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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 are two days of training, a two day meeting, and two to four days of intense collaboration.  The meeting will feature joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events.  GCCBOSC brings together the widest possible community of bioinformatics developers and practitioners into a single event.  GCCBOSC is organized by Oregon Health & Science University and will be at Reed College.

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Sunday, June 24
 

3:00pm

Conference desk open
Checkin to your lodging and pick up your conference badge and materials.

Need to checkin after 10pm?  We'll provide a way.   

Sunday June 24, 2018 3:00pm - 10:00pm
PAB Atrium Performing Arts Building, Reed College
 
Monday, June 25
 

TBA

Training Day 1 - Galaxy

Monday June 25, 2018 TBA
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA

8:00am

Conference desk open
Monday June 25, 2018 8:00am - 10:00pm
PAB Atrium Performing Arts Building, Reed College

9:00am

Galaxy 101 - A gentle introduction to using Galaxy
Key:  BB | XB |  -  |  -  | GG |  -

This workshop will focus on introducing the Galaxy user interface and how it can be used to analyze large datasets. We will cover the basic features of Galaxy, including where to find tools, how to import and use your data, and an introduction to workflows. This session is recommended for anyone who has not used, or only rarely uses Galaxy.
First of 3 sessions in the Introduction to Using Galaxy series.
Prerequisites:
  • Little or no experience using Galaxy.
  • A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best.


Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
University of Freiburg


Monday June 25, 2018 9:00am - 11:30am
PAB 320 Performing Arts Building, Reed Campus

9:00am

Intro to Galaxy Administration 1
Key:  -  |  -  | IP |  -  |  -  | CL

These 3 workshops introduce Galaxy administration, including
  • installing and configuring your own server
  • customizing your set of reference genomes
  • installing tools from the Galaxy Tool Shed
  • defining custom tools with Planemo
  • users and groups
  • storage management and quotas
  • and more 
Prerequisites:
  • Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in these workshops

Speakers
avatar for Martin Čech

Martin Čech

Dev, Galaxy Project, Penn State University
Galaxy Project, Penn State University


Monday June 25, 2018 9:00am - 11:30am
PAB 105 Performing Arts Building, Reed Campus

11:30am

Lunch
Monday lunch will be in the Reed Commons Cafe.  You'll pay for lunch with the swipe card issued to you when you checkin for the conference.

Monday June 25, 2018 11:30am - 12:30pm
Reed Commons Cafe Reed College Commons, Reed Campus

12:30pm

Intro to Galaxy Administration 2
Key:  -  |  -  | IP |  -  |  -  | CL

These 3 workshops introduce Galaxy administration, including
  • installing and configuring your own server
  • customizing your set of reference genomes
  • installing tools from the Galaxy Tool Shed
  • defining custom tools with Planemo
  • users and groups
  • storage management and quotas
  • and more 
Prerequisites:
  • Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in these workshops

Speakers
avatar for Martin Čech

Martin Čech

Dev, Galaxy Project, Penn State University
Galaxy Project, Penn State University


Monday June 25, 2018 12:30pm - 3:00pm
PAB 105 Performing Arts Building, Reed Campus

12:30pm

RNA-Seq Analysis with Galaxy
Key:  BB | XB |  -  |  -  | GG |  -

This workshop will introduce the concepts behind transcriptomics with NGS data and how to analyze this data in Galaxy. Specifically, this workshop will focus on de novo transcriptome reconstruction of RNA-seq data with the following goals:
  • comprehensive identification of all transcripts across an experiment
  • appropriately annotating classes of transcripts
  • generating abundance estimates across a transcriptome
  • significance testing of differentially expressed transcripts
  • visualisation of reads and transcript structures
Second of 3 sessions in the Introduction to Using Galaxy series.
Prerequisites:
  • a general knowledge of Galaxy (for example, you should be familiar with the material in Galaxy 101 or have attended Introduction to Galaxy).
  • a wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best.

Speakers
avatar for Anton Nekrutenko

Anton Nekrutenko

Galaxy Project, Penn State University
Penn State University


Monday June 25, 2018 12:30pm - 3:00pm
PAB 320 Performing Arts Building, Reed Campus

3:00pm

Break
Breaks on Monday will be in the Reed Commons.

Monday June 25, 2018 3:00pm - 3:30pm
Reed Commons Cafe Reed College Commons, Reed Campus

3:30pm

Galaxy For Proteogenomics !
Key:  BB | XB |  -  |  -  | GG |  -

Large-scale ‘omics’ data generation is driven by high throughput genome and transcriptome sequencing, and proteome characterization using mass spectrometry. As a result, many researchers are turning to generating integrative analysis of these ‘multi-omics’ datasets given the great potential to provide novel biological insights. These multi-omics applications are particularly challenging for data analysis, as they require the use of multiple, domain-specific software programs on scalable infrastructure capable of handling the computing and storage needs of this large-scale data.
Galaxy has been shown to solve the problems of software integration and scalability for multi-omics analysis, and additionally offer benefits for sharing complete workflows in a user-friendly environment accessible by wet-bench scientists. In this workshop, we will introduce the use of Galaxy platform for multi-omics data analysis applications. As a representative example, we will focus on the maturing field of proteogenomic applications. Proteogenomics most commonly integrates RNA-Seq data, for generating customized protein sequence databases, with mass spectrometry-based proteomics data, which are matched to these databases to identify novel protein sequence variants. (Cancer Res. (2017); 77(21):e43-e46. doi: 10.1158/0008-5472.CAN-17-0331.)
Workshop Content:
The course will include a basic introduction to proteomics and will include a hands-on session that will cover use of analytical workflows to generate proteomic databases from RNASeq data. The use and understanding of modules for analytical workflows for proteogenomics analysis will be discussed.
Workshop Schedule:
  • Introduction to multi-omic studies
  • RNASeq Data Processing: Generating protein sequence search databases using Galaxy platform
  • Hands-on session for proteomics data analysis using Galaxy
  • Identification of novel proteoforms and visualization
Workshop Goals:
  • Introduce the Galaxy framework as a solution for data analysis across ‘omics’ domains
  • Demonstrate use of Galaxy for a proteogenomic analysis (RNA-seq and proteomic integrative analysis)
  • Lay the foundation for attendees to implement Galaxy at their own facility or institution to meet ‘omics’ data analysis and informatics needs
Third of 3 sessions in the Introduction to Using Galaxy series.
Prerequisites:
  • a general knowledge of Galaxy (for example, you should be familiar with the material in Galaxy 101 or have attended Introduction to Galaxy).
  • a wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best.

Speakers
avatar for Tim Griffin

Tim Griffin

Center for Mass Spectrometry and Proteomics, University of Minnesota
University of Minnesota
avatar for Pratik Jagtap

Pratik Jagtap

Research assistant Professor, University of Minnesota
University of Minnesota
avatar for JJ Johnson

JJ Johnson

Minnesota Supercomputing Institute, University of Minnesota
University of Minnesota
avatar for Praveen Kumar

Praveen Kumar

Graduate Student, University of Minnesota
avatar for Subina Mehta

Subina Mehta

Researcher, University of Minnesota


Monday June 25, 2018 3:30pm - 6:00pm
PAB 320 Performing Arts Building, Reed Campus

3:30pm

Intro to Galaxy Administration 3
Key:  -  |  -  | IP |  -  |  -  | CL

These 3 workshops introduce Galaxy administration, including
  • installing and configuring your own server
  • customizing your set of reference genomes
  • installing tools from the Galaxy Tool Shed
  • defining custom tools with Planemo
  • users and groups
  • storage management and quotas
  • and more 
Prerequisites:
  • Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in these workshops

Speakers
avatar for Martin Čech

Martin Čech

Dev, Galaxy Project, Penn State University
Galaxy Project, Penn State University


Monday June 25, 2018 3:30pm - 6:00pm
PAB 105 Performing Arts Building, Reed Campus

6:00pm

Dinner on your own
Dinner is on your own on Monday night.  The Woodstock neighborhood is nearby and has many choices.  The Reed Commons may also be open for dinner (watch this space).

