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BCC2020

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➞ Registration closed July 15.

BCC2020 is online, global, and affordable. The meeting and training are now done, and the CoFest is under way.

The 2020 Bioinformatics Community Conference brings together the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference into a single event featuring training, a meeting, and a CollaborationFest. Events run from July 17 through July 25, and is held in both the eastern and western hemispheres.

11:00 EDT

Pre-BCC Open House! West

03:00 EDT

Pre-BCC Open House! East

09:00 EDT

West Training 1 Joint

09:01 EDT

Adding Fun(ction) to Microbiome Analysis: Metatranscriptomics and Metaproteomics Workflows in Galaxy Training ETimothy J. Griffin • James Johnson • Saskia Hiltemann • Pratik Jagtap • Subina Mehta Getting started in Git using GitHub Desktop Training AYo Yehudi How to use Reactome data, tools and web services Training BJoel Weiser • Robin Haw • Solomon Shorser • Justin Cook Introduction to Galaxy Administration I Training CThat Other Person • Martin Čech • Nate Coraor • Nicola Soranzo • Helena Rasche Introduction to Using Galaxy Training DDelphine Lariviere • Wolfgang Maier

11:30 EDT

12:15 EDT

West Training 2 Joint

12:16 EDT

From stars to constellations: Scaling analyses in Galaxy Training DMarius van den Beek • Saskia Hiltemann • Helena Rasche Handling integrated biological data using Python, Jupyter, and InterMine Training Asergio contrino • Yo Yehudi • Rachel Lyne Introduction to Galaxy Administration II Training CThat Other Person • Martin Čech • Nate Coraor • Nicola Soranzo R / Bioconductor in the Cloud Training EMartin Morgan • Nitesh Turaga • Lori Shepherd Scaling genomic analysis with Glow and Apache Spark Training BHenry Davidge • Karen Feng • Rishi Ghose • Michael Shtelma • Frank Nothaft • Kiavash Kianfar • Amir Kermany • Will Brandler

14:45 EDT

15:30 EDT

West Training 3 Joint

15:31 EDT

Building communities with open source + open science Training AMalvika Sharan • Yo Yehudi Dockstore Fundamentals: Introduction to Docker and Descriptors for Reproducible Analysis Training DLouise Cabansay • Andrew Duncan • Denis Yuen • Gary Lau • Charles Overbeck • Natalie Perez Import, handle, visualize and analyze biodiversity data in Galaxy Training CYvan Le Bras Introduction to Galaxy Administration III Training BThat Other Person • Martin Čech • Nate Coraor Processing of Single Cell RNA-Seq Data with Galaxy Training EBjorn Gruning • Mehmet Tekman • Hans-Rudolf Hotz

18:00 EDT

Interregnum Joint

21:00 EDT

East Training 1 Joint

21:01 EDT

Command Line Essentials for Bioinformaticians Training EIra Cooke • Wytamma Wirth • Jia Zhang • Legana Fingerhut Dockstore Fundamentals: Introduction to Docker and Descriptors for Reproducible Analysis Training CLouise Cabansay • Andrew Duncan • Denis Yuen How to use Reactome data, tools and web services Training AJoel Weiser • Robin Haw • Solomon Shorser • Justin Cook Introduction to Galaxy Administration I Training DSimon Gladman • Kiran K Telukunta • Nicholas Rhodes • Catherine Bromhead Introduction to Using Galaxy Training BJennifer Hillman-Jackson • Igor Makunin

23:30 EDT

00:15 EDT

East Training 2 Joint

00:16 EDT

Bionitio: building better bioinformatics tools with batteries included. I Training BAnna Syme • Bernie Pope From stars to constellations: Scaling analyses in Galaxy Training CMaria Doyle • Marius van den Beek Getting started in Git using GitHub Desktop Training AThom Cuddihy Introduction to Galaxy Administration II Training DSimon Gladman • Kiran K Telukunta • Nicholas Rhodes • Catherine Bromhead Produce a portable germline variant-calling pipeline in CWL and WDL using Janis and GATK I Training EMichael Franklin • Richard Lupat

02:45 EDT

03:30 EDT

East Training 3 Joint

03:31 EDT

Bionitio: building better bioinformatics tools with batteries included II Training BAnna Syme • Bernie Pope Building communities with open source + open science Training AYo Yehudi High-throughput molecular dynamics with Galaxy Training EChris Barnett • Simon Bray • Tharindu Senapathi Import, handle, visualize and analyze biodiversity data in Galaxy Training CYvan Le Bras Introduction to Galaxy Administration III Training DSimon Gladman • Kiran K Telukunta • Nicholas Rhodes • Catherine Bromhead

06:00 EDT

Interregnum Joint

09:00 EDT

West Training 4 Joint

09:01 EDT

Galaxy Code Architecture Training CJohn Chilton • Nate Coraor How to write a JBrowse 2 plugin Training DColin Diesh • Garrett Stevens Introduction to Machine Learning Training AAlireza Khanteymoori • Anup Kumar RNA-Seq analysis with AskOmics Interactive Tool Training BAnthony Bretaudeau • Xavier Garnier Train the Galaxy Trainer Training ESaskia Hiltemann • Delphine Lariviere • Helena Rasche

11:30 EDT

12:15 EDT

West Training 5 Joint

12:16 EDT

Building communities with open source + open science Training BMalvika Sharan • Yo Yehudi Embedding JBrowse 2 in your website Training CColin Diesh • Garrett Stevens Getting your hands on Climate data Training EAnne Fouilloux Reference data with CVMFS and remote jobs with Pulsar Training DGianmauro Cuccuru • Nate Coraor • Helena Rasche Scripting Galaxy with BioBlend Training AMarius van den Beek • Dannon Baker • Nicola Soranzo

14:45 EDT

15:30 EDT

West Training 6 Joint

15:31 EDT

Bioinformatics in Education Training EUwe Hilgert • Isabella Viney Fit your tools into any platform with Bioconda and BioContainers Training AAndrea Giachetti • Loraine Guéguen • Vincenzo Laveglia • Yi Sun Introduction to Nextflow Training CEvan Floden • Paolo Di Tommaso • Kevin Sayers Proteomic data analysis in Galaxy Training DMelanie Föll • Matthias Fahrner Reproducible Analysis in the Cloud with Dockstore and Terra Training BLouise Cabansay • Beth Sheets • Beri Shifaw

