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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

6:00pm

 
Monday, June 25
 

8:00am

9:00am

11:30am

12:30pm

3:00pm

3:30pm

6:00pm

7:30pm

 
Tuesday, June 26
 

8:00am

9:00am

11:30am

12:30pm

3:00pm

3:30pm

6:20pm

8:00pm

8:10pm

 
Wednesday, June 27
 

8:00am

9:00am

9:01am

10:00am

10:20am

10:50am

10:51am

11:05am

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12:00pm

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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 Irber 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 Goonasekera 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 Lariviére 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 Kalaš 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

4:01pm

4:20pm

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6:00pm

8:00pm

 
Thursday, June 28
 

8:00am

9:00am

9:01am

9:20am

9:40am

9:45am

9:50am

9:55am

10:00am

10:05am

10:10am

10:20am

10:50am

10:51am

11:10am

11:30am

11:35am

11:40am

11:45am

11:50am

11:55am

11:56am

12:02pm

12:10pm

12:30pm

1:40pm

1:41pm

1:50pm

2:00pm

2:07pm

2:10pm

2:16pm

2:22pm

2:27pm

2:28pm

2:34pm

2:40pm

2:46pm

2:52pm

3:00pm

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: 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

4:01pm

5:00pm

5:40pm

7:00pm

 
Friday, June 29
 

8:00am

9:00am

 
Saturday, June 30
 

8:45am

9:00am

 
Sunday, July 1
 

8:45am

9:00am

 
Monday, July 2
 

8:45am

9:00am