Monday June 25, 2018 6:00pm - 7:30pm
TBA

7:30pm

Bioinformatics Training and Education with the Galaxy Training Network
Key:  -  | XB | IP |  -  | GG |  -

Galaxy with its flexibility, reproducibility, and scalability is an ideal environment for teaching and training diverse scientific topics.
The Galaxy Training Network is a community initiative dedicated to high-quality Galaxy-based training around the world. One of its objectives is to support trainers with complete training material and recommendations about bioinformatics training. Templates and best training practices were defined to help trainers create new material, unify the different material, and make training materials more accessible and easy for users to learn and for teachers to teach (https://training.galaxyproject.org).
This workshop will introduce participants to the infrastructure of the GTN training materials and describe how to generate training materials following best practices. Participants will be introduced to the generation of Galaxy Interactive Tours and Docker Galaxy flavors dedicated to teaching and training sessions. The workshop will also cover best practices for running Galaxy-based workshops - how to plan a training session based on number of attendees, time constraints, resource availability, etc.

Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
University of Freiburg


Monday June 25, 2018 7:30pm - 10:00pm
PAB 320 Performing Arts Building, Reed Campus
 
Tuesday, June 26
 

TBA

Training Day 2 - All topics
Tuesday offers 5 parallel tracks and presents a wide range of topics throughout the day.  Topics were nominated and then voted on by the Galaxy and OBF communities.  


Tuesday June 26, 2018 TBA
TBA

8:00am

Conference desk open
Checkin for today or tomorrow and pickup your conference registration materials.

Tuesday June 26, 2018 8:00am - 9:10pm
Vollum College Center Lobby

9:00am

Community built analyses that run everywhere with bcbio
Key:  -  | XB | IP |  -  |  -  | CL

bcbio
 is community built analyses for germline and somatic variant calling, RNA-seq, single cell, smallRNA and ChIP-seq. This workshop will focus on using bcbio to run analysis pipelines in heterogenous environments -- local machines, HPC, cloud providers and commercial services (and also hopefully Galaxy). Attendees will learn how to practically run their analyses on their platform of choice, while discussing how the community can contribute to building, sharing and maintaining workflows across multiple platforms. Recent presentations of bcbio show some of the topics we plan to cover.

Prerequisites


Speakers
avatar for Brad Chapman

Brad Chapman

Bioinformatics Core, Harvard Chan School
Biologist and Programmer
RS

Radhika S. Khetani

Harvard T.H. Chan School of Public Health
avatar for Lorena Pantano Rubino

Lorena Pantano Rubino

Research Scientist, Harvard Chan School
I work with small RNAs, mainly detected through sequencing technology. I like visualization and multi-omic integration methods. :)


Tuesday June 26, 2018 9:00am - 11:30am
Training Venue 2

9:00am

Conda and Containers
Key:  -  |  -  | IP | TD |  -  | CL

This workshop is aimed at people with some desire to develop dependencies for tools (either Galaxy or Common Workflow Language (CWL) tools).
We believe the best practice for declaring dependencies for either Galaxy or the CWL is using Conda and Bioconda. Conda is a cross platform package manager that has minimal requirements to use which makes it ideal for HPC. It can also build isolated environments ideal for platforms like Galaxy or CWL implementations. The Bioconda project is a set of Conda recipes for bioinformatics. The BioContainers project builds best practice containers automatically for all Bioconda recipes, so building a BioConda recipe for a package allows the same binaries to be used by both Galaxy (inside or outside a container) and by any conformant CWL implementation.
We will go through the process of creating, testing, and publishing a Bioconda package and we will work through an example of connecting these packages to a real world tool. Participants will be able to work through the examples using either Galaxy or CWL tools.
Prerequisites
  • Some knowledge of tool development - either CWL or Galaxy.
  • Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in these workshops

Speakers
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
Galaxy Project, Penn State Universtiy
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg
avatar for Martin Čech

Martin Čech

Dev, Galaxy Project, Penn State University
Galaxy Project, Penn State University


Tuesday June 26, 2018 9:00am - 11:30am
Training Venue 1

9:00am

Data Carpentry Genomics Workshop: Data Organization and Automation with Shell I
Key:  BB | XB |  -  |  -  | GG | CL

This is the first session of a 3 session series.

The goal of this one-day, three-part tutorial is to teach participants the fundamental data management and analysis skills and needed to conduct genomics research including: best practices for organization of bioinformatics projects and data as well as use of command line utilities for managing large volumes of genomic data. This tutorial is derived from the Data Carpentry Genomics Workshop, focused on the organization and intro to command line lessons. The tutorial uses active learning and hands-on practice to teach participants the skills and perspectives needed to work effectively with genomic data. Data Carpentry’s aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain.
Lessons:
The tutorial assumes no prior experience with the tools covered. However, learners are expected to have some familiarity with biological concepts, including nucleotide abbreviations. Participants should bring their laptops and plan to participate actively.
Prerequisites



Speakers
avatar for Tracy K. Teal

Tracy K. Teal

Executive Director, The Carpentries
Dr. Teal is the Executive Director of The Carpentries and a co-founder of Data Carpentry. After completing her PhD in Computation and Neural Systems at California Institute of Technology, her work as an NSF Postdoctoral Fellow focused on bioinformatics approaches to metagenomics and microbial community analysis. Then as an Assistant Professor of Microbiology and Molecular Genetics at Michigan State University she continued this work and developed training in bioinformatics and high performance computing. Through these training efforts, she saw that effective data skills are now foundational for research and the need for data training to scale along with data production. She co-founded Data Carpentry to develop and scale this training and Data Carpentry has now joined... Read More →


Tuesday June 26, 2018 9:00am - 11:30am
Training Venue 5

9:00am

Handling integrated biological data using Python (or R) and InterMine
Key:  BB | XB |  -  |  -  | GG | CL

This tutorial will guide you through loading and analyzing integrated biological data (generally genomic or proteomic) in InterMine via an API in Python or R. Topics covered will include automatically generating code to perform queries, customising the code to meet your needs, and automated analysis of sets, e.g gene sets, including enrichment statistics. Skills gained can be re-used in any of the dozens of InterMines available, covering a broad range of organisms and dedicated purposes, from model organisms to plants, drug targets, and mitochondrial DNA.
Prerequisites
  • Basic Python or R skills are advantageous but not required.
  • WiFi-enabled laptop with Python or R Studio.