18:00 EDT

Interregnum Joint

21:00 EDT

East Training 4 Joint

21:01 EDT

Galaxies for Crop Science Training EVenice Juanillas • Dmytro Chebotarov • Ken McNally • Ramil Mauleon Galaxy Code Architecture Training AJohn Chilton • Nate Coraor How to write a JBrowse 2 plugin Training DRob Buels • Peter Xie • Scott Cain R / Bioconductor in the Cloud Training BMartin Morgan • Nitesh Turaga • Lori Shepherd Train the Galaxy Trainer Training CGareth Price • Maria Doyle • Simon Gladman

23:30 EDT

00:15 EDT

East Training 5 Joint

00:16 EDT

Automating Practical Classroom with GitHub Classroom Training CMuhammad Farhan Sjaugi • Abd Rahim Embedding JBrowse 2 in your website Training ARob Buels • Peter Xie • Scott Cain Introduction to RNA-Seq Analysis with Galaxy Training DGareth Price Produce a portable germline variant-calling pipeline in CWL and WDL using Janis and GATK II Training EMichael Franklin • Richard Lupat Reference data with CVMFS and remote jobs with Pulsar Training BSimon Gladman • Catherine Bromhead

02:45 EDT

03:30 EDT

East Training 6 Joint

03:31 EDT

Getting your hands on Climate data Training BAnne Fouilloux Handling integrated biological data using Python, Jupyter, and InterMine Training DDaniela Butano • Yo Yehudi • Rachel Lyne Introduction to Machine Learning Training EAlireza Khanteymoori • Anup Kumar Processing of Single Cell RNA-Seq Data with Galaxy Training ABjorn Gruning • Mehmet Tekman • Hans-Rudolf Hotz Scripting Galaxy with BioBlend Training CMarius van den Beek • Nuwan Goonasekera • Nicola Soranzo • Clare Sloggett

06:00 EDT

Interregnum Joint

10:00 EDT

BCC2020 Conference Day 1: West Joint

10:01 EDT

Welcome JointDave Clements • Nomi Harris

10:30 EDT

West Keynote 1: How Open Source has Changed the World JointLincoln Stein

11:15 EDT

11:30 EDT

BOSC West Session 1a: Sequencing & analysis 🍐 BOSCChris Fields Galaxy West Session 1: Applications and use cases 🌀 GalaxyDelphine Lariviere

11:31 EDT

Cooperative bacteriophage genome annotation in the biologist-friendly Galaxy and Apollo platforms 🌀 GalaxyJolene Ramsey Digital Expression Explorer 2: a repository of 8 trillion uniformly processed RNA-seq reads and still counting 🍐 BOSCMark Ziemann

11:45 EDT

Community genome annotation integrates with Galaxy via Apollo providing greater integration and more functional annotation options 🌀 GalaxyNathan Dunn Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED 🍐 BOSCSam Kovaka

11:50 EDT

THAPBI PICT -- a metabarcoding analysis pipeline developed as a Phytophthora ITS1 Classification Tool 🍐 BOSCPeter Cock Computational chemistry analysis using Galaxy: Exploring antigen-antibody binding patterns for MUC1-AR20.5 🌀 GalaxyChris Barnett

11:55 EDT

Please contribute to FASTQE so I don’t have to 🍐 BOSCAndrew Lonsdale

12:00 EDT

A reproducible workflow for amplicon-based microbial community analysis using the drake R package 🍐 BOSCRodrigo Ortega-Polo

12:05 EDT

Q & A 🌀 GalaxyDelphine Lariviere SigBio-Shiny: A standalone interactive application for detecting biological significance on a set of genes 🍐 BOSCSangram Keshari Sahu

12:10 EDT

Streamlining accessibility and computability of large-scale genomic datasets with the NHGRI genome data science Analysis, Visualization, and Informatics Lab-Space (ANVIL) 🍐 BOSCMichael Schatz Integrating and analyzing genotype, phenotype, and environmental data through CartograTree and Tripal Galaxy 🌀 GalaxyIrene Cobo

12:15 EDT

A comprehensive benchmarking of WGS-based structural variant callers 🍐 BOSCVaruni Sarwal

12:20 EDT

Q&A for session B1a 🍐 BOSCChris Fields

12:24 EDT

BOSC West Session 1b: Open data 🍐 BOSCChris Fields

12:25 EDT

Tripal: an example of successful open-source distributed team development 🍐 BOSCMargaret Staton Automated real-time data analysis and visualizations for the SARS-CoV-2/Covid19 portal 🌀 GalaxyMarius van den Beek

12:30 EDT

BioThings Explorer: A platform for distributed knowledge integration across biomedical APIs 🍐 BOSCJiwen Xin

