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SK

sungyun kang

inidana university
research staff
Saturday, June 25
 

9:00am

Conference desk open LIB: Lobby, Herman B Wells Library

10:00am

Coding Hackathon LIB: Scholars' Commons - IQ-Wall, Herman B Wells Library Data Hackathon LIB: Scholars' Commons - Hazelbaker Lecture Hall, Herman B Wells Library

7:00pm

Training Office Hours LIB: Lobby, Herman B Wells Library
 
Sunday, June 26
 

8:00am

Conference desk open IMU Conference Lounge

9:00am

Introduction to Galaxy IMU Persimmon RoomAnton Nekrutenko Metagenomics with Galaxy IMU Maple RoomDaniel Blankenberg Galaxy Architecture IMU Oak RoomJohn Chilton • Nate Coraor Setting up a Galaxy instance as a service IMU Sassafras RoomJochen Bick • Hans-Rudolf Hotz • Nikolay Aleksandrov Vazov The Galaxy Docker Project IMU Walnut RoomEnis Afgan • Marius van den Beek • Björn Grüning

10:00am

Coding Hackathon LIB: Scholars' Commons - IQ-Wall, Herman B Wells Library Data Hackathon LIB: Scholars' Commons - Hazelbaker Lecture Hall, Herman B Wells Library

11:30am

Training lunch (catered) IMU Conference Lounge

12:30pm

Beyond the Intro: Further adventures in using Galaxy IMU Sassafras RoomDaniel Blankenberg Human Variant Calling with Galaxy IMU Persimmon RoomJessica Chung • Simon Gladman • Pip Griffin • Annette McGrath • Torsten Seemann Get your own Galaxy within minutes IMU Maple RoomEnis Afgan • Nuwan Goonasekera • Nitesh Turaga The Galaxy Database Schema IMU Oak RoomDave Clements • Hans-Rudolf Hotz Writing & Publishing Galaxy Tools IMU Walnut RoomMarius van den Beek • Dave Bouvier • John Chilton • Björn Grüning • Nicola Soranzo

3:00pm

Training Break IMU Conference Lounge

3:30pm

ChIPseq analysis using deepTools and MACS IMU Walnut RoomDevon Ryan RNA-seq analysis with Galaxy, using advanced workflows IMU Oak RoomJessica Chung • Simon Gladman • Pip Griffin • Annette McGrath • Torsten Seemann BioinforMagic: Marrying Galaxy and Bioconductor IMU Sassafras RoomMallory Freeberg • Nitesh Turaga How to use Galaxy Ansible Playbooks IMU Maple RoomEnis Afgan • Nate Coraor Introduction to Galaxy Interactive Environments IMU Persimmon RoomMarius van den Beek • John Chilton • Björn Grüning

7:30pm

Galactically Speaking: Best Practices and Resources for Galaxy Training IMU Oak RoomGalaxy Training Network Members

8:30pm

Training Office Hours IMU Hoosier Room
 
Monday, June 27
 

8:00am

Conference desk open IMU Conference Lounge

9:00am

Introduction to Galaxy IMU Sassafras RoomAnton Nekrutenko Small Genomes de novo Assembly and Scaffolding IMU Persimmon RoomJessica Chung • Simon Gladman • Pip Griffin • Annette McGrath • Torsten Seemann Dynamic prototyping of tools with Galaxy ProTo IMU Walnut RoomAbdulrahman Azab • Boris Simovski Galaxy on the Cloud: build it IMU Maple RoomEnis Afgan • Nuwan Goonasekera The Galaxy Docker Project IMU Oak RoomMarius van den Beek • Björn Grüning

11:30am

Training lunch (catered) IMU East Lounge Birds-of-a-Feather Flocking IMU: Indiana Memorial Union

12:30pm

Beyond the Intro: Further adventures in using Galaxy IMU Persimmon RoomDaniel Blankenberg Small Genome Annotation IMU Maple RoomJessica Chung • Simon Gladman • Pip Griffin • Annette McGrath • Torsten Seemann Using Galaxy for proteomic and integrative multi-omic data analysis IMU Walnut RoomTimothy Griffin • Pratik Jagtap • James (JJ) Johnson Advanced Topics in Galaxy Tool Development IMU Oak RoomMarius van den Beek • Dave Bouvier • John Chilton • Björn Grüning • Nicola Soranzo Contributing Code to the Galaxy Project IMU Sassafras RoomDannon Baker

3:00pm

Training Break IMU Conference Lounge

3:30pm

RADseq Data Analysis Through STACKS on Galaxy IMU Sassafras RoomYvan Le Bras • Anthony Bretaudeau • Gildas Le Corguillé RNA-seq analysis with Galaxy, using advanced workflows IMU Persimmon RoomJessica Chung • Simon Gladman • Pip Griffin • Annette McGrath • Torsten Seemann Visualization of Omics Datasets in Galaxy IMU Maple RoomJeremy Goecks • Aysam Guerler Advanced Topics in Galaxy Interactive Environments IMU Oak RoomMarius van den Beek • Dave Bouvier • John Chilton • Björn Grüning Scripting Galaxy using the API and BioBlend IMU Walnut RoomDannon Baker • Nicola Soranzo