Speakers
avatar for Daniela Butano

Daniela Butano

Research SofwareEngineer, InterMine, University of Cambridge
LR

Leyla Ruzicka

ZFIN, University of Oregon
avatar for Yo Yehudi

Yo Yehudi

Software Developer, InterMine (University of Cambridge)
Integrated genomic data (InterMine)


Tuesday June 26, 2018 9:00am - 11:30am
Training Venue 4

9:00am

WDL: the Workflow Description Language
Key:  -  | XB | IP | TD |  -  | CL

The advent of open, portable workflow languages is an exciting development which allows for the definition of a workflow to be decoupled from the execution. One can create workflows which can run unmodified on local compute, HPC clusters, or the cloud. As these languages are not tied to a specific execution environment, the descriptions can easily be shared, discovered and even composed together to form more complex workflows. The Workflow Description Language (WDL) is an open, community driven standard that is designed from the ground up as a human-readable and -writable way to express portable tasks and workflows.
In this session we’ll walk through the lifecycle of writing, sharing and discovering portable workflows in WDL. We’ll introduce the WDL syntax. You’ll learn how to write and run a workflow locally. We’ll demonstrate how to use EPAM’s Pipeline Builder toolto visualize WDL workflows. We’ll look at Dockstore, an open platform where one can publish, share and discover workflows. Finally we’ll put everything together and see how we can compose workflows we find on Dockstore together with our own additions to create new, more powerful workflows.
Prerequisites:
  • Mac or Linux computer
  • Java 8 installed and runnable from the command line
  • A workshop bundle downloaded from TBD

Speakers
avatar for Geraldine Van der Auwera

Geraldine Van der Auwera

Associate Director of Outreach and Communications, Broad Institute
I run outreach and communication efforts to the global scientific research community on behalf of the Data Sciences Platform (DSP) at the Broad Institute. My team's efforts include technical support, documentation, social media presence and user education events for users of soft... Read More →
avatar for Jeff Gentry

Jeff Gentry

Senior Principal Software Engineer, Broad Institute
Jeff leads the development of the Cromwell workflow engine at the Broad Institute and is in the leadership groups for both the Workflow Description Language (WDL) as well as the Common Workflow Language (CWL). He has over 15 years of experience developing software for the bioinfo... Read More →
CL

Chris Llanwarne

Broad Institute


Tuesday June 26, 2018 9:00am - 11:30am
Training Venue 3

11:30am

Lunch
Tuesday lunch will be in the Reed Commons Cafe.  You pay for lunch with the swipe card issued to you when you checkin for the conference.

Tuesday June 26, 2018 11:30am - 12:30pm
Reed Commons Cafe Reed College Commons, Reed Campus

12:30pm

Data Carpentry Genomics Workshop: Data Organization and Automation with Shell II
Key:  BB | XB |  -  |  -  | GG | CL

This is the second session of a 3 session series.

The goal of this one-day, three-part tutorial is to teach participants the fundamental data management and analysis skills and needed to conduct genomics research including: best practices for organization of bioinformatics projects and data as well as use of command line utilities for managing large volumes of genomic data. This tutorial is derived from the Data Carpentry Genomics Workshop, focused on the organization and intro to command line lessons. The tutorial uses active learning and hands-on practice to teach participants the skills and perspectives needed to work effectively with genomic data. Data Carpentry’s aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain.
Lessons:
The tutorial assumes no prior experience with the tools covered. However, learners are expected to have some familiarity with biological concepts, including nucleotide abbreviations. Participants should bring their laptops and plan to participate actively.
Prerequisites

Speakers
avatar for Tracy K. Teal

Tracy K. Teal

Executive Director, The Carpentries
Dr. Teal is the Executive Director of The Carpentries and a co-founder of Data Carpentry. After completing her PhD in Computation and Neural Systems at California Institute of Technology, her work as an NSF Postdoctoral Fellow focused on bioinformatics approaches to metagenomics and microbial community analysis. Then as an Assistant Professor of Microbiology and Molecular Genetics at Michigan State University she continued this work and developed training in bioinformatics and high performance computing. Through these training efforts, she saw that effective data skills are now foundational for research and the need for data training to scale along with data production. She co-founded Data Carpentry to develop and scale this training and Data Carpentry has now joined... Read More →


Tuesday June 26, 2018 12:30pm - 3:00pm
Training Venue 5

12:30pm

Galaxy Interactive Environments
Key:  -  |  -  | IP |  -  |  -  | CL

In this session you will get in-depth introduction to Interactive Environments (IE). You will learn how to setup and secure IE’s (JupyterRStudio, etc.) in a production Galaxy instance. Moreover, we will create an IE on-the-fly to get you started in creating your own Interactive Environments.In this session you will get an introduction to Interactive Environments (IE) as an easy and powerful way to integrate arbitrary interactive web services into Galaxy. We will demonstrate the IPython Galaxy Project and the general concept of IE’s.
Prerequisites:
  • Basic understanding of Galaxy from a developer point of view.
  • General knowledge about Docker
  • Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in this workshop.
  • A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best.

Speakers
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg


Tuesday June 26, 2018 12:30pm - 3:00pm
Training Venue 1

12:30pm

Introduction to Common Workflow Language
Key:  -  | XB | IP | TD |  -  | CL

Common Workflow Language (http://commonwl.org) is a standard for writing portable scientific workflows that can execute on a variety of compute environments and workflow systems.
  • What is CWL, history
  • Status of CWL implementations (Arvados, Toil, Rabix, Galaxy, Cromwell, cwtool, ...)
  • Wrapping bioinformatics tools in CWL
  • Connecting tools together into workflows
  • Best practices for writing portable workflows
  • Hands on "bring your own pipeline" session
  • Q&A on advanced topics based on audience
Prerequisites
  • Unix command line experience
  • Experience with Docker

Speakers
avatar for Michael R. Crusoe

Michael R. Crusoe

Project Lead & Co-founder, Common Workflow Language
Michael R. Crusoe is one of the co-founders of the CWL project and is the CWL Project Lead. His facilitation, technical contributions, and training on behalf of the project draw from his time as the former lead developer of C. Titus Brown's k-h-mer project, his previous career as... Read More →


Tuesday June 26, 2018 12:30pm - 3:00pm
Training Venue 2

12:30pm

Practical use of the Galaxy API command line tools
Key:  -  | XB | IP | TD |  -  | CL

How to use the Galaxy API to automate workflows.
Galaxy has an always-growing API that allows for external programs to upload and download data, manage histories and datasets, run tools and workflows, and even perform admin tasks. This session will cover various approaches to access the API, in particular using the BioBlend Python library.
Prerequisites
  • Unix command line
  • Basic understanding of Galaxy from a developer point of view.
  • Python programming.
  • A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best.

Speakers
avatar for Dannon Baker

Dannon Baker

Galaxy Project, Johns Hopkins University
Galaxy Project, Johns Hopkins University
avatar for Marius van den Beek

Marius van den Beek

Institut Curie, Paris
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute


Tuesday June 26, 2018 12:30pm - 3:00pm
Training Venue 4

12:30pm

Setting up for success: Everything you need to know when planning for an RNA-seq analysis I
Key:  BB | XB |  -  |  -  |  -  |  -

Note: This is the first session of a two-session workshop.


This two-part workshop is geared towards researchers who are thinking about conducting an RNA-seq experiment and are interested in knowing more about what is involved. The planning process requires taking a step back to evaluate various factors and ultimately assess the feasibility of the experiment, including thinking about potential pitfalls and how to avoid them. The workshop will go into detail about the different strategies for working with RNA-seq data depending on the biological question being addressed. Specific topics include:
  • Best practice guidelines for experimental design (Biological replicates, Paired-end vs Single-end, Sequencing depth).
  • Data storage and computational requirements.
  • Overview of commonly used workflows for differential gene expression, de-novo assembly, isoform quantification and other uses of RNA sequencing.
The focus of this workshop is to outline current standards and required resources for the analysis of RNA sequencing data. This workshop will not provide an exhaustive list of software tools or pipelines available; rather it aims to provide a fruitful discussion on how best to prepare for performing RNA-seq data analysis from the lab to manuscript preparation.
Prerequisites:
  • None

Speakers
MM

Meeta Mistry

Bioinformatics Analyst and Trainer, Harvard T.H Chan School of Public Health
I'm a wet-lab bench scientist turned bioinformatician who loves to play with data. When I am not consulting in bioinformatics analysis, I am teaching it.
MP

Mary Piper

Harvard T.H. Chan School of Public Health


Tuesday June 26, 2018 12:30pm - 3:00pm
Training Venue 3

3:00pm

Break
Breaks on Tuesday will be close the training venues.