12:35 EDT

Don’t worry about data management - use Cenzontle 🍐 BOSCAsis Hallab

12:40 EDT

Q & A 🌀 GalaxyDelphine Lariviere Q&A for session B1b 🍐 BOSCChris Fields

12:45 EDT

13:00 EDT

Broad Institute Data Sciences Platform Sponsor Table JointGeraldine Van der Auwera eLife Innovation Sponsor Table JointEmmy Tsang GigaScience Sponsor Table JointLaurie Goodman • Ken Cho • Scott Edmunds P1-03: : A somatic variant-calling pipeline for the support of molecular tumor boards at German university hospitals 🍐 JointWolfgang Maier • Patrick Metzger P1-07: : Automating the annotation of biological data through semantic technologies and machine learning 🍐 JointLorcán Pigott-Dix P1-08: : BioThings Explorer: A platform for distributed knowledge integration across biomedical APIs 🍐 JointJiwen Xin P1-10: : BLAST in a container 🍐 JointTom Madden P2-10: : Deploying Galaxy workflows in containers 🌀 JointBert Droesbeke P3-01: : Earth System Modelling and data analysis with Galaxy Climate Science Workbench 🌀 JointAnne Fouilloux P3-04: : Enabling computational workflows with Tripal and Galaxy 🌀 JointSean Buehler P3-09: : Exploring chromatogram library-based data independent acquisition analysis using EncyclopeDIA within Galaxy framework 🌀 JointPratik Jagtap P3-10: : Extensions of READemption for the analysis of several RNA-seq based protocols 🍐 JointTill Sauerwein P3-12: : Full-factorial examination of high-throughput microbiome sequencing workflows from sample preparation to bioinformatic analysis 🍐 JointTravis J. De Wolfe P4-06: : GraphClust2: a galaxy-based solution for clustering RNA sequences to discover conserved and common secondary structures 🌀 JointMilad Miladi P4-07: : GVL Demo: from Administrators to End-users 🌀 JointNuwan Goonasekera P5-04: : Magic-BLAST an accurate RNA-seq mapper 🍐 JointGrzegorz Boratyn P5-07: : Open-Source, Large-Scale Set Similarity Search with Sketch 🍐 JointDaniel Baker P5-10: : Planet Microbe: Toward the reintegration of oceanographic ‘omics dataset in their environmental and physiochemical context 🍐 JointAlise Jany Ponsero P5-12: : Progerin expression induces a significant downregulation of transcription from human repetitive sequences in iPSC-derived dopaminergic neurons 🌀 JointWalter Arancio P6-01: : pyGenomeTracks: Reproducible plots for multivariate genomic data sets 🍐 JointLucille Delisle P6-02: : Reproducible, collaborative and exploratory data analysis using CyVerse VICE 🍐 JointReetu Tuteja P6-03: : Running and sharing the ENCODE atac-seq pipeline on Truwl 🍐 JointKarl Sebby P6-04: : SigBio-Shiny: A standalone interactive application for detecting biological significance on a set of genes 🍐 JointSangram Keshari Sahu P6-08: : Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED 🍐 JointSam Kovaka P6-12: : Towards more FAIR research software 🍐 JointMateusz Kuzak Poster / Demo West Session 1 Joint

13:45 EDT

14:00 EDT

BOSC West Session 2: Reproducibility and standards 🍐 BOSCMoni Muñoz-Torres • Jessica Maia Galaxy West Session 2: Extending the Galaxy ecosystem 🌀 GalaxyJennifer Harrow

14:01 EDT

Automated generation of training materials from markdown documents 🌀 GalaxyDelphine Lariviere Bionitio: building better bioinformatics tools with batteries included 🍐 BOSCBernie Pope

14:15 EDT

Enhancing rigor and reproducibility in biomedical research 🍐 BOSCJaqueline J. Brito Integrating refgenie and Galaxy for reference data management: a proposal for IDC 🌀 GalaxyIgnacio Eguinoa

14:20 EDT

Galaxy and its Tool Shed on Python 3: conclusion of a long journey 🌀 GalaxyNicola Soranzo Secondary analysis of publicly available omics data across almost 3 million publications 🍐 BOSCNicholas Darci-Maher

14:25 EDT

Q & A 🌀 GalaxyJennifer Harrow Q&A 🍐 BOSC

14:30 EDT

CrowdGO: Gene Ontology prediction using a meta approach 🍐 BOSCMaarten Reijnders Implementation of the IEEE-2791-2020 standard (BioCompute Objects) in Galaxy via workflow invocations 🌀 GalaxyCharles Hadley King

14:35 EDT

Goslin - A grammar of succinct lipid nomenclature 🍐 BOSCNils Hoffmann Porting the rCASC workflow for scRNA-Seq data analysis to Galaxy and the Laniakea Galaxy on-demand system 🌀 Galaxypietro mandreoli

14:40 EDT

Executable Research Article (ERA): Enrich a research paper with code and data 🍐 BOSCEmmy Tsang Galaxy, Selenium, and End-to-end Testing 🌀 GalaxyOleg Zharkov

14:55 EDT

Q & A 🌀 GalaxyJennifer Harrow Q&A 🍐 BOSC

15:00 EDT

Break! Joint Interregnum Joint

15:15 EDT

Birds of a Feather (BOFs) Joint BoF: Board games Social JointDelphine Lariviere BoF: IWC - Intergalactic Workflow Commission JointBrad Langhorst BoF: Parenting during Coronavirus JointAssunta DeSanto BoF: Where is the bar? JointUla Afgan

17:00 EDT

Galaxy Social One! JointDave Clements

22:00 EDT

BCC2020 Conference Day 1: East Joint

22:01 EDT

Welcome JointNomi Harris • Gareth Price

22:30 EDT

East Keynote 1: Open minds bring open collaborations JointPrashanth Suravajhala

23:15 EDT

23:30 EDT

BOSC East Session 1a: Sequencing & analysis 🍐 BOSCMoni Muñoz-Torres Galaxy East Session 1: Applications and use cases 🌀 GalaxyMaria Doyle

23:31 EDT

Cooperative bacteriophage genome annotation in the biologist-friendly Galaxy and Apollo platforms 🌀 GalaxyJolene Ramsey Digital Expression Explorer 2: a repository of 8 trillion uniformly processed RNA-seq reads and still counting 🍐 BOSCMark Ziemann

23:45 EDT

Community genome annotation integrates with Galaxy via Apollo providing greater integration and more functional annotation options 🌀 GalaxyNathan Dunn Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED 🍐 BOSCSam Kovaka

23:50 EDT

THAPBI PICT -- a metabarcoding analysis pipeline developed as a Phytophthora ITS1 Classification Tool 🍐 BOSCPeter Cock Computational chemistry analysis using Galaxy: Exploring antigen-antibody binding patterns for MUC1-AR20.5 🌀 GalaxyChris Barnett

23:55 EDT

Please contribute to FASTQE so I don’t have to 🍐 BOSCAndrew Lonsdale

00:00 EDT

A reproducible workflow for amplicon-based microbial community analysis using the drake R package 🍐 BOSCRodrigo Ortega-Polo

