚡
4:00pm •
Session 8 - Joint BOSC & GCC Closing
4:01pm •
Closing Keynote: Confound it! Reproducible biology from "omics" data analysis
5:00pm •
Conference Closing
Timezone
GCC BOSC 2018
America/Los Angeles
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Southeast Reed College Place, Portland, Oregon, United States
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Eliot Chapel
Gigantic Brewing
PAB 104
PAB 130
PAB 131
PAB 320
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PAB Atrium
Performing Arts Building
Reed College Campus
Reed Commons Cafe
Sitka Dorm, Ground Floor
TBA
Vollum Lecture Hall
Vollum Lounge
Woodstock Neighborhood
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Eliot Chapel
Gigantic Brewing
PAB 104
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PAB Atrium
Performing Arts Building
Reed College Campus
Reed Commons Cafe
Sitka Dorm, Ground Floor
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Vollum Lecture Hall
Vollum Lounge
Woodstock Neighborhood
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