7:00pm

Opening Reception with Bus Schedule Cyberinfrastructure Building
 
Tuesday, June 28
 

9:00am

Opening and Welcome IMU Alumni HallRobert Ping Session 1 IMU Alumni HallRobert Ping

9:15am

Keynote: Genomic variation. Impact of regulatory variation from RNA to protein IMU Alumni HallYoav Gilad

10:00am

Proteogenomics in Galaxy: Identifying novel ‘constellations’ of proteoforms using transcriptomic and proteomic data. IMU Alumni HallPratik Jagtap

10:20am

An Interactive Tool for Reproducible Analysis of Affinity Proteomics Data IMU Alumni HallPaul A. Stewart

10:40am

Break IMU Solarium

11:10am

Session 2 IMU Alumni HallTea Muelia

11:40am

Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics IMU Alumni HallDaniel Blankenberg

12:00pm

FROGS: Find Rapidly OTU with Galaxy Solution IMU Alumni HallYvan Le Bras

12:20pm

Ktoolu and idFusion - Galaxy Solutions for Plant Immunity and Pathogen Informatics IMU Alumni HallChristian Schudoma

12:40pm

Birds-of-a-Feather Flocking IMU: Indiana Memorial Union Lunch (catered) IMU Solarium

1:40pm

Galaxy Community Update IMU Alumni HallJeremy Goecks • Anton Nekrutenko • James Taylor Session 3 IMU Alumni HallChris Hemmerich

2:15pm

GSuite Tools: integrative genomic analyses across cells and epigenetic factors using Galaxy IMU Alumni HallBoris Simovski

2:35pm

The Galaxy workflow for epigenetic profiling of progressing melanoma IMU Alumni HallKatarzyna Murat • Krzysztof Poterlowicz

3:10pm

Poster Session 1: Odd numbers IMU Solarium

4:25pm

The LAPPS Grid and Galaxy IMU Alumni HallKeith Suderman Session 4 IMU Alumni HallSuzanna Lewis

5:30pm

Dinner & Socializing (on your own) TBA

7:00pm

Birds-of-a-Feather Flocking IMU: Indiana Memorial Union
 
Wednesday, June 29
 

8:00am

Conference desk open IMU Alumni Hall

9:00am

Session 5 IMU Alumni HallScott Michaels Welcome Day 2 IMU Alumni Hall

9:10am

Enhancements to Galaxy for delivering on NIH Commons IMU Alumni HallRavi K. Madduri

9:30am

Moving data from the warehouse to the workbench: a bridge to Galaxy from the Tripal community genome database software platform IMU Alumni HallMargaret Staton

9:50am

Apollo: Collaborative Manual Annotation for Genomic Sequencing Projects IMU Alumni HallNathan Dunn

10:10am

Accurate and Complete Gene Construction with EvidentialGene Pipeline IMU Alumni HallDon Gilbert

10:30am

Break IMU Solarium

11:00am

Galaxy security practices in an age of clinical data for point of care services IMU Alumni HallCarrie Ganote Session 6 IMU Alumni HallMargaret Staton

11:20am

Increasing Beer Time: Decreasing the Galaxy System Administration Burden IMU Alumni HallNate Coraor

11:40am

The Intergalactic Utilities Commission - driving Galaxy tool development IMU Alumni HallBjörn Grüning

12:00pm

Planemo – A Scientific Workflow SDK IMU Alumni HallJohn Chilton

12:20pm

CloudLaunch as a multi-cloud, multi-application launch platform IMU Alumni HallEnis Afgan

12:40pm

Birds-of-a-Feather Flocking IMU: Indiana Memorial Union Lunch (catered) IMU Solarium

1:40pm

FlowGalaxy: Developing a workflow for Flow Cytometry Analysis in Galaxy IMU Alumni HallCristel G. Thomas Session 7 IMU Alumni HallCarrie Ganote

2:00pm

Outbreak surveillance and investigation using IRIDA and SNVPhyl IMU Alumni HallAaron Petkau

2:20pm

Metavisitor, a suite of Galaxy tools and workflows for detection or discovery of viruses in NGS datasets IMU Alumni HallChristophe Antoniewski • Marius van den Beek

2:40pm

Chemflow, chemometrics using Galaxy IMU Alumni HallVirginie Rossard

3:15pm

Poster Session 2: Even numbers IMU Solarium Sponsor Exhibition IMU Solarium

4:30pm

Session 8 IMU Alumni HallNancy Wilkins-Diehr

7:00pm

Conference Dinner IMU Tudor Room