00:05 EDT

Q & A 🌀 GalaxyMaria Doyle SigBio-Shiny: A standalone interactive application for detecting biological significance on a set of genes 🍐 BOSCSangram Keshari Sahu

00:10 EDT

Streamlining accessibility and computability of large-scale genomic datasets with the NHGRI genome data science Analysis, Visualization, and Informatics Lab-Space (ANVIL) 🍐 BOSCMichael Schatz Integrating and analyzing genotype, phenotype, and environmental data through CartograTree and Tripal Galaxy 🌀 GalaxyIrene Cobo

00:15 EDT

A comprehensive benchmarking of WGS-based structural variant callers 🍐 BOSCVaruni Sarwal

00:20 EDT

Q&A for session B1a 🍐 BOSCMoni Muñoz-Torres

00:25 EDT

Tripal: an example of successful open-source distributed team development 🍐 BOSCMargaret Staton Automated real-time data analysis and visualizations for the SARS-CoV-2/Covid19 portal 🌀 GalaxyMarius van den Beek BOSC East Session 1b: Open data 🍐 BOSCMoni Muñoz-Torres

00:30 EDT

BioThings Explorer: A platform for distributed knowledge integration across biomedical APIs 🍐 BOSCJiwen Xin

00:35 EDT

Don’t worry about data management - use Cenzontle 🍐 BOSCAsis Hallab

00:40 EDT

Q & A 🌀 GalaxyMaria Doyle Q&A for session B1b 🍐 BOSCMoni Muñoz-Torres

00:45 EDT

01:00 EDT

eLife Innovation Sponsor Table JointEmmy Tsang GigaScience Sponsor Table JointKen Cho • Scott Edmunds • Laurie Goodman P1-01: : A composable rootless container system for genomic analysis pipelines 🍐 JointXu Yang P2-02: : Computational meta-analysis of transcriptome in Tetrology of Fallot reveals dysregulated hubs and pathways 🌀 JointSona Charles P2-07: : Data integration promises robust and faster discovery of COVID-19 drug targets 🍐 JointTyrone Chen P4-07: : GVL Demo: from Administrators to End-users 🌀 JointNuwan Goonasekera P6-01: : pyGenomeTracks: Reproducible plots for multivariate genomic data sets 🍐 JointLucille Delisle P6-04: : SigBio-Shiny: A standalone interactive application for detecting biological significance on a set of genes 🍐 JointSangram Keshari Sahu P6-12: : Towards more FAIR research software 🍐 JointMateusz Kuzak Poster / Demo East Session 1 Joint

01:45 EDT

02:00 EDT

BOSC East Session 2: Reproducibility and standards 🍐 BOSCHeather Wiencko Galaxy Session 2: Extending the Galaxy Ecosystem 🌀 GalaxySimon Gladman

02:01 EDT

Automated generation of training materials from markdown documents 🌀 GalaxyDelphine Lariviere Bionitio: building better bioinformatics tools with batteries included 🍐 BOSCBernie Pope

02:15 EDT

Enhancing rigor and reproducibility in biomedical research 🍐 BOSCJaqueline J. Brito Integrating refgenie and Galaxy for reference data management: a proposal for IDC 🌀 GalaxyIgnacio Eguinoa

02:20 EDT

Galaxy and its Tool Shed on Python 3: conclusion of a long journey 🌀 GalaxyNicola Soranzo Secondary analysis of publicly available omics data across almost 3 million publications 🍐 BOSCNicholas Darci-Maher

02:25 EDT

Q & A 🌀 GalaxySimon Gladman Q&A 🍐 BOSCHeather Wiencko

02:30 EDT

CrowdGO: Gene Ontology prediction using a meta approach 🍐 BOSCMaarten Reijnders Implementation of the IEEE-2791-2020 standard (BioCompute Objects) in Galaxy via workflow invocations 🌀 GalaxyCharles Hadley King

02:35 EDT

Goslin - A grammar of succinct lipid nomenclature 🍐 BOSCNils Hoffmann Porting the rCASC workflow for scRNA-Seq data analysis to Galaxy and the Laniakea Galaxy on-demand system 🌀 Galaxypietro mandreoli

02:40 EDT

Executable Research Article (ERA): Enrich a research paper with code and data 🍐 BOSCEmmy Tsang Galaxy, Selenium, and End-to-end Testing 🌀 GalaxyOleg Zharkov

02:55 EDT

Q & A 🌀 GalaxySimon Gladman Q&A 🍐 BOSCHeather Wiencko

03:00 EDT

Break! Joint Interregnum Joint

03:15 EDT

Birds of a Feather (BOFs) Joint

05:00 EDT

Galaxy Social East! JointGareth Price

09:00 EDT

Birds of a Feather (BOFs) Joint BoF: A code of conduct for the OBF JointBastian Greshake Tzovaras • Malvika Sharan BoF: Celestial Masses: Galaxy for mass spectrometry-based research JointTimothy J. Griffin • Pratik Jagtap • Yves Vandenbrouck • Oliver Schilling BoF: Computational Immunoinformatics Worflows Over Galaxy Server JointAmbarish Kumar BoF: Galaxy Africa - Outreach Plans JointPeter van Heusden BoF: Galaxy-India: Launch and Outreach Plans JointAnshu Bhardwaj • Harpreet Singh

10:00 EDT

BCC2020 Conference Day 2: West Joint

10:01 EDT

Day 2 Welcome JointDave Clements • Morgan Taschuk

10:15 EDT

West Keynote 2: Open minds bring open collaborations JointPrashanth Suravajhala

11:00 EDT

11:15 EDT

BOSC West Session 3: Building Open Source Communities (BOSC) 🍐 BOSCYo Yehudi Galaxy West Session 3: Galaxy Administration 🌀 GalaxyJohn Chilton

11:16 EDT

Building open source communities and empowering new contributors 🍐 BOSCYo Yehudi The cloud-native Galaxy: Galaxy on Kubernetes 🌀 GalaxyAlexandru Mahmoud

11:30 EDT

Codeathons as a tool for improving diversity in computer science 🍐 BOSCAllissa Dillman Custos: Enabling User Authentication via External Institutional Identities 🌀 GalaxyJuleen Graham