Tuesday June 26, 2018 3:00pm - 3:30pm
TBA

3:30pm

Command line workflow management systems: Snakemake and Nextflow
Key:  -  | XB | IP | TD |  -  | CL

This session introduces command line and text based workflow management systems by the examples of Snakemake and Nextflow. We will start with an overview of concepts and challenges then spend an hour on each of these platforms.
Snakemake
We will show how to define a workflow in the Snakemake workflow language, and how to execute it using the Snakemake command line interface. In particular, we will show how Snakemake enables reproducible science by allowing
  • automation of every step of a data analysis from raw data to final figures
  • scalability of the workflow to any major computing architecture (compute server, cluster, grid, cloud) without having to modify the workflow definition
  • portability of the workflow by integration with the Conda package manager and Singularity containers.
Nextflow
This session will introduce the Nextflow framework, the tool basic concepts and how it enables the definition and the deployment of large-scale distributed computational pipeline in a portable and reproducible manner across cloud and clusters. In particular it will be discussed:
  • installation and introduction to the dataflow processing model
  • workflows parallelisation and scalability
  • portable workflows containerisation with Docker, Singularity and Shifter
  • cloud deployment strategies
Prerequisites
  • Linux command line experience

Speakers
JK

Johannes Köster

Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen | Department of Medical Oncology, Harvard Medical School | https://koesterlab.github.io
avatar for Paolo Di Tommaso

Paolo Di Tommaso

Research Software engineer, Center for Genomic Regulation (CRG)


Tuesday June 26, 2018 3:30pm - 6:00pm
Training Venue 1

3:30pm

Data Carpentry Genomics Workshop: Data Organization and Automation with Shell III
Key:  BB | XB |  -  |  -  | GG | CL

This is the third session of a 3 session series.

The goal of this one-day, three-part tutorial is to teach participants the fundamental data management and analysis skills and needed to conduct genomics research including: best practices for organization of bioinformatics projects and data as well as use of command line utilities for managing large volumes of genomic data. This tutorial is derived from the Data Carpentry Genomics Workshop, focused on the organization and intro to command line lessons. The tutorial uses active learning and hands-on practice to teach participants the skills and perspectives needed to work effectively with genomic data. Data Carpentry’s aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain.
Lessons:
The tutorial assumes no prior experience with the tools covered. However, learners are expected to have some familiarity with biological concepts, including nucleotide abbreviations. Participants should bring their laptops and plan to participate actively.
Prerequisites

Speakers
avatar for Tracy K. Teal

Tracy K. Teal

Executive Director, The Carpentries
Dr. Teal is the Executive Director of The Carpentries and a co-founder of Data Carpentry. After completing her PhD in Computation and Neural Systems at California Institute of Technology, her work as an NSF Postdoctoral Fellow focused on bioinformatics approaches to metagenomics and microbial community analysis. Then as an Assistant Professor of Microbiology and Molecular Genetics at Michigan State University she continued this work and developed training in bioinformatics and high performance computing. Through these training efforts, she saw that effective data skills are now foundational for research and the need for data training to scale along with data production. She co-founded Data Carpentry to develop and scale this training and Data Carpentry has now joined... Read More →


Tuesday June 26, 2018 3:30pm - 6:00pm
Training Venue 5

3:30pm

Galaxy Architecture
Key:  -  |  -  | IP |  -  |  -  |  -

Want to know the big picture about what is going on inside Galaxy? This workshop will give participants a practical introduction to the Galaxy code base with a focus on changing those parts of Galaxy most often modified by local deployers and new contributors.
The workshop will include the following specific content:
  • A description of the various file and top-level directories in the Galaxy code base.
  • An overview of important Python modules - including models, tools, jobs, workflows, visualisations, and API controllers.
  • An overview of important Python objects and concepts in the Galaxy codebase - including the Galaxy transaction object ("trans"), the application object ("app") , and the configuration object ("config").
  • An overview of various plugin extension points. - An overview of important JavaScript modules that power the front-end.
  • An overview of important JavaScript concepts used by Galaxy - in particular Backbone MVC, Webpack, ES6, and Vue.
  • An overview of the client build system used to generate compressed JavaScript, cascading stylesheets, and other static web assets.
  • A demonstration of a complete start-to-finish modification of Galaxy - including forking the project on Github, modifying files, running the tests, checking style guidelines, committing the change, pushing it back to your local Github fork, and opening a pull request.
  • A brief description of other projects in the Galaxy ecosystem (CloudMan, the Tool Shed, Ephemeris, bioblend, docker-galaxy-stable, Pulsar, and Planemo).
Prerequisites:
  • Your interest.

Speakers
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
Galaxy Project, Penn State Universtiy
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University
Galaxy Project, Penn State University


Tuesday June 26, 2018 3:30pm - 6:00pm
Training Venue 4

3:30pm

GATK4: What's new and how to run it
Key:  BB | XB |  -  |  -  | GG | CL

The advent of open, portable workflow languages is an exciting development which allows for the definition of a workflow to be decoupled from the execution. One can create workflows which can run unmodified on local compute, HPC clusters, or the cloud. As these languages are not tied to a specific execution environment, the descriptions can easily be shared, discovered and even composed together to form more complex workflows. The Workflow Description Language (WDL) is an open, community driven standard that is designed from the ground up as a human-readable and -writable way to express portable tasks and workflows.
In this session we’ll walk through the lifecycle of writing, sharing and discovering portable workflows in WDL. We’ll introduce the WDL syntax. You’ll learn how to write and run a workflow locally. We’ll demonstrate how to use EPAM’s Pipeline Builder toolto visualize WDL workflows. We’ll look at Dockstore, an open platform where one can publish, share and discover workflows. Finally we’ll put everything together and see how we can compose workflows we find on Dockstore together with our own additions to create new, more powerful workflows.
Prerequisites:
  • Mac or Linux computer
  • Java 8 installed and runnable from the command line
  • A workshop bundle downloaded from TBD

Speakers
avatar for Geraldine Van der Auwera

Geraldine Van der Auwera

Associate Director of Outreach and Communications, Broad Institute
I run outreach and communication efforts to the global scientific research community on behalf of the Data Sciences Platform (DSP) at the Broad Institute. My team's efforts include technical support, documentation, social media presence and user education events for users of soft... Read More →


Tuesday June 26, 2018 3:30pm - 6:00pm
Training Venue 2

3:30pm

Setting up for success: Everything you need to know when planning for an RNA-seq analysis II
Key:  BB | XB |  -  |  -  |  -  |  -

Note: This is the second session of a two-session workshop.


This two-part workshop is geared towards researchers who are thinking about conducting an RNA-seq experiment and are interested in knowing more about what is involved. The planning process requires taking a step back to evaluate various factors and ultimately assess the feasibility of the experiment, including thinking about potential pitfalls and how to avoid them. The workshop will go into detail about the different strategies for working with RNA-seq data depending on the biological question being addressed. Specific topics include:
  • Best practice guidelines for experimental design (Biological replicates, Paired-end vs Single-end, Sequencing depth).
  • Data storage and computational requirements.
  • Overview of commonly used workflows for differential gene expression, de-novo assembly, isoform quantification and other uses of RNA sequencing.
The focus of this workshop is to outline current standards and required resources for the analysis of RNA sequencing data. This workshop will not provide an exhaustive list of software tools or pipelines available; rather it aims to provide a fruitful discussion on how best to prepare for performing RNA-seq data analysis from the lab to manuscript preparation.
Prerequisites:
  • None

Speakers
RS

Radhika S. Khetani

Harvard T.H. Chan School of Public Health
MM

Meeta Mistry

Bioinformatics Analyst and Trainer, Harvard T.H Chan School of Public Health
I'm a wet-lab bench scientist turned bioinformatician who loves to play with data. When I am not consulting in bioinformatics analysis, I am teaching it.
MP

Mary Piper

Harvard T.H. Chan School of Public Health


Tuesday June 26, 2018 3:30pm - 6:00pm
Training Venue 3

6:20pm

Birds-of-a-Feather (BoFs), With Your Dinner!
Birds-of-a-feather are infornal gatherings or participants with a shared interest.  Anyone can organize a BoF session.  The BoF call will go out this spring, and we will accept BoF topics from then until we run out of space for them.