11:35 EDT

CyVerse Learning Institute’s foundational open science skills workshop 🍐 BOSCTyson Swetnam On-demand Galaxy with Laniakea: results and future perspectives 🌀 GalaxyMarco Antonio Tangaro

11:40 EDT

HiSCiAp and Human Cell Atlas Galaxy instance: User-friendly, scalable tools and workflows for single-cell analysis 🌀 GalaxyPablo Moreno Open Life Science: Empowering early career researchers to become open science leaders 🍐 BOSCBérénice Batut • Yo Yehudi • Malvika Sharan

11:55 EDT

Q & A 🌀 GalaxyJohn Chilton Q&A 🍐 BOSCYo Yehudi

12:00 EDT

12:15 EDT

Sponsor Session West JointDave Clements

12:20 EDT

AWS Gold Sponsor Talk: Scalable genomics data analysis in the cloud JointLee Pang

12:40 EDT

Software Sustainability Institute Gold Sponsor Talk: Most code is cr#p and that’s okay JointNeil Chue Hong

13:00 EDT

eLife Innovation Sponsor Table JointEmmy Tsang GigaScience Sponsor Table JointKen Cho • Scott Edmunds • Laurie Goodman P1-05: : Automated generation of training materials from markdown documents 🌀 JointDelphine Lariviere P1-06: : Automated real-time data analysis and visualizations for the SARS-CoV-2/Covid19 portal 🌀 JointMarius van den Beek P1-09: : BioViz Connect: Web application linking CyVerse cloud resources to genomic visualization in the Integrated Genome Browser 🍐 JointNowlan Freese P1-12: : Codeathons as a tool for improving diversity in computer science 🍐 JointAllissa Dillman P2-01: : Community genome annotation integrates with Galaxy via Apollo providing greater integration and more functional annotation options 🌀 JointNathan Dunn P2-05: : CrowdGO: a wisdom of the crowd-based Gene Ontology prediction tool 🍐 JointMaarten Reijnders P3-03: : EDAM: the ontology of bioinformatics operations, topics, data, and formats (update 2020) 🍐 JointMatúš Kalas P3-06: : eSPiGA: a population genomic analyses package with graphical interface 🍐 JointSebastian E. Ramos-Onsins P4-01: : Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Land Model in Galaxy 🌀 JointAnne Fouilloux • Hui Tang • Sonya Geange P4-05: : Goslin - A grammar of succinct lipid nomenclature 🍐 JointNils Hoffmann P4-09: : HiSCiAp and Human Cell Atlas Galaxy instance: User-friendly, scalable tools and workflows for single-cell analysis 🌀 JointPablo Moreno P4-11: : Implementation of the IEEE-2791-2020 standard (BioCompute Objects) in Galaxy via workflow invocations 🌀 JointCharles Hadley King P5-01: : Integrating refgenie and Galaxy for reference data management: a proposal for IDC 🌀 JointIgnacio Eguinoa P5-03: : Jasmine: Fast and accurate structural variant comparison across many individuals 🍐 JointMelanie Kirsche P5-08: : OpenBio.eu: An extrovert bioinformatics research object repository and workflow management system 🍐 JointAlexandros Kanterakis P5-09: : Pan-cancer Aberrant Pathway Activity Analysis (PAPAA): A Galaxy Operable Machine Learning-Based Pipeline. 🌀 JointVijay Krishna Nagampalli P6-06: : sRNAflow: a tool for analysis of small RNA-seq data 🍐 JointPawel Zayakin P6-10: : The cloud-native Galaxy: Galaxy on Kubernetes 🌀 JointNuwan Goonasekera • The Other Enis Afgan • Alexandru Mahmoud P7-01: : ViPRA-Haplo: de novo reconstruction of viral populations using paired end sequencing data) 🍐 JointWeiling Li P7-03: : Visualization of gene regulation in endothelial cells that are programmed to human pluripotent stem cells and differentiated to endothelial or neuronal cells 🍐 JointLuke Trinity P7-07: Modern Data Visualization in Galaxy with Higlass 🌀 JointAlex Ostrovsky P7-09: Leveraging machine learning techniques and microbiota data for accessible and reproducible biological classification 🌀 JointJayadev Joshi Poster / Demo West Session 2 Joint

13:45 EDT

14:00 EDT

BOSC West Session 4a: Developer tools & libraries 🍐 BOSCKarsten Hokamp Galaxy West Session 4: The big picture 🌀 GalaxyPeter van Heusden

14:01 EDT

Applying Pulsar: a democratised national and international remote compute network for Galaxy 🌀 GalaxyGianmauro Cuccuru Shesmu: A bioinformatics orchestration tool 🍐 BOSCAndre Masella

14:15 EDT

SIMD Everywhere: portable implementations of SIMD intrinsics 🍐 BOSCEvan Nemerson Galaxy Community Update 🌀 GalaxySimon Gladman • Gareth Price • Bjorn Gruning • Michael Schatz • Anton Nekrutenko • Jeremy Goecks • The Other Enis Afgan • Daniel Blankenberg

14:20 EDT

Biopython Project Update 2020 🍐 BOSCPeter Cock

14:25 EDT

Q&A for session B4a 🍐 BOSCKarsten Hokamp

14:29 EDT

BOSC West Session 4b: Visualization 🍐 BOSCKarsten Hokamp

14:30 EDT

Introducing App Store for IGB, a site for sharing and installing extensions for Integrated Genome Browser from BioViz.org 🍐 BOSCAnn Loraine

14:35 EDT

pyGenomeTracks: Reproducible plots for multivariate genomic data sets 🍐 BOSCLucille Delisle

14:40 EDT

MultiQC updates: Visualising results from common bioinformatics tools 🍐 BOSCPhil Ewels

14:45 EDT

The Xena Geneset Viewer provides a visual comparison of pathways over public genomic cancer data 🍐 BOSCNathan Dunn

14:50 EDT

New features for GRNsight: a web application for visualizing models of small- to medium-scale gene regulatory networks 🍐 BOSCKam D. Dahlquist Q & A 🌀 GalaxyPeter van Heusden