While BoFs tend to be informal, BoFsWYD! will be especially informal, as these will meet over dinner at a restaurant in the nearby Woodstock neighborhood.  Interactions and conversation will likely happen in smaller groups much of the time.

We suggest that BoFsWYD! groups flock outside of the Vollum College Center and depart on foot for Woodstock at 6:20.  You can talk along the way too.

Tuesday June 26, 2018 6:20pm - 7:40pm
TBA

8:00pm

Joint BOSC & GCC: Opening Session
Conference welcome and opening keynote address.  Anyone registered for training on Tuesday or for the meeting on Wednesday and Thursday is welcome to attend this session.

Tuesday June 26, 2018 8:00pm - 9:10pm
Vollum Lecture Hall Vollum College Center, Reed Campus

8:10pm

Opening Keynote: Tracy K. Teal
Dr. Teal is the Executive Director of The Carpentries and a co-founder of.  She co-founded Data Carpentry to develop and scale this training. Data Carpentry has now joined with Software Carpentry to form The Carpentries and more broadly meet training and community needs. She is involved in the open source software and reproducible research communities, including as an Editor at the Journal for Open Source Software.

Tracy's keynote is sponsored by BOSC.

Speakers
avatar for Tracy K. Teal

Tracy K. Teal

Executive Director, The Carpentries
Dr. Teal is the Executive Director of The Carpentries and a co-founder of Data Carpentry. After completing her PhD in Computation and Neural Systems at California Institute of Technology, her work as an NSF Postdoctoral Fellow focused on bioinformatics approaches to metagenomics and microbial community analysis. Then as an Assistant Professor of Microbiology and Molecular Genetics at Michigan State University she continued this work and developed training in bioinformatics and high performance computing. Through these training efforts, she saw that effective data skills are now foundational for research and the need for data training to scale along with data production. She co-founded Data Carpentry to develop and scale this training and Data Carpentry has now joined... Read More →


Tuesday June 26, 2018 8:10pm - 9:10pm
Vollum Lecture Hall Vollum College Center, Reed Campus
 
Wednesday, June 27
 

8:00am

Help Desk Open
The help desk will be in the Performing Arts Building on Wednesday and Thursday during select times.  You owon't be able to register at the Help Desk, but you will be able to get information about the conference, and sponsor, poster, and demo setup as well (all are in the PAB Atrium).

Wednesday June 27, 2018 8:00am - 10:50am
PAB Atrium Performing Arts Building, Reed College

8:00am

Conference desk open
Pick up your registration materials here.

Wednesday June 27, 2018 8:00am - 5:30pm
Vollum College Center Lobby

9:00am

Keynote: Fernando Pérez
Dr. Pérez is an assistant professor in Statistics at UC Berkeley and a Faculty Scientist in the Department of Data Science and Technology at Lawrence Berkeley National Laboratory. He created IPython and co-founded its successor, Project Jupyter.

Fernando's keynote is sponsored by BOSC and GCC.

Speakers
avatar for Fernando Pérez

Fernando Pérez

Assistant Professor, Berkeley Institute for Data Science, University of California Berkeley
Dr. Pérez is an assistant professor in Statistics at UC Berkeley and a Faculty Scientist in the Department of Data Science and Technology at Lawrence Berkeley National Laboratory. After completing a PhD in particle physics at the University of Colorado at Boulder, his postdoctoral research in applied mathematics centered on the development of fast algorithms for the solution of partial differential equations in multiple dimensions. Today, his research focuses on creating tools for modern computational research and data science across domain disciplines, with an emphasis on high-level languages, interactive and literate computing, and reproducible research. He created IPython while a graduate student in 2001 and co-founded its... Read More →


Wednesday June 27, 2018 9:00am - 10:00am
Vollum Lecture Hall Vollum College Center, Reed Campus

9:00am

Joint BOSC & GCC Session 1
This joint session will start with a keynote, followed by an accepted talk.
 

Wednesday June 27, 2018 9:00am - 10:20am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:00am

The journey of a team of engineers in learning packaging technology
Authors
Laure Quintric 1, Patrick Durand 1, Olivier Inizan 2, Valentin Marcon 2, Caroline Dussart 1, Valentin Loux 2, Maria Bernard 3, Géraldine Pascal 4

  1. IRSI-RIC-Cellule Bioinformatique, IFREMER, 29280 Plouzané, France.
  2. INRA, UR1404,MaIAGE,Université Paris-Saclay, Jouy en Josas, France. 
  3. GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France. 
  4. GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France.


Wednesday June 27, 2018 10:00am - 10:20am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:20am

Break
Head over to the Performing Arts building for a stretch, refreshments, and conversation.

Wednesday June 27, 2018 10:20am - 10:50am
PAB Atrium Performing Arts Building, Reed College

10:20am

Sponsors
Sponsors make GCCBOSC possible and affordable, and they are your potential partners in research.  Take some time during the Poster and Demo sessions to visit them and find out how they can help you do your research.


Wednesday June 27, 2018 10:20am - 10:50am
PAB Atrium Performing Arts Building, Reed College

10:50am

Storage Media Federation for Galaxy
Authors
Vahid Jalili 1, Enis Afgan 2, Nuwan Goonasekera 3, Dannon Baker 2, Jeremy Goecks 1

  1. Oregon Health and Science University, Portland, OR, USA, 
  2. Johns Hopkins University, Baltimore, MD, USA
  3. University of Melbourne, Melbourne, Australia.


A GCC Talk

Speakers
VJ

Vahid Jalili

Galaxy Project, Oregon Health & Science University


Wednesday June 27, 2018 10:50am - 11:10am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:50am

BOSC: Session 2
The first BOSC session of GCCBOSC 2018.  The session will include accepted oral presentations from BOSC community members. 

Wednesday June 27, 2018 10:50am - 12:10pm
Eliot Chapel Eliot Hall, Reed Campus

10:50am

GCC Session 2: Galaxy Infrastructure
The first Galaxy Community Conference session of GCCBOSC 2018.  The session will include accepted oral presentations from the Galaxy community. 

Wednesday June 27, 2018 10:50am - 12:10pm
Vollum Lecture Hall Vollum College Center, Reed Campus

11:10am

From laptop to super-computer: standardizing installation and management of Galaxy
Authors
Nuwan Goonasekera 1, Enis Afgan 2, Vahid Jalili 3

  1. University of Melbourne, Melbourne, Australia
  2. Johns Hopkins University, Baltimore, MD, USA
  3. Oregon Health and Science University, Portland, OR, USA

Speakers
NG

Nuwan Goonasekera

University of Melbourne


Wednesday June 27, 2018 11:10am - 11:30am
Vollum Lecture Hall Vollum College Center, Reed Campus

11:30am

Testing Wide-Area Lustre File Systems for Sharing load in Galaxy
Authors
CarrieGanote 1, Philip Blood 2, Bhavya NP 1, Sheri Sanders 1, Thomas Doak 1

  1. Indiana University Bloomington.
  2. PittsburghSupercomputingCenter.


Speakers
avatar for Carrie Ganote

Carrie Ganote

Indiana University Bloomington


Wednesday June 27, 2018 11:30am - 11:50am
Vollum Lecture Hall Vollum College Center, Reed Campus

11:50am

Lightning Talks ⚡
Lightning talks are short talks that concisely communicate resources, work in progress and other topics that lend themselves to just a few minutes coverage and a few slides.