14:55 EDT

Q&A for session B4b 🍐 BOSCKarsten Hokamp

15:00 EDT

Break! Joint Interregnum Joint

15:15 EDT

Birds of a Feather (BOFs) Joint BoF: Computational Biology in the Cloud JointLydia Fleischmann • Yuriy Skripchenko

17:00 EDT

BOSC Happy Hour West! Joint

21:00 EDT

Birds of a Feather (BOFs) Joint BoF: Celestial Masses: Galaxy for mass spectrometry-based research JointPratik Jagtap BoF: Computational Immunoinformatics Worflows Over Galaxy Server JointAmbarish Kumar

22:00 EDT

BCC2020 Conference Day 2: East Joint

22:01 EDT

Day 2 East Welcome JointGareth Price

22:15 EDT

East Keynote 2: How Open Source has Changed the World JointLincoln Stein

23:00 EDT

23:15 EDT

BOSC East Session 3: Building Open Source Communities (BOSC) 🍐 BOSCNomi Harris Galaxy East Session 3: Galaxy Administration 🌀 GalaxyNuwan Goonasekera

23:16 EDT

Building open source communities and empowering new contributors 🍐 BOSCYo Yehudi The cloud-native Galaxy: Galaxy on Kubernetes 🌀 GalaxyAlexandru Mahmoud

23:30 EDT

Codeathons as a tool for improving diversity in computer science 🍐 BOSCAllissa Dillman Custos: Enabling User Authentication via External Institutional Identities 🌀 GalaxyJuleen Graham

23:35 EDT

CyVerse Learning Institute’s foundational open science skills workshop 🍐 BOSCTyson Swetnam On-demand Galaxy with Laniakea: results and future perspectives 🌀 GalaxyMarco Antonio Tangaro

23:40 EDT

HiSCiAp and Human Cell Atlas Galaxy instance: User-friendly, scalable tools and workflows for single-cell analysis 🌀 GalaxyPablo Moreno Open Life Science: Empowering early career researchers to become open science leaders 🍐 BOSCBérénice Batut • Yo Yehudi • Malvika Sharan

23:55 EDT

Q & A 🌀 GalaxyNuwan Goonasekera Q&A 🍐 BOSCNomi Harris

00:00 EDT

00:15 EDT

Sponsor Session East JointGareth Price

00:20 EDT

AWS Gold Sponsor Talk: Scalable genomics data analysis in the cloud JointLee Pang

00:40 EDT

Software Sustainability Institute Gold Sponsor Talk: Most code is cr#p and that’s okay JointNeil Chue Hong

01:00 EDT

eLife Innovation Sponsor Table JointEmmy Tsang GigaScience Sponsor Table JointKen Cho • Scott Edmunds • Laurie Goodman P2-04: : CoxBase an online platform for epidemiological surveillance, visualization, analysis and typing of Coxiella burnetii genomic sequence 🍐 JointAkinyemi Mandela Fasemore P2-08: : Deep-EMSCAN: Deep Learning Approach to Recover Combination of Biologically Significant DNA Motifs 🍐 JointSonika Tyagi P3-03: : EDAM: the ontology of bioinformatics operations, topics, data, and formats (update 2020) 🍐 JointMatúš Kalas P4-03: : Genome-wide variant analysis of dwarf soybean lines derived from normal F5 RILs obtained from crossing cultivated and wild soybean 🌀 JointNeha Roy P4-04: : Genpei: an implementation of GA4GH Workflow Execution Service Standard as a microservice 🍐 JointHirotaka Suetake P7-06: The comparative gene expression to delay flowering in the maturing mutation derived from the soybean crossing F8 RIL 🌀 JointChae Won Yu P7-07: Modern Data Visualization in Galaxy with Higlass 🌀 JointAlex Ostrovsky Poster / Demo East Session 2 Joint

01:45 EDT

02:00 EDT

BOSC East Session 4a: Developer tools & libraries 🍐 BOSCHeather Wiencko Galaxy East Session 4: The big picture 🌀 GalaxyHarpreet Singh

02:01 EDT

Applying Pulsar: a democratised national and international remote compute network for Galaxy 🌀 GalaxyGianmauro Cuccuru Shesmu: A bioinformatics orchestration tool 🍐 BOSCAndre Masella

02:15 EDT

SIMD Everywhere: portable implementations of SIMD intrinsics 🍐 BOSCEvan Nemerson Galaxy Community Update 🌀 GalaxySimon Gladman • Gareth Price • Michael Schatz • Bjorn Gruning • Anton Nekrutenko • Jeremy Goecks • The Other Enis Afgan • Daniel Blankenberg

02:20 EDT

Biopython Project Update 2020 🍐 BOSCPeter Cock

02:25 EDT

Q&A for session B4a 🍐 BOSCHeather Wiencko

02:30 EDT

Introducing App Store for IGB, a site for sharing and installing extensions for Integrated Genome Browser from BioViz.org 🍐 BOSCAnn Loraine BOSC East Session 4b: Visualization 🍐 BOSCHeather Wiencko

02:35 EDT

pyGenomeTracks: Reproducible plots for multivariate genomic data sets 🍐 BOSCLucille Delisle

02:40 EDT

MultiQC updates: Visualising results from common bioinformatics tools 🍐 BOSCPhil Ewels

02:45 EDT

The Xena Geneset Viewer provides a visual comparison of pathways over public genomic cancer data 🍐 BOSCNathan Dunn

02:50 EDT

New features for GRNsight: a web application for visualizing models of small- to medium-scale gene regulatory networks 🍐 BOSCKam D. Dahlquist Q & A 🌀 GalaxyHarpreet Singh

02:55 EDT

Q&A for session B4b 🍐 BOSCHeather Wiencko

03:00 EDT

Break! Joint Interregnum Joint

03:15 EDT

Birds of a Feather (BOFs) Joint BoF: Galaxy-India: Launch and Outreach Plans JointHarpreet Singh • Anshu Bhardwaj

09:00 EDT

Birds of a Feather (BOFs) Joint BoF: FAIR Computational Workflows JointIgnacio Eguinoa BoF: Galaxy and Kubernetes JointNuwan Goonasekera • The Other Enis Afgan • Alexandru Mahmoud

10:00 EDT

BOSC West Session 5: Workflow management systems 🍐 BOSCPeter Cock Galaxy West Session 5: Galaxy beyond genomics 🌀 GalaxyYvan Le Bras BCC2020 Conference Day 3: West Joint

10:01 EDT

Evolution of the Nextflow workflow management system 🍐 BOSCEvan Floden

10:02 EDT

Producing biodiversity indicators from citizen science projects: update of birds and bats monitoring schemes on Galaxy-E 🌀 GalaxyColine Royaux

10:15 EDT

Essential biodiversity variables on Galaxy: implementing the PAMPA application 🌀 GalaxyColine Royaux What’s new with nf-core: community-built bioinformatics pipelines 🍐 BOSCPhil Ewels

10:20 EDT

H3AGWAS: Portable GWAS workflows for African science 🍐 BOSCBrandenburg Jean-Tristan VINYL: Variant prIoritizatioN bY survivaL analysis 🌀 GalaxyMatteo Chiara

10:25 EDT

Evaluating customized database generation methods for metaproteomics analysis within the Galaxy platform. 🌀 GalaxySubina Mehta Q&A 🍐 BOSCPeter Cock

10:30 EDT

An automated, accessible proteogenomic pipeline for high confidence detection and rigorous validation of novel peptide sequence variants in Galaxy-P 🌀 GalaxyAndrew T. Rajczewski CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language 🍐 BOSCMichael Kotliar

10:35 EDT

Q & A 🌀 GalaxyYvan Le Bras

10:40 EDT

Galaxy enables FAIR mass spectrometry imaging data analysis of urothelial carcinoma tissues 🌀 GalaxyMelanie Föll

10:45 EDT

Challenges in implementing Janis: A generator for CWL and WDL pipelines 🍐 BOSCMichael Franklin Democratizing DIA analysis on public cloud infrastructures via Galaxy 🌀 GalaxyMatthias Fahrner

10:50 EDT

EOSC-Nordic Climate Science Workbench roadmap 🌀 GalaxyAnne Fouilloux Rapidly creating portable pipelines with aCLImatise 🍐 BOSCMichael Milton

10:55 EDT

Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Land Model in Galaxy 🌀 GalaxyAnne Fouilloux • Hui Tang • Sonya Geange The all-new Genomics Virtual Lab 🍐 BOSCThe Other Enis Afgan

11:10 EDT

Q & A 🌀 GalaxyYvan Le Bras Q&A 🍐 BOSCPeter Cock

11:15 EDT

11:30 EDT

GigaScience Sponsor Table JointKen Cho • Scott Edmunds • Laurie Goodman P1-02: : A data model approach to data coordination in the Human Tumor Atlas Network project 🍐 JointXengie Doan P1-04: : An automated, accessible proteogenomic pipeline for high confidence detection and rigorous validation of novel peptide sequence variants in Galaxy-P 🌀 JointAndrew T. Rajczewski P2-03: : COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource 🍐 JointAndrea Guarracino P2-06: : CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language 🍐 JointMichael Kotliar P2-09: : Democratizing DIA analysis on public cloud infrastructures via Galaxy 🌀 JointMatthias Fahrner P2-11: : Development of TranSMART and Applications in Biomedical Research 🍐 JointPeter Rice P2-12: : Dnpatterntools suite for nucleosome positioning sequence patterns 🌀 JointErinija Pranckeviciene P3-05: : EOSC-Nordic Climate Science Workbench roadmap 🌀 JointAnne Fouilloux P3-07: : Evaluating customized database generation methods for metaproteomics analysis within the Galaxy platform 🌀 JointSubina Mehta P3-08: : Evolution of the Nextflow workflow management system 🍐 JointEvan Floden P4-02: : Galaxy enables FAIR mass spectrometry imaging data analysis of urothelial carcinoma tissues 🌀 JointMelanie Föll P4-08: : H3AGWAS: Portable GWAS workflows for African science 🍐 JointBrandenburg Jean-Tristan P4-12: : In silico characterization of FK506-binding proteins in wheat 🌀 JointAnantika Suri P5-02: : Introducing App Store for IGB, a site for sharing and installing extensions for Integrated Genome Browser from BioViz.org 🍐 JointAnn Loraine P5-05: : Nebulizer: a command-line utility for remote Galaxy admin tasks 🌀 JointPeter Briggs P5-06: : New features for GRNsight: a web application for visualizing models of small- to medium-scale gene regulatory networks 🍐 JointKam D. Dahlquist P5-11: : Producing biodiversity indicators from citizen science projects: update of birds and bats monitoring schemes on Galaxy-E 🌀 JointColine Royaux P6-05: : SIMD Everywhere: portable implementations of SIMD intrinsics 🍐 JointEvan Nemerson P6-07: : Survey of metaproteomics software tools for functional microbiome analysis 🌀 JointRay Sajulga P6-09: : Testing and investigating deep learning models for promoter recognition 🍐 JointRaul Ivan Perez Martell P6-11: : The Xena Geneset Viewer provides a visual comparison of pathways over public genomic cancer data 🍐 JointNathan Dunn P7-02: : ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes 🍐 JointNiema Moshiri P7-04: : What’s new with nf-core: community-built bioinformatics pipelines 🍐 JointPhil Ewels Poster / Demo West Session 3 Joint

12:15 EDT

12:30 EDT

Joint West Session 6: COVID-19 JointMorgan Taschuk

12:31 EDT

Serratus: Ultra-deep search for novel coronaviruses 🍐 JointArtem Babaian

12:45 EDT

MALVIRUS: viral variant calling made easy 🍐 JointYuri Pirola

12:50 EDT

Development of TranSMART and Applications in Biomedical Research 🍐 JointPeter Rice

12:55 EDT

ViPRA-Haplo: de novo reconstruction of viral populations using paired end sequencing data 🍐 JointWeiling Li

13:00 EDT

Q&A JointMorgan Taschuk

13:05 EDT

COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource 🍐 JointAndrea Guarracino