Wednesday June 27, 2018 11:50am - 12:10pm
Vollum Lecture Hall Vollum College Center, Reed Campus

12:10pm

Help Desk Open
The help desk will be in the Performing Arts Building on Wednesday and Thursday during select times.  You owon't be able to register at the Help Desk, but you will be able to get information about the conference, and sponsor, poster, and demo setup as well (all are in the PAB Atrium) during breaks and lunch.

Wednesday June 27, 2018 12:10pm - 1:40pm
PAB Atrium Performing Arts Building, Reed College

12:10pm

Lunch
Lunches during the meeting will be served in the Performing Arts Building.

Birds-of-a-feather session will start at 12:30 in several PAB classrooms.  If you aren't planning to attend a BoF, you are encouraged to arrive at lunch a few minutes late, and then to use the extra time for networking and for catching up on your morning email.

Wednesday June 27, 2018 12:10pm - 1:40pm
PAB Atrium Performing Arts Building, Reed College

12:10pm

Sponsors
Sponsors make GCCBOSC possible and affordable, and they are your potential partners in research.  Take some time during the Poster and Demo sessions to visit them and find out how they can help you do your research.


Wednesday June 27, 2018 12:10pm - 1:40pm
PAB Atrium Performing Arts Building, Reed College

12:30pm

Birds-of-a-Feather (BoFs), with Lunch!
Birds-of-a-feather are infornal gatherings or participants with a shared interest.  Anyone can organize a BoF session.  The BoF call will go out this spring, and we will accept BoF topics from then until we run out of space for them.

These BoF sessions will start 20 minutes into lunch.  Rooms will be available in the Performing Arts Building, where lunch is served.

Wednesday June 27, 2018 12:30pm - 1:30pm
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA

12:30pm

BoF: JBrowse
Configuring and using JBrowse; JBrowse development priorities.

JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools.

Planning to attend?  Please login add yourself to this session.

Moderators
RB

Rob Buels

JBrowse Project, University of California Berkeley


Wednesday June 27, 2018 12:30pm - 1:30pm
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA

1:40pm

Galaksio, a more user friendly interface for Galaxy using workflows
Authors
Tomas Klingström, Oskar Danielsson, Rafael Hernández-de-Diego and Erik Bongcam-Rudloff

Speakers
TK

Tomas Klingström

SLU-Global Bioinformatics Centre, Swedish University of Agricultural Sciences


Wednesday June 27, 2018 1:40pm - 2:00pm
Vollum Lecture Hall Vollum College Center, Reed Campus

1:40pm

BOSC Session 3
The latest and greatest from BOSC community members. 

Wednesday June 27, 2018 1:40pm - 3:00pm
Eliot Chapel Eliot Hall, Reed Campus

1:40pm

GCC Session 3: Challenges & Opportunities
The session will include accepted oral presentations from the Galaxy community. 

Wednesday June 27, 2018 1:40pm - 3:00pm
Vollum Lecture Hall Vollum College Center, Reed Campus

2:00pm

Large scale analyses with improved dataset collections
Authors
Marius van den Beek 1, John Chilton 2, Nicola Soranzo 3, Anil S. Thanki 3, Martin Čech 2, and the Galaxy Team

  1. Institut Curie, 26 rue d’Ulm, F-75248 Paris, France.
  2. Department of Biochemistry and Molecular Biology, Penn State University, University Park PA USA .
  3. Earlham Institute (EI), Norwich Research Park, Norwich NR4 7UZ, UK.

Speakers
avatar for Marius van den Beek

Marius van den Beek

Institut Curie, Paris


Wednesday June 27, 2018 2:00pm - 2:20pm
Vollum Lecture Hall Vollum College Center, Reed Campus

2:20pm

A fruitful year for the Galaxy Training materials
Authors
Bérénice Batut, Saskia Hiltemann, Björn Grüning and the Galaxy Training Network

Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
University of Freiburg


Wednesday June 27, 2018 2:20pm - 2:40pm
Vollum Lecture Hall Vollum College Center, Reed Campus

2:40pm

The usegalaxy.* servers: democratizing computational resources for life sciences at a new level
Authors
Simon Gladman 1, Eric Rasche 2, Björn Grüning 2, Nate Coraor 3, Derek Benson 4, Andrew Lonie 1 and James Taylor5
  1. Melbourne Bioinformatics, The University of Melbourne, Australia.
  2. University of Freiburg, Freiburg, Germany.
  3. Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
  4. Research Computing Centre, The University of Queensland, Brisbane, Australia
  5. Department of Biology, Johns Hopkins University, Baltimore, MD, USA

Speakers
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne


Wednesday June 27, 2018 2:40pm - 3:00pm
Vollum Lecture Hall Vollum College Center, Reed Campus

3:00pm

Demos
Demos will be presented on two days and concurrently with posters and the sponsor exhibits.

Wednesday June 27, 2018 3:00pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:00pm

Help Desk Open
The help desk will be in the Performing Arts Building on Wednesday and Thursday during select times.  You owon't be able to register at the Help Desk, but you will be able to get information about the conference during this session.

Wednesday June 27, 2018 3:00pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:00pm

Posters
Posters will be presented on two days and concurrently with demos and the sponsor exhibits.

Wednesday June 27, 2018 3:00pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:00pm

Sponsors
Sponsors make GCCBOSC possible and affordable, and they are your potential partners in research.  Take some time during the Poster and Demo sessions to visit them and find out how they can help you do your research.


Wednesday June 27, 2018 3:00pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

4:00pm

Improving the Bioinformatics Curriculum
Author
Jason Williams, Cold Spring Harbor Laboratory, Williams@cshl.edu

Speakers
JW

Jason Williams

Cold Spring Harbor Laboratory


Wednesday June 27, 2018 4:00pm - 4:20pm
Vollum Lecture Hall Vollum College Center, Reed Campus

4:00pm

Session 4 - Joint BOSC & GCC
The last session of the first day of the GCCBOSC 2018 meeting

Wednesday June 27, 2018 4:00pm - 5:20pm
Vollum Lecture Hall Vollum College Center, Reed Campus

4:20pm

Panel: Training and Documentation in Bioinformatics
Yes, we are looking for a snazzier title.

Wednesday June 27, 2018 4:20pm - 5:20pm
Vollum Lecture Hall Vollum College Center, Reed Campus

5:40pm

Birds-of-a-Feather (BoFs), With Your Dinner!
Birds-of-a-feather are infornal gatherings or participants with a shared interest.  Anyone can organize a BoF session.  The BoF call will go out this spring, and we will accept BoF topics from then until we run out of space for them.

While BoFs tend to be informal, BoFsWYD! will be especially informal, as these will meet over dinner at a restaurant in the nearby Woodstock neighborhood.  Interactions and conversation will likely happen in smaller groups much of the time.

We suggest that BoFsWYD! groups flock outside of the Vollum College Center and depart on foot for Woodstock at 5:40.  You can talk along the way too.

Wednesday June 27, 2018 5:40pm - 7:40pm
TBA

5:40pm

Dinner on your own (or join a BoF)
Dinner on Wednesday night is on your own.  There are numerous good options in the nearby Woodstock neighborhood.

You can also join a Birds-of-a-feather for dinner

Wednesday June 27, 2018 5:40pm - 7:40pm
TBA

8:00pm

Birds-of-a-Feather (BoFs), wherever you want!
Birds-of-a-feather are infornal gatherings or participants with a shared interest.  Anyone can organize a BoF session.  The BoF call will go out this spring, and we will accept BoF topics from then until we run out of space for them.

This is the second BoF session of Wednesday evening.  Rooms will be available on campus in the Performing Arts Building.  You can also meet in a location of your choice in the nearby Woodstock neighborhood.