13:10 EDT

Designing and executing workflows for virtual screening of the SARS-CoV-2 main protease 🍐 JointSimon Bray

13:25 EDT

Analyzing the Nanopore data of SARS-CoV-2 within the Galaxy framework 🌀 JointNathan Roach

13:40 EDT

Q&A JointMorgan Taschuk

13:45 EDT

14:00 EDT

West Keynote 3: Biased by Default: Exploring Discrimination in Research Code JointAbigail Cabunoc Mayes

14:45 EDT

Closing remarks JointDave Clements • Nomi Harris • Peter Cock • Michael Heuer • Frederik Coppens

15:00 EDT

Interregnum Joint

15:15 EDT

Birds of a Feather (BOFs) Joint BoF: Dynamic Visualization of Bioinformatic Data JointNathan Dunn • Rob Buels • Colin Diesh BoF: Machine learning and parasites genomics diversity JointBoï Kone

21:00 EDT

Birds of a Feather (BOFs) Joint BoF: IWC - Intergalactic Workflow Commission JointBrad Langhorst

22:00 EDT

BOSC East Session 5: Workflow management systems 🍐 BOSCChris Fields Galaxy East Session 5: Galaxy beyond genomics 🌀 GalaxyAnshu Bhardwaj BCC2020 Conference Day 3: East Joint

22:01 EDT

Evolution of the Nextflow workflow management system 🍐 BOSCEvan Floden

22:02 EDT

Producing biodiversity indicators from citizen science projects: update of birds and bats monitoring schemes on Galaxy-E 🌀 GalaxyColine Royaux

22:15 EDT

Essential biodiversity variables on Galaxy: implementing the PAMPA application 🌀 GalaxyColine Royaux What’s new with nf-core: community-built bioinformatics pipelines 🍐 BOSCPhil Ewels

22:20 EDT

H3AGWAS: Portable GWAS workflows for African science 🍐 BOSCBrandenburg Jean-Tristan VINYL: Variant prIoritizatioN bY survivaL analysis 🌀 GalaxyMatteo Chiara

22:25 EDT

Evaluating customized database generation methods for metaproteomics analysis within the Galaxy platform. 🌀 GalaxySubina Mehta Q&A 🍐 BOSCChris Fields

22:30 EDT

An automated, accessible proteogenomic pipeline for high confidence detection and rigorous validation of novel peptide sequence variants in Galaxy-P 🌀 GalaxyAndrew T. Rajczewski CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language 🍐 BOSCMichael Kotliar

22:35 EDT

Q & A 🌀 GalaxyAnshu Bhardwaj

22:40 EDT

Galaxy enables FAIR mass spectrometry imaging data analysis of urothelial carcinoma tissues 🌀 GalaxyMelanie Föll

22:45 EDT

Challenges in implementing Janis: A generator for CWL and WDL pipelines 🍐 BOSCMichael Franklin Democratizing DIA analysis on public cloud infrastructures via Galaxy 🌀 GalaxyMatthias Fahrner

22:50 EDT

EOSC-Nordic Climate Science Workbench roadmap 🌀 GalaxyAnne Fouilloux Rapidly creating portable pipelines with aCLImatise 🍐 BOSCMichael Milton

22:55 EDT

Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Land Model in Galaxy 🌀 GalaxyAnne Fouilloux • Hui Tang • Sonya Geange The all-new Genomics Virtual Lab 🍐 BOSCThe Other Enis Afgan

23:10 EDT

Q & A 🌀 GalaxyAnshu Bhardwaj Q&A 🍐 BOSCChris Fields

23:15 EDT

23:30 EDT

GigaScience Sponsor Table JointKen Cho • Scott Edmunds • Laurie Goodman P3-02: : ECRcentral: A central platform for early-career researchers 🍐 JointAziz Khan P3-11: : FASE: Finding Alternative Splicing Events and analysis of RNA-Sequencing Data. 🍐 JointHarsh Sharma P4-10: : Identification of differentially expressed genes between cultivar and weedy type in soybean plant 🌀 JointPrakash Basnet P7-04: : What’s new with nf-core: community-built bioinformatics pipelines 🍐 JointPhil Ewels P7-05: RNA-seq analyses of the hydrated and dehydrated leaves of the resurrection plant, Selaginella tamariscina 🌀 JointEunchae Kwon P7-08: Molecular Property Diagnostic Suite (MPDS): Development of Disease-Specific Web Portals Based on Galaxy Platform 🌀 JointAnamika Singh Gaur Poster / Demo East Session 3 Joint

00:15 EDT

00:30 EDT

Joint East Session 6: COVID-19 JointDieter Bulach

00:31 EDT

Serratus: Ultra-deep search for novel coronaviruses 🍐 JointArtem Babaian

00:45 EDT

MALVIRUS: viral variant calling made easy 🍐 JointYuri Pirola

00:50 EDT

Development of TranSMART and Applications in Biomedical Research 🍐 JointPeter Rice

00:55 EDT

ViPRA-Haplo: de novo reconstruction of viral populations using paired end sequencing data 🍐 JointWeiling Li

01:00 EDT

Q&A Joint

01:05 EDT

COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource 🍐 JointAndrea Guarracino

01:10 EDT

Designing and executing workflows for virtual screening of the SARS-CoV-2 main protease 🍐 JointSimon Bray

01:25 EDT

Analyzing the Nanopore data of SARS-CoV-2 within the Galaxy framework 🌀 JointNathan Roach

01:40 EDT

Q&A Joint

01:45 EDT

02:00 EDT

East Keynote 3: Biased by Default: Exploring Discrimination in Research Code JointAbigail Cabunoc Mayes

02:45 EDT

Closing JointGareth Price • Frederik Coppens • Peter Cock • Harpreet Singh • Nomi Harris

03:15 EDT

Birds of a Feather (BOFs) Joint BoF: Computational Chemistry JointChris Barnett BoF: Microbial Bioinformatics with Galaxy JointPeter van Heusden

04:15 EDT

CollaborationFest: Core Joint

01:00 EDT

CollaborationFest: Encore Joint

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