Wednesday June 27, 2018 8:00pm - 10:00pm
TBA
 
Thursday, June 28
 

8:00am

Help Desk Open
The help desk will be in the Performing Arts Building on Wednesday and Thursday during select times.  You won't be able to register at the Help Desk, but you will be able to get information about the conference, and get sponsor, poster, and demo setup help as well (all are in the PAB Atrium).

Thursday June 28, 2018 8:00am - 10:20am
PAB Atrium Performing Arts Building, Reed College

8:00am

Conference desk open
Pick up your registration materials and otherwise find help.

Thursday June 28, 2018 8:00am - 12:10pm
Vollum College Center Lobby

9:00am

Galaxy Enables Integrated Analysis of Phenotypic, Genotypic, and Environmental Data for Geo-referenced Trees in CartograTree
Authors
Nic Herndon∗, Peter Richter†, Taylor Falk†, Sean Buehler†, Emily Grau†, Dorrie Main‡,Sook Jung‡, Stephen Ficklin‡, Margaret Staton§, Alex Feltus¶, Jill Wegrzyn†

∗ Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA. Email: nic.herndon@uconn.edu
† Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
‡ Department of Horticulture, Washington State University, Pullman, WA, USA
§ Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
¶ Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA

Speakers

Thursday June 28, 2018 9:00am - 9:20am
Vollum Lecture Hall Vollum College Center, Reed Campus

9:00am

BOSC Session 5
Talks and lightning of interest to the BOSC community.

Thursday June 28, 2018 9:00am - 10:20am
Eliot Chapel Eliot Hall, Reed Campus

9:00am

GCC Session 5: Galaxy in situ
Talks and lightning of interest to the Galaxy community.

Thursday June 28, 2018 9:00am - 10:20am
Vollum Lecture Hall Vollum College Center, Reed Campus

9:20am

G-OnRamp: Create UCSC Assembly Hubs and JBrowse/Apollo Archives for Collaborative Eukaryotic Genome Annotations
Authors
Luke Sargent 1, Yating Liu 2, Wilson Leung 2, Sarah C.R. Elgin 2,Jeremy Goecks 1

1 Oregon Health & Science University
2 Washington University in St. Louis

Speakers
LS

Luke Sargent

Oregon Health and Science University (OHSU)


Thursday June 28, 2018 9:20am - 9:40am
Vollum College Center Lobby

9:40am

Canada's Integrated Rapid Infectious Disease Analysis Platform (IRIDA)
Authors
Thomas Matthews 1, Franklin Bristow 2, Aaron Petkau 1, Josh Adam 1, Peter Kruczkiewicz 1, Jen Cabral 1, Damion Dooley 4, Emma Griffiths 3, Dan Fornika 4, Geoff Winsor 3, Morag Graham 1, The IRIDA consortium, Eduardo Taboada 1, Robert Beiko 5, William Hsiao 4, Fiona Brinkman 3, Gary Van Domselaar 1,2

1. Public Health Agency of Canada, Canada
2. University of Manitoba, Winnipeg, Canada
3. Simon Fraser University, Burnaby, Canada
4. BC Public Health Microbiology and Reference Laboratory, Vancouver, Canada
5. Dalhousie University, Halifax, Canada

Speakers
TM

Thomas Matthews

Public Health Agency of Canada


Thursday June 28, 2018 9:40am - 10:00am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:00am

Galaxy in a proteomics core facility
Authors
Jeremy D Volkening 1, Grzegorz Sabat 1, Gregory A Barrett-Wilt 1, and Michael R Sussman 1

1. Biotechnology Center, University of Wisconsin-Madison

Speakers

Thursday June 28, 2018 10:00am - 10:20am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:20am

Break
Head over to the Performing Arts building for a stretch, refreshments, and conversation.

Thursday June 28, 2018 10:20am - 10:50am
PAB Atrium Performing Arts Building, Reed College

10:20am

Sponsors
Sponsors make GCCBOSC possible and affordable, and they are your potential partners in research.  Take some time during the Poster and Demo sessions to visit them and find out how they can help you do your research.


Thursday June 28, 2018 10:20am - 10:50am
PAB Atrium Performing Arts Building, Reed College

10:50am

Quantifying Functional Microbiomes: An integrated, quantitative metaproteomics approach reveals connections between taxa, function and protein expression in complex microbiomes
Authors
Caleb W Easterly 1; Nadia Szeinbaum 2; Bjoern Gruening 3; Lee S Parsons 1; Shane L Hubler 4; Subina Mehta 1; Ray Sajulga 1; Bart Mesuere 5; James E Johnson 1; Alessandro Tanca6; Carolin Kolmeder 7; Praveen Kumar 1; Jennifer Glass 2; Joel Rudney 1; Brook L Nunn 8; Timothy J. Griffin 1; Pratik D. Jagtap 1

  1. University of Minnesota, Minneapolis, MN
  2. Georgia Institute of Technology, Atlanta,GA
  3. University of Freiburg, Freiburg, Germany
  4. Rhapsody Data LLC, Madison, WI
  5. Ghent University, Ghent, Belgium
  6. Porto Conte Ricerche Science & Technology Park of Sardinia, Alghero, Italy
  7. Universityof Helsinki, Helsinki, Finland
  8. University of Washington Department of Genome Sciences, Seattle, WA.

Speakers
CE

Caleb Easterly

University of Minnesota
avatar for Pratik Jagtap

Pratik Jagtap

Research assistant Professor, University of Minnesota
University of Minnesota


Thursday June 28, 2018 10:50am - 11:10am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:50am

BOSC Session 6
The second day of BOSC continues with more accepted talks, and other content.

Thursday June 28, 2018 10:50am - 12:10pm
Eliot Chapel Eliot Hall, Reed Campus

10:50am

GCC Session 6: Galaxy in situ
Galaxy Community Conference continues on Thursday.

Thursday June 28, 2018 10:50am - 12:10pm
Vollum Lecture Hall Vollum College Center, Reed Campus

11:10am

GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline
Authors
Anil S. Thanki, Nicola Soranzo, Wilfried Haerty, Robert P. Davey

Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK

Speakers
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute


Thursday June 28, 2018 11:10am - 11:30am
Vollum Lecture Hall Vollum College Center, Reed Campus

11:30am

Galaxy HiCExplorer: HiCExplorer, deepTools3 and pyGenomeTracks
Authors
Joachim Wolff 1, Devon Ryan 2, Fidel Ramirez 2, Bjoern Gruening 1
  1. Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
  2. Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg im Breisgau, Germany

Speakers
JW

Joachim Wolff

Albert-Ludwigs-University Freiburg


Thursday June 28, 2018 11:30am - 11:50am
Vollum Lecture Hall Vollum College Center, Reed Campus

11:50am

Lightning Talks ⚡
Lightning talks are short talks that concisely communicate resources, work in progress and other topics that lend themselves to just a few minutes coverage and a few slides.

Thursday June 28, 2018 11:50am - 12:10pm
Vollum Lecture Hall Vollum College Center, Reed Campus

12:10pm

Help Desk Open
The help desk will be in the Performing Arts Building on Wednesday and Thursday during select times.  You won't be able to register at the Help Desk, but you will be able to get information about the conference, and help with sponsor, poster, and demo setup as well (all are in the PAB Atrium).

Thursday June 28, 2018 12:10pm - 1:40pm
PAB Atrium Performing Arts Building, Reed College

12:10pm

Lunch
Lunches during the meeting will be served in the Performing Arts Building.

Birds-of-a-feather session will start at 12:30 in several PAB classrooms.  If you aren't planning to attend a BoF, you are encouraged to arrive at lunch a few minutes late, and then to use the extra time for networking and for catching up on your morning email.

Thursday June 28, 2018 12:10pm - 1:40pm
PAB Atrium Performing Arts Building, Reed College

12:10pm

Sponsors
Sponsors make GCCBOSC possible and affordable, and they are your potential partners in research.  Take some time during the Poster and Demo sessions to visit them and find out how they can help you do your research.


Thursday June 28, 2018 12:10pm - 1:40pm
PAB Atrium Performing Arts Building, Reed College

12:30pm

Birds-of-a-Feather (BoFs), with Lunch!
Birds-of-a-feather are infornal gatherings or participants with a shared interest.  Anyone can organize a BoF session.  The BoF call will go out this spring, and we will accept BoF topics from then until we run out of space for them.

This BoF session will start 20 minutes into lunch. Rooms will be available in the Performing Arts Building, where lunch is served.

Thursday June 28, 2018 12:30pm - 1:30pm
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA

1:40pm

Galaxy Community Update
What's happened, what's happening, and what's going to happen in the Galaxy Community - the annual project update.

Speakers
DB

Dan Blankenberg

Cleveland Clinic Lerner College of Medicine of Case Western Reserve University
JG

Jeremy Goecks

Oregon Health & Science University (OHSU)
avatar for Anton Nekrutenko

Anton Nekrutenko

Galaxy Project, Penn State University
Penn State University
avatar for James Taylor

James Taylor

Johns hopkins University


Thursday June 28, 2018 1:40pm - 2:10pm
Vollum Lecture Hall Vollum College Center, Reed Campus

1:40pm

BOSC Session 7
The latest and greatest from BOSC community members. 

Thursday June 28, 2018 1:40pm - 3:00pm
Eliot Chapel Eliot Hall, Reed Campus

1:40pm

GCC Session 7
The session includes the Galaxy Project update talk, and lightning talks from the Galaxy community. 

Thursday June 28, 2018 1:40pm - 3:00pm
Vollum Lecture Hall Vollum College Center, Reed Campus

2:10pm

Lightning Talks ⚡
Lightning talks are short talks that concisely communicate resources, work in progress and other topics that lend themselves to just a few minutes coverage and a few slides.

Thursday June 28, 2018 2:10pm - 3:00pm
Vollum Lecture Hall Vollum College Center, Reed Campus

3:00pm

Demos
Demos will be presented on two days and concurrently with posters and the sponsor exhibits.

Thursday June 28, 2018 3:00pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:00pm

Help Desk Open
The help desk will be in the Performing Arts Building on Wednesday and Thursday during select times.  You won't be able to register at the Help Desk, but you will be able to get information about the conference during this session.

Thursday June 28, 2018 3:00pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:00pm

Posters
Posters will be presented on two days and concurrently with demos and the sponsor exhibits.

Thursday June 28, 2018 3:00pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:00pm

Sponsors
Sponsors make GCCBOSC possible and affordable, and they are your potential partners in research.  Take some time during the Poster and Demo sessions to visit them and find out how they can help you do your research.


Thursday June 28, 2018 3:00pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

4:00pm

Closing Keynote: Confound it! Reproducible biology from "omics" data analysis
Dr. Peixoto is an Assistant Professor at the Elson S. Floyd College of Medicine at Washington State University. Her research focuses on using genomic and computational biology approaches to study brain function. She also advises the WSU Spokane Genomics Core, and has published work on how analysis of complex datasets affects power and reproducibly in RNA-seq and Epigenomic-seq.

Lucia's keynote is sponsored by GCC.

Speakers
avatar for Lucia Peixoto

Lucia Peixoto

Assistant Professor, Elson S. Floyd College of Medicine, Washington State University
Dr. Peixoto is an Assistant Professor at the Elson S. Floyd College of Medicine at Washington State University. Her research focuses on using genomic and computational biology approaches to study brain function. In particular, understanding the underlying molecular basis of Autism Spectrum Disorders and their comorbidity with Intellectual Disability and Sleep Impairments. Her lab uses mouse models for functional genomic studies of behavior and patient samples to study genetic contributions to disease. She also advises... Read More →


Thursday June 28, 2018 4:00pm - 5:00pm
Vollum Lecture Hall Vollum College Center, Reed Campus

4:00pm

Session 8 - Joint BOSC & GCC Closing
The closing session for GCCBOSC 2018.  
 

Thursday June 28, 2018 4:00pm - 5:20pm
Vollum Lecture Hall Vollum College Center, Reed Campus

5:00pm

Conference Closing
Where we bring it all together by wrapping up this year, talking about the coming year, and maybe even give away a prize or two.

Thursday June 28, 2018 5:00pm - 5:20pm
Vollum Lecture Hall Vollum College Center, Reed Campus

5:20pm

Conference desk open
Got questions for the organizers?  This is your last chance before the conference dinner.

Thursday June 28, 2018 5:20pm - 5:40pm
Vollum College Center Lobby

5:40pm

Birds-of-a-Feather (BoFs), the Final Flight!
Birds-of-a-feather are infornal gatherings or participants with a shared interest.  Anyone can organize a BoF session.  The BoF call will go out this spring, and we will accept BoF topics from then until we run out of space for them.

This is the last BoF session of GCCBOSC 2018!



Thursday June 28, 2018 5:40pm - 7:00pm
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA

7:00pm

Conference Dinner!
The meeting is done!  Please relax and join us for dinner under the setting sun of a glorious (really) Oregon summer evening. The conference dinner is included with your meeting registration.

Didn't register for the two day meeting but still want to attend (or bring a guest)?  You can order additional tickets on the conference registration site.

Thursday June 28, 2018 7:00pm - 10:00pm
TBA
 
Friday, June 29
 

9:00am

GCC OBF CollaborationFest: Core
The GCCBOSC meeting will be followed by CollaborationFest: Core, two days with lots of opportunities and emphasis on  learning about open source bioinformatics projects and software.
CollaborationFest will have three tracks:
  • Galaxy development (Galaxy Dev): Learn how Galaxy and Galaxy code development works, and contribute to the Galaxy code base
  • Galaxy documentation, analysis, and training (Galaxy DAT): Focus on expanding Galaxy community resources like training materials and documentation.
  • OBF: Contribute to any open source bioinformatics project.

These groups will be fluid and highly interactive with each other. There will be a joint gathering of all communities at least once a day.

See the CollaborationFest page for more.

Friday June 29, 2018 9:00am - 6:00pm
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA
 
Saturday, June 30
 

9:00am

GCC OBF CollaborationFest: Core
The GCCBOSC meeting will be followed by CollaborationFest: Core, two days with lots of opportunities and emphasis on  learning about open source bioinformatics projects and software.
CollaborationFest will have three tracks:
  • Galaxy development (Galaxy Dev): Learn how Galaxy and Galaxy code development works, and contribute to the Galaxy code base
  • Galaxy documentation, analysis, and training (Galaxy DAT): Focus on expanding Galaxy community resources like training materials and documentation.
  • OBF: Contribute to any open source bioinformatics project.
These groups will be fluid and highly interactive with each other. There will be a joint gathering of all communities at least once a day.
See the CollaborationFest page for more.

Saturday June 30, 2018 9:00am - 6:00pm
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA
 
Sunday, July 1
 

9:00am

GCC OBF CollaborationFest: Encore
The first two days, CollaborationFest: Core emphasize collaboration and learning.  The next two days, CollaborationFest: Encore lean heavily towards collaboration (although, trust us, organizers won't stop you from learning either).  We expect CollaborationFest: Encore to be a smaller group of contributors.
See the CollaborationFest page for more.

Sunday July 1, 2018 9:00am - 6:00pm
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA
 
Monday, July 2
 

9:00am

GCC OBF CollaborationFest: Encore
The first two days, CollaborationFest: Core emphasize collaboration and learning.  The next two days, CollaborationFest: Encore lean heavily towards collaboration (although, trust us, organizers won't stop you from learning either).  We expect CollaborationFest: Encore to be a smaller group of contributors.
See the CollaborationFest page for more.

Monday July 2, 2018 9:00am - 6:00pm
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA