Loading…
GCC BOSC 2018 has ended
The 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) are meeting together in Portland, Oregon, United States, June 25-30, 2018.  There will be two days of training, a two+ day meeting, and four days of intense collaboration.  The meeting features joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events.  GCCBOSC is organized by Oregon Health & Science University and will be at Reed College.


( #GCCBOSC / Chat )
View analytic

Sign up or log in to bookmark your favorites and sync them to your phone or calendar.

Sunday, June 24
 

3:00pm

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

The registration desk is on the first floor of the Performing Arts Building.

Need to checkin after 11pm?  We'll provide a way.   

Sunday June 24, 2018 3:00pm - 11:00pm
PAB Atrium Performing Arts Building, Reed College

6:00pm

BoF: Genome Browsers and visualization in Galaxy
Galaxy's architecture supports genomic data visualization with a plugin mechanism that enables integration with tools like JBrowse and Apollo, and call-out visualization with tools like the UCSC Genome Browser, IGV and IGB.  

This BoF will discuss the Galaxy genomic data viz ecosystem, and options for improving it.

Meet us at Gigantic Brewing, starting at 6pm.  Gigantic has a large beverage selection and two adjacent, pretty darn good, food cart options.

Moderators
Sunday June 24, 2018 6:00pm - 8:00pm
Gigantic Brewing 5224 SE 26th Ave, Portland, OR 97202
 
Monday, June 25
 

8:00am

Conference desk open
Pick up your conference package and checkin to on-campus lodging.  The registration desk is on the first floor of the Performing Arts Building.

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

8:00am

Training Day 1 - Galaxy

Monday June 25, 2018 8:00am - 10:00pm
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA

9:00am

Galaxy 101 - A gentle introduction to using Galaxy
→ Tutorial

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
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy. | Bérénice is also passionate about training. She regularly gives workshops on... Read More →
JW

Joachim Wolff

Albert-Ludwigs-University Freiburg



Monday June 25, 2018 9:00am - 11:30am
PAB 104 Performing Arts Building, Reed Campus

9:00am

Intro to Galaxy Administration 1
→ Training Material

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

Computational infrastructure for this workshop is generously provided by Jetstream, NSF's user-friendly cloud computing environment  for researchers.

Speakers
avatar for Enis Afgan

Enis Afgan

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

Marius van den Beek

Institut Curie, Paris
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University
avatar for Carrie Ganote

Carrie Ganote

Indiana University Bloomington
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne
NG

Nuwan Goonasekera

University of Melbourne
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 320 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
→ Training Material

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

Computational infrastructure for this workshop is generously provided by Jetstream, NSF's user-friendly cloud computing environment  for researchers.

Speakers
avatar for Enis Afgan

Enis Afgan

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

Marius van den Beek

Institut Curie, Paris
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University
avatar for Carrie Ganote

Carrie Ganote

Indiana University Bloomington
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne
NG

Nuwan Goonasekera

University of Melbourne
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 320 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 104 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 !
Workshop Slides
Workshop Tutorial
Workshop Server (will go away at some point)

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.

Computational infrastructure for this workshop is generously provided by Jetstream, NSF's user-friendly cloud computing environment  for researchers.

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

Senior Software Developer, Minnesota Supercomputing Institute, University of Minnesota
Galaxy for genomics and proteomics
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 104 Performing Arts Building, Reed Campus

3:30pm

Intro to Galaxy Administration 3
→ Training Material

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

Computational infrastructure for this workshop is generously provided by Jetstream, NSF's user-friendly cloud computing environment  for researchers.

Speakers
avatar for Enis Afgan

Enis Afgan

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

Marius van den Beek

Institut Curie, Paris
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University
avatar for Carrie Ganote

Carrie Ganote

Indiana University Bloomington
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne
NG

Nuwan Goonasekera

University of Melbourne
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 320 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
Slides

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
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy. | Bérénice is also passionate about training. She regularly gives workshops on... Read More →


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

8:00am

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 8:00am - 6:00pm
Reed College Campus

8:00am

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

Tuesday June 26, 2018 8:00am - 10:00pm
PAB Atrium Performing Arts Building, Reed College

9:00am

Community built analyses that run everywhere with bcbio
Slides

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
Brad is a senior research scientist in the Bioinformatics Core at Harvard T.H. Chan School of Public Health. He develops open source community built infrastructure for analyzing biological data, focusing on multi platform interoperability and automated validation against heterogeneous... Read More →
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
PAB 332 Performing Arts Building, Reed Campus

9:00am

Conda and Containers
→ Tool Dependencies and Conda:          Slides, PDF
→ Tool Dependencies and Containers:  
SlidesPDF

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
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
PAB 320 Performing Arts Building, Reed Campus

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... Read More →


Tuesday June 26, 2018 9:00am - 11:30am
PAB 131 Performing Arts Building, Reed Campus

9:00am

Handling integrated biological data using Python (or R) and InterMine
→ Tutorial and slides

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
PAB 104 Performing Arts Building, Reed Campus

9:00am

WDL: the Workflow Description Language
Training Materials

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 software... 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 bioinformatics... Read More →
CL

Chris Llanwarne

Broad Institute



Tuesday June 26, 2018 9:00am - 11:30am
Vollum Lounge Vollum College Center, Reed Campus

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... Read More →


Tuesday June 26, 2018 12:30pm - 3:00pm
PAB 131 Performing Arts Building, Reed Campus

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
PAB 332 Performing Arts Building, Reed Campus

12:30pm

Introduction to Common Workflow Language
Slides

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 →
KH

Kenzo-Hugo Hillion

Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI); Institut Pasteur de Paris
avatar for Hervé Ménager

Hervé Ménager

Research Engineer, Institut Pasteur
Bioinformatics and Biostatistics Hub of the C3BI, Institut Pasteur



Tuesday June 26, 2018 12:30pm - 3:00pm
PAB 320 Performing Arts Building, Reed Campus

12:30pm

Practical use of the Galaxy API command line tools
→ Slides
→ All Training Material

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
Talk to me about Galaxy Development, especially the UI!
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
Vollum Lounge Vollum College Center, Reed Campus

12:30pm

Setting up for success: Everything you need to know when planning for an RNA-seq analysis I
→ Training Materials

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
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 12:30pm - 3:00pm
PAB 104 Performing Arts Building, Reed Campus

3:00pm

Break
Breaks on Tuesday will be close the training venues.

Tuesday June 26, 2018 3:00pm - 3:30pm
PAB Atrium Performing Arts Building, Reed College

3:30pm

Command line workflow management systems: Snakemake and Nextflow
Snakemake Tutorial

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-EssenDepartment of Medical Oncology, Harvard Medical Schoolhttps://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
Vollum Lounge Vollum College Center, Reed Campus

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... Read More →


Tuesday June 26, 2018 3:30pm - 6:00pm
PAB 131 Performing Arts Building, Reed Campus

3:30pm

Galaxy Architecture
Slides (PDF)

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
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University



Tuesday June 26, 2018 3:30pm - 6:00pm
PAB 320 Performing Arts Building, Reed Campus

3:30pm

GATK4: What's new and how to run it
→ Prep
Tutorial

Key:  BB | XB |  -  |  -  | GG | CL

GATK4 is the brand new version of the Genome Analysis Toolkit (GATK), an open-source genomics software package focused on variant discovery. This workshop will highlight the key changes and updates in the new 4.0 version which was released in January 2018 (see https://software.broadinstitute.org/gatk/gatk4).

The goal of the workshop is to equip participants with the essential know-how to get started with GATK4, whether they have previously used GATK or not. We will walk participants through hands-on exercises aimed at developing familiarity with the GATK4 command line. We will also guide participants through several different ways of running GATK4 tools and pipelines on publicly available platforms including but not limited to Galaxy. We hope this will help participants understand what are their options and choose the platform that best suits their needs and abilities.

The workshop will cover the following topics:

1. Introduction to GATK and the Best Practices:
  • Purpose, variant calling basics and standard data types

2. What's new in GATK4:
  • New syntax/invocations, performance improvements and tips & tricks for using GATK effectively
  • Expanded scope of analysis:
    • Scaling germline variant discovery with GenomicsDB
    • Calling somatic short variants with the new and improved Mutect2
    • Calling somatic copy number variants with GATK CNV

3. Options for running GATK
  • Running tools individually on a laptop (with Docker)
  • Running Spark-capable tools individually on a Spark cluster (via Google Dataproc)
  • Running pipelines on a laptop using Cromwell
  • Running pipelines on Google Cloud using Cromwell + Pipelines API
  • Running pipelines on the FireCloud analysis portal through the web GUI
  • Running pipelines on FireCloud through the API + Python bindings
  • Running tools and pipelines on Galaxy

Free credits will be provided for running on Google Cloud. For more information on FireCloud, see https://software.broadinstitute.org/firecloud.

Prerequisites:
  • Basic familiarity with terms and concepts of genetics and genomics, including high-level understanding of high-throughput sequencing technologies and file formats used in genomic analysis.
  • Basic familiarity with the command line environment and usage of command line tools.
  • NO familiarity is expected with Spark or cloud computing concepts.


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 software... Read More →
KN

Kate Noblett

Broad Institute



Tuesday June 26, 2018 3:30pm - 6:00pm
PAB 332 Performing Arts Building, Reed Campus

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
PAB 104 Performing Arts Building, Reed Campus

6:20pm

Birds-of-a-Feather (BoFs), With Your Dinner!
Organize/Submit a BoF!

Birds-of-a-feather are informal 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 either 1) meet in the Reed Campus Commons for dinner, or 2) flock outside PAB and depart on foot for Woodstock at 6:15 (you can talk along the way too).

BoFs offered during this flocking:



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

6:20pm

BoF: Galaxy for proteomics interest group
BoF is for those interested either developing, wrapping or using proteomics tools in Galaxy.  Informal discussion on current state of available tools for proteomics in Galaxy, suggestions for additional tools and other topics.  We may also discuss an idea to develop a community study for testing and demonstrating reproducibility of sophisticated proteomics analyses using Galaxy.

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

Organize/Submit a BoF!

Moderators
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

Tuesday June 26, 2018 6:20pm - 7:40pm
Reed Commons Cafe Reed College Commons, Reed Campus

8:00pm

Opening & Welcome
Conference welcome, logistics, and information.

Speakers
avatar for Dave Clements

Dave Clements

Training and Outreach Coordinator, Galaxy Project, Johns Hopkins University
avatar for Nomi Harris

Nomi Harris

BOSC 2018 Chair, Lawrence Berkeley National Laboratory
Nomi Harris is a bioinformatics program manager at LBNL. She has chaired or co-chaired BOSC since 2011.



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

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.

Moderators
avatar for Nicole Vasilevsky

Nicole Vasilevsky

Lead Biocurator, OHSU
avatar for Heather Wiencko

Heather Wiencko

Software Engineer, Hosted Graphite
I'm a software engineer working for Hosted Graphite in the heart of Dublin, Ireland. As co-chair of BOSC, I'm excited about partnering with GCC to put on a conference the likes of which the world has never seen. I also serve as a member-at-large on the OBF Board of Directors. If you're... Read More →

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

8:10pm

Opening Keynote: Tracy K. Teal--"Democratizing Data"
Abstract:
Data is no longer the bottleneck for discovery. Instead it our ability and capacity to work with data, to turn data into information and knowledge, that is limiting. The question then becomes, how do we empower researchers and enable discovery, by scaling people's capacity to work with data? First we must recognize the importance of valuing the people by investing in training and valuing the people who create the tools and software. We need to view software not as a service to research, but an integral part of the research process. Then we must develop and provide training, access to computational resources, and give credit for and support research software development. With this support and training, everyone can have the tools and perspectives to work effectively and reproducibly with data. People are empowered to answer the questions that are important to them, allowing us to address more and more diverse questions, and broadening the impact on science and society. We talk about bringing compute to data or data to compute. We also need to bring people to data. It is only by democratizing data that it will reach its potential.

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... Read More →



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

8:00am

Conference desk open
Pick up your registration materials here. Get help with poster and sponsor setup too.

The Conference Desk is on the first floor of the Performing Arts Building

Wednesday June 27, 2018 8:00am - 4:00pm
PAB Atrium Performing Arts Building, Reed College

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

9:01am

Keynote: Fernando Pérez--"Sustainable development of scientific open source tools: a view from Jupyter"
Slides

Abstract

It is by now well established that software plays an increasingly important role in scientific research. We are gradually recognizing the importance of tools that are robust, well-tested, documented, and that support reproducible research practices. However, the development of such tools is a complex,resource-intensive process for which most scientists are poorly trained, and that is rarely recognized by the incentive structures of professional research.
In this talk, I will discuss some of the work we have done in Project Jupyter from the perspective of these issues.  I will highlight some recent technical developments in Jupyter that may be of interest to the GCC/BOSC audience, and will discuss lessons we have learned in over 15 years of building these tool sat the intersection of research, education and industrial partnerships.

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... Read More →



Wednesday June 27, 2018 9:01am - 10:00am
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

BOSC: Session 2: Translational & Medical Informatics
The first BOSC session of GCCBOSC 2018.  The session will include accepted oral presentations focusing on translational and medical research.

Moderators
avatar for Hilmar Lapp

Hilmar Lapp

Director of Informatics, Duke University, Center for Gemonic and Computational Biology

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

Speakers
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne


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

10:51am

Cloud-based data ingest for the Human Cell Atlas
Speakers
avatar for Daniel Vaughan

Daniel Vaughan

Tech Lead, EMBL-EBI



Wednesday June 27, 2018 10:51am - 11:05am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:51am

Storage Media Federation for Galaxy
Slides @ F1000 (and @ Slideshare)

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 10:51am - 11:10am
Eliot Chapel Eliot Hall, Reed Campus

11:05am

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
Eliot Chapel Eliot Hall, Reed Campus

11:20am

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
Eliot Chapel Eliot Hall, Reed Campus

11:40am

Enabling Machine Learning at Scale with “Tiled” Human Genomes
Speakers
avatar for Sarah Wait Zaranek

Sarah Wait Zaranek

President, Curoverse Research
Interested in large data, WGS, machine learning, open source standards.



Wednesday June 27, 2018 11:40am - 11:45am
Vollum Lecture Hall Vollum College Center, Reed Campus

11:45am

JASS: a free and open source software for the joint analysis and interactive analysis of GWAS results

Speakers
avatar for Hervé Ménager

Hervé Ménager

Research Engineer, Institut Pasteur
Bioinformatics and Biostatistics Hub of the C3BI, Institut Pasteur



Wednesday June 27, 2018 11:45am - 11:50am
Vollum Lecture Hall Vollum College Center, Reed Campus

11:50am

Building a community menagerie of automated variant validations
Speakers
avatar for Brad Chapman

Brad Chapman

Bioinformatics Core, Harvard Chan School
Brad is a senior research scientist in the Bioinformatics Core at Harvard T.H. Chan School of Public Health. He develops open source community built infrastructure for analyzing biological data, focusing on multi platform interoperability and automated validation against heterogeneous... Read More →



Wednesday June 27, 2018 11:50am - 11:55am
Vollum Lecture Hall Vollum College Center, Reed Campus

11:50am

Galaxy for AnswerALS on Microsoft Azure and Kubernetes
Authors:
RC Carter, Microsoft; Abhik Ghosh, Applied Information Systems; Alex Lenail, MIT; Enis Afgan, Johns Hopkins University; Gaurav Hind, Microsoft; Nuwan Goonasekera, University of Melbourne

Speakers
RC

RC Carter

Microsoft



Wednesday June 27, 2018 11:50am - 11:56am
Eliot Chapel Eliot Hall, 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
Eliot Chapel Eliot Hall, Reed Campus

11:55am

11:56am

Adding Python 3 support to Galaxy: a status report
Slides @ F1000

Authors:
Nicola Soranzo1, Marius van den Beek2, John Chilton3

  1. Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK. 
  2. Institut Curie, Paris, France.
  3. The Pennsylvania State University, University Park, PA, USA.

Speakers
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute



Wednesday June 27, 2018 11:56am - 12:02pm
Eliot Chapel Eliot Hall, Reed Campus

12:00pm

Q&A for lightning talks in this session ⚡
Got questions for this session's lightning talk speakers?  Ask them now.

Wednesday June 27, 2018 12:00pm - 12:08pm
Vollum Lecture Hall Vollum College Center, Reed Campus

12:02pm

Aurora Galaxy Tools: Using R Markdown as a framework to build interactive Galaxy tool output reports
Authors:
Ming Chen 1, Bradford Condon 1, Abdullah Almsaeed 1, Connor Wytko 2, Stephen Ficklin 2, MargaretStaton 1

  1. University of Tennessee, Knoxville, Tennessee (USA)
  2. Washington State University, Pullman, Washington (USA)

Speakers


Wednesday June 27, 2018 12:02pm - 12:08pm
Eliot Chapel Eliot Hall, Reed Campus

12:10pm

Lunch, sponsored by Lenovo + Intel
Lunches during the meeting will be served in the Performing Arts Building.

Wednesday's lunch is sponsored by Lenovo + Intel.  Please visit them in the PAB Atrium and find out how they can help you move your research forward.

Birds-of-a-feather sessions 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!
Organize/Submit a BoF!

Birds-of-a-feather are informal 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.

BoFs offered during this flocking:
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: Getting contributors to your open project
BoF Notes

Anyone who works on open projects (or would like to) is welcome. Do you want to learn how to gain new contributors for your project? Better yet, what do you do to keep them and help them grow to life-long contributors? Come, share your tips, ask your questions and learn what others do. If you're a recent / new / want to be open contributor, we'd love to hear your questions, thoughts, and fears too!

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

Organize/Submit a BoF!

Moderators
avatar for Yo Yehudi

Yo Yehudi

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

Wednesday June 27, 2018 12:30pm - 1:30pm
PAB 130 Performing Arts Building

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.

Organize/Submit a BoF!

Moderators

Wednesday June 27, 2018 12:30pm - 1:30pm
PAB 104 Performing Arts Building, Reed Campus

12:30pm

BoF: Let's talk about WDL
Whether you’re already a user or simply interested, come join us as we discuss the Workflow Description Language (WDL) and the OpenWDL organization. In particular we’ll be looking at what’s new in WDL 1.0 and what would be good to include for 1.1 and beyond.

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

Organize/Submit a BoF!

Moderators
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 software... Read More →
CL

Chris Llanwarne

Broad Institute

Speakers
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 bioinformatics... Read More →



Wednesday June 27, 2018 12:30pm - 1:30pm
PAB 332 Performing Arts Building, Reed Campus

12:30pm

BoF: Stable and persistent URIs in biological data integration systems
FAIR principles state that each entity needs a stable and persistent URI.  This translates into links that always point to the same information (gene, organism, ... )  and are valid forever, thus making experiments  reproducible.

More easily said than done!

Same data providers have solved it, and we can look at their approach for inspiration although for data integrators there are different challenges, as well as the need for easy of creation and maintenance.

Please come and discuss with us on possible solutions.

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

Organize/Submit a BoF!

Moderators
avatar for Daniela Butano

Daniela Butano

Research SofwareEngineer, InterMine, University of Cambridge

Wednesday June 27, 2018 12:30pm - 1:30pm
PAB 131 Performing Arts Building, Reed Campus

1:40pm

BOSC Session 3: All About Data
The latest and greatest from BOSC community members, focusing on the data. 

Moderators
avatar for Bastian Greshake Tzovaras

Bastian Greshake Tzovaras

co-founder, openSNP

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

1:40pm

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

Moderators
JG

Jeremy Goecks

Assistant Professor of Biomedical Engineering and Computational Biology, Oregon Health & Science University (OHSU)

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

1:41pm

miRTop: An open source community project for the development of a unified format file for miRNA data

Speakers
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. :)



Wednesday June 27, 2018 1:41pm - 2:00pm
Vollum Lecture Hall Vollum College Center, Reed Campus

1:41pm

Galaksio, a more user friendly interface for Galaxy using workflows
Slides @ F1000

Authors
Tomas Klingström, Oskar Danielsson, Rafael Hernández-de-Diego and Erik Bongcam-Rudloff

Speakers
avatar for Tomas Klingström

Tomas Klingström

Project manager, SLU-Global Bioinformatics Centre, Swedish University of Agricultural Sciences
Biobanking, data management from sampling to publication, support infrastructures, and Africa.



Wednesday June 27, 2018 1:41pm - 2:00pm
Eliot Chapel Eliot Hall, Reed Campus

2:00pm

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
Eliot Chapel Eliot Hall, Reed Campus

2:20pm

InterMine 2.0: More than fifteen years of open biological data integration
Speakers
avatar for Yo Yehudi

Yo Yehudi

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



Wednesday June 27, 2018 2:20pm - 2:40pm
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
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy. | Bérénice is also passionate about training. She regularly gives workshops on... Read More →



Wednesday June 27, 2018 2:20pm - 2:40pm
Eliot Chapel Eliot Hall, Reed Campus

2:40pm

GRADitude: A computational tool for the analysis of Grad-seq data
Speakers
SD

Silvia Di Giorgio

PhD-student, University of Würzburg



Wednesday June 27, 2018 2:40pm - 2:45pm
Vollum Lecture Hall Vollum College Center, Reed Campus

2:40pm

The usegalaxy.* servers: democratizing computational resources for life sciences at a new level
Slides @ F1000

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
Eliot Chapel Eliot Hall, Reed Campus

2:45pm

2:50pm

Reproducible data analysis with Snakemake
Speakers
JK

Johannes Köster

Genome Informatics, Institute of Human Genetics, University of Duisburg-EssenDepartment of Medical Oncology, Harvard Medical Schoolhttps://koesterlab.github.io



Wednesday June 27, 2018 2:50pm - 2:55pm
Vollum Lecture Hall Vollum College Center, Reed Campus

2:55pm

Q&A for lightning talks in this session⚡
Got questions for this session's lightning talk speakers?  Ask them now.

Wednesday June 27, 2018 2:55pm - 2:59pm
Vollum Lecture Hall Vollum College Center, Reed Campus

3:00pm

Posters & Demos: Odd Numbered
Posters and demos will be presented on two days and concurrently with 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

3:01pm

B01: Association Mapping and Landscape Genomics of Georeferenced Forest Trees via CartograTree and TreeGenes
Poster @ F1000

Authors
Taylor Falk, Nic Herndon, Emily Grau, Sean Buehler, Peter Richter and Jill Wegrzyn

Speakers
avatar for Taylor Falk

Taylor Falk

Researcher, University of Connecticut
Plant genomics researcher, working on managing bioinformatics databases, annotation, and helping create CartograTree and TreeGenes.



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B03: CRI iAtlas: an interactive portal for immuno-oncology research
Authors
James Eddy, Vesteinn Thorsson, Andrew Lamb, David Gibbs, Ilya Shmulevich and Justin Guinney

Speakers
avatar for James Eddy

James Eddy

Senior Scientist, Sage Bionetworks
I'm a data scientist, systems biologist, and an advocate for reproducible, open source, open access science and software. In collaboration with colleagues at Sage Bionetworks and across genomics and health research networks, I'm focused on developing infrastructure, standards, and... Read More →


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B05: One Week to 1,000 Whole Genomes with Open Source: Arvados, CWL, and bcbio
Authors
Peter Amstutz and Tom Morris

Speakers

Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B07: Classification of short read alignments from xenograft samples
Authors
Lawrence Heisler, Heather D'Souza, Séverine Cathelin, Steven Chan, Morgan Taschuk, Jessica Miller and Lars Jorgensen

Speakers
avatar for Lawrence Heisler

Lawrence Heisler

Manager, Bioinformatics Support, Ontario Institute for Cancer Research


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B09: Enabling Machine Learning at Scale with “Tiled” Human Genomes
Authors
Sarah Wait Zaranek, Abram Connelly and Alexander Wait Zaranek

Speakers
avatar for Sarah Wait Zaranek

Sarah Wait Zaranek

President, Curoverse Research
Interested in large data, WGS, machine learning, open source standards.


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B11: flowDashboard: An Interactive Dashboard for Comparative Flow Analysis
Poster @ F1000

Authors
Ted Laderas, Gwendolyn Swarbrick, David Lewinsohn, Deborah Lewinsohn, Evan Lind and Shannon McWeeney

Speakers
avatar for Ted Laderas

Ted Laderas

Assistant Professor, Oregon Health & Science University
I am an Assistant Professor in Medical Informatics. I am active in teaching data science and visualization to our graduate, staff, and postdocs at OHSU. I do my best to be a good collaborator.



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B13: READemption - from reads to knowledge
Authors
Till Sauerwein, Diarmaid Tobin, Thorsten Bischler and Konrad Förstner

Speakers

Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B15: RyuGoo-Saba: a CWL-based execution engine utilizing cloud resources for big data analysis in life science
Poster @ F1000

Authors
Hirotaka Suetake and Ryo Nakaki

Speakers
avatar for Hirotaka Suetake

Hirotaka Suetake

Research, Rhelixa Inc.



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B17: High-performance computing service in the Health Science and Human Services Library at University of Maryland Baltimore
Poster @ F1000

Authors
Jean-Paul Courneya and Alexa Mayo

Speakers
avatar for Jean-Paul Courneya

Jean-Paul Courneya

Bioinformationist, University of Maryland - Baltimore HS/HSL
RNA seq, Galaxy Administration, learning bioinformatics, skateboarding.



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B19: Reproducible big data science: A case study in continuous FAIRness
Authors
Ravi Madduri

Speakers

Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B21: FAIRsharing: Working with the community to map the landscape of standards, databases and data policies
Authors
Peter McQuilton, Massimiliano Izzo, Alejandra Gonzalez-Beltran, Allyson Lister, Rocca-Serra Philippe, Thurston Milo and Susanna-Assunta Sansone


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B23: Oxidizing Python: writing extensions in Rust
Poster @ F1000

Authors
Luiz Irber

Speakers

Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B25: The GTrack ecosystem: expressive file formats for genomic track data and metadata - through compilation, exchange, storage and analysis
Poster

Authors
Sveinung Gundersen, Matúš Kalaš, Boris Simovski, Brynjar Rongved, Henrik Glasø Skifjeld, Sivert Kronen Hatteberg, Osman Abul, Arnoldo Frigessi, Geir Kjetil Sandve and Eivind Hovig



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B27: JASS: a free and open source software for the joint analysis and interactive analysis of GWAS results
Poster @ F1000

Authors
Hervé Ménager, Vincent Guillemot, Pierre Lechat, Hanna Julienne, Carla Lasry, Vincent Laville, Bjarni Vilhjalmsson and Hugues Aschard

Speakers
avatar for Hervé Ménager

Hervé Ménager

Research Engineer, Institut Pasteur
Bioinformatics and Biostatistics Hub of the C3BI, Institut Pasteur


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B29: Extended Extraction Transform Load: A novel framework for batch jobs on cloud computing resources
Poster @ F1000

Authors
Hiromu Ochiai, Kenichi Chiba, Ai Okada, Satoru Miyanoand Yuichi Shiraishi

Speakers
avatar for Hiromu Ochiai

Hiromu Ochiai

Researcher, National Cancer Center Japan
https://github.com/otiai10



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B31: The Arachne Graph Database Server
Authors
Alexander Buchanan, Ryan Spangler, Brian Walsh and Kyle Ellrott

Speakers

Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B33: BioThings Hub: An API Gateway for Biomedical Knowledge
Poster @ F1000

Authors
Sebastien Lelong, Cyrus Afrasiabi, Jiwen Xin, Ginger Tsueng, Andrew Su and Chunlei Wu

Speakers
avatar for Sébastien Lelong

Sébastien Lelong

Research Programmer, Scripps Research Institute



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B35: Modernising somatic mutation calling pipelines with Open Source tools and Containers.
Authors
Keiran Raine, Adam Butler, Peter J. Campbell, Peter Clapham, David Jones, Jon W. Teague, Andrew Menzies, Lucy Stebbings, Luca Barbon, Matt Lane and Yaobo Xu

Speakers
avatar for Mr Keiran M Raine

Mr Keiran M Raine

Principal Bioinformatician, Wellcome Sanger Institute
Docker, Dockstore, cwl, perl, python, javascript, react, JBrowse, NGS sequencing. | https://keiranmraine.github.io/


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B37: Accumulating computational resource usage of data analysis workflow to select suitable cloud instance
Poster @ F1000

Authors
Tazro Ohta, Tomoya Tanjo and Osamu Ogasawara

Speakers
avatar for Tazro Ohta

Tazro Ohta

Researcher, DBCLS


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B39: CWL-Airflow pipeline manager as a backend for BioWardrobe data analysis platform
Poster @ F1000

Authors
Andrey Kartashov, Michael Kotlair and Artem Barski

Speakers
avatar for Andrey Kartashov

Andrey Kartashov

Senior Software Developer, Cincinnati Childrens Hospital
I am a scientific programmer who performed data analysis in areas ranging from space science to physical chemistry and now for functional genomics. I am the developer behind BioWardrobe, an integrated platform for analysis of epigenomics and transcriptomics data that helps researchers... Read More →



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B41: Scaling bioinformatics analysis using Nextflow and AWS
Authors
Francesco Strozzi, Paolo Di Tommaso, Evan Floden and Cedric Notredame


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B43: CWLProv - Interoperable retrospective provenance capture and its challenges
Poster @ F1000

Authors
Farah Zaib Khan, Stian Soiland-Reyes, Richard O. Sinnott, Andrew Lonie and Michael R. Crusoe

Speakers
avatar for Farah Zaib Khan

Farah Zaib Khan

The University of Melbourne
Bioinformatics Workflow developer | CWL enthusiast | Working on Provenance of bioinformatics workflows


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B45: CWL Community Update
Authors
Peter Amstutz, John Chilton, Kaushik Ghose, Brandi Davis Dusenbery, Jeff Gentry, Hervé Ménager, Stian Soiland-Reyes and Michael Crusoe

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 →


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

D01: From laptop to super-computer: standardizing installation and management of Galaxy
Authors
Nuwan Goonasekera, Enis Afgan and Vahid Jalili

Speakers
NG

Nuwan Goonasekera

University of Melbourne


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

D03: Aurora Galaxy Tools: Using R Markdown as a framework to build interactive Galaxy tool output reports
Authors
Ming Chen, Bradford Condon, Abdullah Almsaeed, Connor Wytko, Stephen Ficklin and Margaret Staton

Speakers

Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

D05: Open Humans - connecting, sharing and analyzing personal data that enables community-driven research
Authors

Speakers
avatar for Bastian Greshake Tzovaras

Bastian Greshake Tzovaras

co-founder, openSNP


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

D07: Building a community menagerie of automated variant validations
Authors

Speakers
avatar for Brad Chapman

Brad Chapman

Bioinformatics Core, Harvard Chan School
Brad is a senior research scientist in the Bioinformatics Core at Harvard T.H. Chan School of Public Health. He develops open source community built infrastructure for analyzing biological data, focusing on multi platform interoperability and automated validation against heterogeneous... Read More →


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

D09: taxa: taxonomic data standards and methods for R and Python
Authors


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G01: Galaxy-E, a first stage towards collaborative data analysis by citizens
Authors
Yvan Le Bras, Valentin Chambon, Alan Amosé, Julien Sananikone, Elise Brax, Marianne Linares, Marie Delannoy, Grégoire Loïs and Romain Julliard

Speakers
avatar for Yvan Le Bras

Yvan Le Bras

French National Museum of Natural History



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G03: Predicting Galaxy Tool Runtimes with Random Forests
Poster @ F1000

Authors
Anastasia Tyryshkina and Anton Nekrutenko

Speakers
AT

Anastasia Tyryshkina

Penn State University



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G05: Galaksio, a more user friendly interface for Galaxy using workflows
Poster @ F1000

Authors
Tomas Klingström, Oskar Danielsson, Rafael Hernández-De-Diego and Erik Bongcam-Rudloff

Speakers
avatar for Tomas Klingström

Tomas Klingström

Project manager, SLU-Global Bioinformatics Centre, Swedish University of Agricultural Sciences
Biobanking, data management from sampling to publication, support infrastructures, and Africa.



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G07: Identifying suitable spliced mapper and genomic assembly for variant detection
Poster @ F1000

Authors
Akila Parvathy Dharshini, Michael Gromiha M and Taguchi Y.H

Speakers
avatar for Akila Parvathy Dharshini

Akila Parvathy Dharshini

PhD student, Indian institute of technology
Hi All, | I am a research scholar. Currently, I am Working on RNA-seq analysis of neurodegenerative disorders and large-scale gene network analysis. I would like to talk about the variant effect in regulatory elements.



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G09: EWAS-Galaxy: a tool suite for population epigenetics integrated into the Galaxy
Poster

Authors
Katarzyna Murat and Krzysztof Poterlowicz

Speakers
avatar for Krzysztof Poterlowicz

Krzysztof Poterlowicz

University of Bradford



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G11: Candidate Gene Methylation quantification (CandiMeth) Within the Galaxy Bioinformatics Interface
Poster @ F1000

Authors
Sara-Jayne Thursby, Sarah-Jayne Mackin, Rachelle Irwin and Colum Walsh

Speakers
ST

Sara-Jayne Thursby

University of Ulster



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G13: Bacterial genomics in Galaxy
Poster 

Authors
Delphine Larivière, Han Mei, Mallory Freeberg, James Taylor and Anton Nekrutenko



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G15: Galaxy in a proteomics core facility
Poster

Authors
Jeremy Volkening, Grzegorz Sabat, Gregory Barrett-Wilt and Michael Sussman

See also

Speakers


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G17: Evaluation of moFF and FlashLFQ for label-free peptide quantification in proteomic workflows within the Galaxy-P framework
Poster @ F1000

Authors
Subina Mehta, Caleb Easterly, James Johnson, Bjoern Gruening, Andrea Argentini, Robert Millikin, Michael Shortreed, Thomas McGowan, Praveen Kumar, Lennart Martens, Lloyd Smith, Timothy Griffin and Pratik Jagtap

Speakers
avatar for Subina Mehta

Subina Mehta

Researcher, University of Minnesota



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G19: Implementation of machine learning algorithms for medulloblastoma classification in a local galaxy server
Poster @ F1000

Authors
Luciane Sussuchi Da Silva, Letícia Ferro Leal, Thais Hosokawa, Murilo Machado, Michael Taylor, Adriane Feijó Evangelista and Rui Manuel Reis

Speakers
avatar for Luciane Sussuchi Da Silva

Luciane Sussuchi Da Silva

Postdoc, Barretos Cancer Hospital



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G21: The Mammalian Ortholog and Annotation Database: enhanced ortholog information with an accurate identifier mapping between NCBI and Ensembl accessible from a Galaxy-server
Poster

Authors
Jochen Bick¹, Susanne Ulbrich¹ and Stefan Bauersachs²

  1. ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland
  2. University of Zurich, Genetics and Functional Genomics, Clinic for Animal Reproduction Medicine, Zurich, Switzerland


Speakers
avatar for Jochen Bick

Jochen Bick

ETH Zürich



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G23: SECIMTools: A suite of Metabolomics Data Analysis Tools
Poster @ F1000

Authors
Oleksandr Moskalenko, Alison Morse, Alexander Kirpich, Miguel Ibarra, Justin Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi and Lauren McIntyre



Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G25: VKMZ: Visualizing Metabolomics on a van Krevelen Diagram through Galaxy
Poster

Authors
Mark Esler, Stephen Brockman, Arthur Eschenlauer, Tim Griffin and Adrian Hegeman

Speakers


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G27: BioXSD | BioJSON | BioYAML – towards unified formats for sequences, alignments, features, and annotations
Poster @ F1000

Authors
Matúš Kalaš, Sveinung Gundersen, Inge Jonassen and The Bioxsd And Gtrack Contributors

Speakers
avatar for Matúš Kalaš

Matúš Kalaš

University of Bergen
Open science & society, EDAM ontology, ELIXIR Norway, Bio.Tools, BioXSD|GTrack


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G29: ELIXIR contributions to the FAIRness of Bioinformatics resources, with bio.tools, Galaxy and CWL
Authors
Kenzo-Hugo Hillion, Fabien Mareuil, Olivia Doppelt Azeroual, Hervé Ménager, Galaxy, CWL and bio.tools communities

Speakers
KH

Kenzo-Hugo Hillion

Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI); Institut Pasteur de Paris


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G31: A fruitful year for the Galaxy Training materials
Poster

Authors
Bérénice Batut, Saskia Hiltemann, Bjoern Gruening and Galaxy Training Network

Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy. | Bérénice is also passionate about training. She regularly gives workshops on... Read More →


poster png

Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G33: Refinery: a data management, analysis, and visualization platform utilizing the Galaxy workbench
Poster @ F1000

Authors
Nils Gehlenborg 1,3, Shannan J Ho Sui 2,3, David R Jones 4, Jennifer K Marx 1, Chuck McCallum 1, Sarah Morgan 4, Geoffrey M Nelson 1, Scott Ouellette 1, Ilya Sytchev 2, Winston Hide 2,3,4, Peter J Park 1,3

  1. Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
  2. Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
  3. Harvard Stem Cell Institute, Cambridge, MA, USA
  4. Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK

Speakers


Wednesday June 27, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

4:00pm

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

Moderators
avatar for Brad Chapman

Brad Chapman

Bioinformatics Core, Harvard Chan School
Brad is a senior research scientist in the Bioinformatics Core at Harvard T.H. Chan School of Public Health. He develops open source community built infrastructure for analyzing biological data, focusing on multi platform interoperability and automated validation against heterogeneous... Read More →

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

4:01pm

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

Speakers
avatar for Jason Williams

Jason Williams

Cold Spring Harbor Laboratory
Jason is Assistant Director, External Collaborations of Cold Spring Harbor Laboratory’s DNA Learning Center, and is the Education, Outreach, and Training lead for CyVerse (A U.S. national life science cyberinfrastructure funded by NSF). Jason organizes, instructs, and speaks at... Read More →



Wednesday June 27, 2018 4:01pm - 4:20pm
Vollum Lecture Hall Vollum College Center, Reed Campus

4:20pm

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

Moderators
avatar for Brad Chapman

Brad Chapman

Bioinformatics Core, Harvard Chan School
Brad is a senior research scientist in the Bioinformatics Core at Harvard T.H. Chan School of Public Health. He develops open source community built infrastructure for analyzing biological data, focusing on multi platform interoperability and automated validation against heterogeneous... Read More →

Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy. | Bérénice is also passionate about training. She regularly gives workshops on... Read More →
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... Read More →
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... Read More →
avatar for Jason Williams

Jason Williams

Cold Spring Harbor Laboratory
Jason is Assistant Director, External Collaborations of Cold Spring Harbor Laboratory’s DNA Learning Center, and is the Education, Outreach, and Training lead for CyVerse (A U.S. national life science cyberinfrastructure funded by NSF). Jason organizes, instructs, and speaks at... Read More →


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!
Organize/Submit a BoF!

Birds-of-a-feather are infornal gatherings or participants with a shared interest.  Anyone can organize a BoF session.  BoFs will be accepted until we run out of space for them.

BoFs offered in this session:


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

BoF: Educating Funders/PIs on Open Science
What would a Carpentries style workshop look like to help educate persons in academia on open source and open science to make them better funders, reviewers (grants/publications/etc.)? We have an outline started but want your thoughts. Educating these folks would (we hope) accelerate policy change and foster better science.

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

Organize/Submit a BoF!

Moderators
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... Read More →
avatar for Jason Williams

Jason Williams

Cold Spring Harbor Laboratory
Jason is Assistant Director, External Collaborations of Cold Spring Harbor Laboratory’s DNA Learning Center, and is the Education, Outreach, and Training lead for CyVerse (A U.S. national life science cyberinfrastructure funded by NSF). Jason organizes, instructs, and speaks at... Read More →


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

5:40pm

BoF: Open Bioinformatics Foundation Community (OBF)
BoF Report

The BoF for Open Bioinformatics Foundation members and prospective members! You probably know of the OBF as the organisers of BOSC, but maybe you'd like to learn a little more about us? Or maybe you're an experienced OBF member and BOSC attendee, and you'd like to come hang out -  or perhaps you'd even like to get involved more, or pitch a nifty community idea. Come and chat over dinner!

Anyone who is involved in open source or open science is welcome to join the OBF, and there is no membership fee--see  https://www.open-bio.org/wiki/Main_Page

Planning to attend this BoF?  Please login and add yourself to this session.
---------------------------
Organize/Submit a BoF!

Moderators
avatar for Yo Yehudi

Yo Yehudi

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


Wednesday June 27, 2018 5:40pm - 7:40pm
Reed Commons Cafe Reed College Commons, Reed Campus

5:40pm

BoF: Sharing and Leveraging Galaxy Tool Execution Data
How long will this bwa_mem job take? How much memory will it consume? Can we set dynamic walltimes? Is it efficient for us to give this tool more cpu cores?

We are moving closer to having better answers for these based on the job metadata mined from the Galaxies that opt-in to share and on a machine learning project spearheaded by Anastasia Tyryshkina.

Let's discuss what we can do with this and how to participate in this emerging database of unprecedented depth.

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

Organize/Submit a BoF!

Moderators
avatar for Martin Čech

Martin Čech

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

Anastasia Tyryshkina

Penn State University

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

5:40pm

BoF: Using Galaxy in bioinformatics support infrastructures
Bioinformatics support facilities at universities are becoming increasingly common and Galaxy is being used or considered by several universities. The role of core facility scientists supporting researchers in bioinformatics can provide a first line of support for Galaxy and also help shape the further development of the ecosystem. Reaching out to discuss key Galaxy servers, other suitable tools and how to obtain user feedback will therefore hopefully make for a pleasant and constructive dinner.

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

Organize/Submit a BoF!

Moderators
avatar for Tomas Klingström

Tomas Klingström

Project manager, SLU-Global Bioinformatics Centre, Swedish University of Agricultural Sciences
Biobanking, data management from sampling to publication, support infrastructures, and Africa.

Wednesday June 27, 2018 5:40pm - 7:40pm
Reed Commons Cafe Reed College Commons, Reed Campus

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

6:00pm

BOSC & GCC Social Mixer | by Lifebit
Lifebit's mission would not be possible without the diverse Bioinformatics Open Source community.

We admire everyone who is involved in contributing to the ecosystem and therefore, we would like to give it back to you and get a chance to meet over drinks during GCCBOSC, in Portland.

Join us for a GCCBOSC side-event and let us show our gratitude for your contributions. Feel free to come any time from 6PM onwards.

Interested?  Please sign up here.

Sponsors
avatar for Lifebit

Lifebit

Lifebit is on a mission to build a cloud-based cognitive system that can reason about omics data like humans do.  Lifebit is developing the first platform that brings the computation to your omics data and learns from it. It connects with your existing cloud providers - your data stays... Read More →


Wednesday June 27, 2018 6:00pm - 10:00pm
Woodstock Neighborhood

8:00pm

Birds-of-a-Feather (BoFs), wherever you want!
Organize/Submit a BoF!

Birds-of-a-feather are informal 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.

BoFs offered during this flocking:


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

8:00pm

BoF: Nextflow Gathering
General meet up for Nextflow users, developers and any one interested in discussing new features, use cases and plans for the future of the project. Current idea is for an informal gathering at one of the local brew pubs.

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

Organize/Submit a BoF!

Moderators
Wednesday June 27, 2018 8:00pm - 10:00pm
Sitka Dorm, Ground Floor Sitka Residence Hall

8:00pm

BoF: Snakemake get together
Let's go to a bar and talk about future development and contributions to Snakemake itself and all the community projects like workflows, wrappers, and profiles.

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

Organize/Submit a BoF!

Moderators
JK

Johannes Köster

Genome Informatics, Institute of Human Genetics, University of Duisburg-EssenDepartment of Medical Oncology, Harvard Medical Schoolhttps://koesterlab.github.io

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

8:00am

Conference desk open
Need help?  Here's where to get it.  You can also checkin for the following day too.


Thursday June 28, 2018 8:00am - 6:00pm
PAB Atrium Performing Arts Building, Reed College

9:00am

BOSC Session 5: Developer Tools and Libraries
Talks and lightning of interest to the BOSC community.

Moderators
avatar for Peter Cock

Peter Cock

The James Hutton Institute
Bioinformatician at the James Hutton Institute, a member of the BOSC organizing committee, treasurer of the Open Bioinformatics Foundation, and a core developer on the Biopython project.

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

9:00am

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

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

9:01am

9:01am

Galaxy Enables Integrated Analysis of Phenotypic, Genotypic, and Environmental Data for Geo-referenced Trees in CartograTree
Slides @ F1000

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 9:01am - 9:20am
Eliot Chapel Eliot Hall, Reed Campus

9:20am

The Funnel Task Execution Server


Thursday June 28, 2018 9:20am - 9:40am
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
Slides @ F1000

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
avatar for Luke Sargent

Luke Sargent

Oregon Health and Science University (OHSU)
Hello, I am a developer on the G-OnRamp project (gonramp.org). I am happy to talk about all manifestations of the logical majesty of the Machine Spirit.



Thursday June 28, 2018 9:20am - 9:40am
Eliot Chapel Eliot Hall, Reed Campus

9:40am

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
avatar for Thomas Matthews

Thomas Matthews

Public Health Agency of Canada



Thursday June 28, 2018 9:40am - 10:00am
Eliot Chapel Eliot Hall, Reed Campus

9:45am

Extended Extraction Transform Load: A novel framework for batch jobs on cloud computing resources
Speakers
avatar for Hiromu Ochiai

Hiromu Ochiai

Researcher, National Cancer Center Japan
https://github.com/otiai10



Thursday June 28, 2018 9:45am - 9:50am
Vollum Lecture Hall Vollum College Center, Reed Campus

9:50am

9:55am

The Arachne Graph Database Server
Speakers

Thursday June 28, 2018 9:55am - 10:00am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:00am

Owlery: An easily deployable web service for making reasoning queries over OWL ontologies web-native
Speakers
avatar for Hilmar Lapp

Hilmar Lapp

Director of Informatics, Duke University, Center for Gemonic and Computational Biology



Thursday June 28, 2018 10:00am - 10:05am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:00am

Galaxy in a proteomics core facility
→ Slides @ F1000

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
Eliot Chapel Eliot Hall, Reed Campus

10:05am

taxa: taxonomic data standards and methods for R and Python

Thursday June 28, 2018 10:05am - 10:10am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:10am

Q&A for lightning talks in this session⚡
Got questions for this session's lightning talk speakers?  Ask them now.

Thursday June 28, 2018 10:10am - 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

BOSC Session 6: Workflows
The second day of BOSC continues with more accepted talks, and other content, this time focusing on workflow.

Moderators
avatar for Karsten Hokamp

Karsten Hokamp

Bioinformatics Research Officer, Trinity College Dublin
You can talk to me about bioinformatics and the soccer world cup in Russia. Also, let me know if you ever saw Greg Sage and the Wipers live!

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

10:50am

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

Moderators
MD

Maria Doyle

Application and Training Specialist, Peter MacCallum Cancer Centre

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

10:51am

CWLProv - Interoperable retrospective provenance capture and its challenges
Speakers
avatar for Farah Zaib Khan

Farah Zaib Khan

The University of Melbourne
Bioinformatics Workflow developer | CWL enthusiast | Working on Provenance of bioinformatics workflows


Thursday June 28, 2018 10:51am - 11:10am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:51am

Quantifying Functional Microbiomes: An integrated, quantitative metaproteomics approach reveals connections between taxa, function and protein expression in complex microbiomes
→ Slides @ F1000

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 10:51am - 11:10am
Eliot Chapel Eliot Hall, Reed Campus

11:10am

11:10am

GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline
Slides @ F1000

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
Eliot Chapel Eliot Hall, Reed Campus

11:30am

The GA4GH/DREAM Workflow Execution Challenge
Speakers
avatar for James Eddy

James Eddy

Senior Scientist, Sage Bionetworks
I'm a data scientist, systems biologist, and an advocate for reproducible, open source, open access science and software. In collaboration with colleagues at Sage Bionetworks and across genomics and health research networks, I'm focused on developing infrastructure, standards, and... Read More →



Thursday June 28, 2018 11:30am - 11:35am
Vollum Lecture Hall Vollum College Center, Reed Campus

11:30am

Galaxy HiCExplorer: HiCExplorer, deepTools3 and pyGenomeTracks
Slides @ F1000

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
Eliot Chapel Eliot Hall, Reed Campus

11:35am

11:40am

CWL-Airflow pipeline manager as a backend for BioWardrobe data analysis platform
Speakers
avatar for Andrey Kartashov

Andrey Kartashov

Senior Software Developer, Cincinnati Childrens Hospital
I am a scientific programmer who performed data analysis in areas ranging from space science to physical chemistry and now for functional genomics. I am the developer behind BioWardrobe, an integrated platform for analysis of epigenomics and transcriptomics data that helps researchers... Read More →



Thursday June 28, 2018 11:40am - 11:45am
Vollum Lecture Hall Vollum College Center, Reed Campus

11:45am

11:50am

11:50am

Using Galaxy to analyze TCGA data: the experience of a Brazilian center
Slides @ F1000

Thais Talarico1, Murilo Machado1, Luciane Sussuchi da Silva1, José Humberto Tavares GuerreiroFregnani1,RuiManuelReis1,AdrianeFeijóEvangelista1

  1. Barretos Cancer Hospital

Speakers
avatar for Thais Talarico

Thais Talarico

Project assistant/Student, Barretos Cancer Hospital
I'm a Pharmacist who works with project design, development, and management. I'm also a master candidate in Oncology focused on Bioinformatics and a Systems analysis and development student.



Thursday June 28, 2018 11:50am - 11:56am
Eliot Chapel Eliot Hall, 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
Eliot Chapel Eliot Hall, Reed Campus

11:55am

Q&A for lightning talks in this session⚡
Got questions for this session's lightning talk speakers?  Ask them now.

Thursday June 28, 2018 11:55am - 12:05pm
Vollum Lecture Hall Vollum College Center, Reed Campus

11:56am

ImmPort Galaxy, facilitating analysis and meta-analysis of flow cytometry data
Slides @ F1000

Authors:
Cristel G Thomas1, Elizabeth Thomson1, Henry Schaefer2, Patrick Dunn1, John C Campbell1

  1. Northrop Grumman TS, Rockville, MD USA
  2. ESAC, Inc, Rockville, MD, USA

Speakers


Thursday June 28, 2018 11:56am - 12:02pm
Eliot Chapel Eliot Hall, Reed Campus

12:02pm

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
→ Slides @ Prezi

Authors:
Boris Simovski 1, Chakravarthi Kanduri 1,2, Sveinung Gundersen 1,3, Dmytro Titov 1,3, Diana Domanska 1, Christoph Bock 4,5,6, Lara Bossini-Castillo 7, Maria Chikina 8, Alexander Favorov 9,10, Ryan M. Layer 11,12, Andrey A. Mironov 13,14,15, Aaron R. Quinlan 11,12,16, Nathan C. Sheffield 17, Gosia Trynka 7 and Geir K. Sandve 1,2

  1. Department of Informatics, University of Oslo, Gaustadalleen 23 B, N-0373 Oslo, Norway
  2. K. G. Jebsen Centre for Coeliac Disease Research, Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway
  3. Elixir Norway - Oslo node, Department of Informatics, University of Oslo, Gaustadalleen 23 B, N-0373 Oslo, Norway
  4. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
  5. Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
  6. Max Planck Institute for Informatics, 66123 Saarbrucken, Germany
  7. 7Cellular Genetics Programme, Wellcome Sanger Institute, CB10 1SA Hinxton, UK
  8. University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15213, USA, 
  9. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, 550 N Broadway, Baltimore, MD 21205, USA
  10. Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Gubkina Street 3, Moscow 119333, Russia
  11. Department of Human Genetics, University of Utah, 15 N 2030 E, Salt Lake City, UT 84112, USA 
  12. USTAR Center for Genetic Discovery, University of Utah, 15 N 2030 E, Salt Lake City, UT 84112, USA
  13. Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Lab. Bldg B, Vorobiovy Gory 1-73, Moscow 119992, Russia
  14. Skolkovo Institute of Science and Technology, Nobelya ul. 3, Moscow 121205, Russia
  15. Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karenty per. 19, Moscow 127994, Russia
  16. Department of Biomedical Informatics, University of Utah, 421 Wakara Way, Salt Lake City, UT 84108, USA and 
  17. Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903 USA





Thursday June 28, 2018 12:02pm - 12:08pm
Eliot Chapel Eliot Hall, Reed Campus

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!
Organize/Submit a BoF!

Birds-of-a-feather are informal 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.

BoFs offered during this flocking:


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

12:30pm

BoF: Common Workflow Language community chat
Meet other CWL users and learn more about CWL v1.1 and beyond!

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

Organize/Submit a BoF!

Moderators
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
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 →
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 bioinformatics... Read More →
avatar for Hervé Ménager

Hervé Ménager

Research Engineer, Institut Pasteur
Bioinformatics and Biostatistics Hub of the C3BI, Institut Pasteur

Thursday June 28, 2018 12:30pm - 1:30pm
PAB 332 Performing Arts Building, Reed Campus

12:30pm

BoF: Galaxy Training Material: Let's improve the contributions!
Notes from BoF (thanks to Simon Gladman)

The Galaxy Training Network has developed an infrastructure to deliver interactive training based on Galaxy: one central place to aggregate training materials covering many current research topics. The tutorials are developed and maintained by the community via a GitHub repository.

Given all our effort, contributing to the Galaxy Training material may be sometimes cumbersome and not always easy. Let's discuss how we could improve the contributor experience!

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

Organize/Submit a BoF!

Moderators
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy. | Bérénice is also passionate about training. She regularly gives workshops on... Read More →

Thursday June 28, 2018 12:30pm - 1:30pm
PAB 130 Performing Arts Building

12:30pm

BoF: Preparing for the next steps in AI
We'll discuss applying AI to bioinformatics analysis.   Some challenges that can be addressed with AI:

  • Efficient data management 
  • Optimizing workflow and analysis
  • Future-proofing infrastructure
  • Scalability / availability

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

Organize/Submit a BoF!

Moderators
Thursday June 28, 2018 12:30pm - 1:30pm
PAB 131 Performing Arts Building, Reed Campus

12:30pm

BoF: Standardizing Galaxy deployments
There's a lot of repeated effort out there regarding Galaxy setup, configuration, maintenance, upgrades, etc. Let's talk about some ideas, requirements, and directions for providing a framework to standardize how a vast majority of Galaxy servers can set up. This is primarily intended for individuals maintaining Galaxy instances. Please come with some requirements for your environments so we can discuss corner cases and desires.

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

Organize/Submit a BoF!

Moderators
avatar for Enis Afgan

Enis Afgan

Research scientist, Galaxy Project, Johns Hopkins University
NG

Nuwan Goonasekera

University of Melbourne

Thursday June 28, 2018 12:30pm - 1:30pm
PAB 104 Performing Arts Building, Reed Campus

1:40pm

BOSC Session 7: Project Updates and Late-Breaking Research
Updates on projects in the BOSC community.  Plus, Late Breaking Lightning Talks.

Moderators
avatar for Chris Fields

Chris Fields

Associate Director, HPCBio, University of Illinois Urbana-Champaign
I am a reformed molecular microbiologist associatively directing a moderately sized group of very smart people from crazy diverse backgrounds, and we all work on anything and everything sequence-related. No, really.

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

1:40pm

GCC Session 7: Community Update(s)
The session includes the Galaxy Project update talk, and lightning talks from the Galaxy community. 

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

1:41pm

OBF update
Speakers
avatar for Hilmar Lapp

Hilmar Lapp

Director of Informatics, Duke University, Center for Gemonic and Computational Biology


Thursday June 28, 2018 1:41pm - 1:50pm
Vollum Lecture Hall Vollum College Center, Reed Campus

1:41pm

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

Speakers
avatar for Dan Blankenberg

Dan Blankenberg

Assistant Professor, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University
JG

Jeremy Goecks

Assistant Professor of Biomedical Engineering and Computational Biology, 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 1:41pm - 2:10pm
Eliot Chapel Eliot Hall, Reed Campus

1:50pm

GSOC update
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 →



Thursday June 28, 2018 1:50pm - 2:00pm
Vollum Lecture Hall Vollum College Center, Reed Campus

2:00pm

Biopython Project Update 2018

Speakers
avatar for Peter Cock

Peter Cock

The James Hutton Institute
Bioinformatician at the James Hutton Institute, a member of the BOSC organizing committee, treasurer of the Open Bioinformatics Foundation, and a core developer on the Biopython project.



Thursday June 28, 2018 2:00pm - 2:07pm
Vollum Lecture Hall Vollum College Center, Reed Campus

2:07pm

2:10pm

Integrative proteo-transcriptomics workflows within the Galaxy framework to explore the correlation between the expression of RNA and proteins
Poster @ F1000

Authors:
Praveen Kumar 1,2, Priyabrata Panigrahi 3, James Johnson 4, Caleb Easterly 2, Subina Mehta 2, Andrew Rajczewski 2, RaySajulga 2, Mohammad Heydarian 5, Krishanpal Anamika 3, Timothy Griffin 2, Pratik Jagtap 2

  1. Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, USA
  2. Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA
  3. LABS, Persistent Systems, Pingala-Aryabhata, Erandwane, Pune 411004, India
  4. Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, USA
  5. Department of Biology, Johns Hopkins University, Baltimore, USA

Speakers
avatar for Praveen Kumar

Praveen Kumar

Graduate Student, University of Minnesota



Thursday June 28, 2018 2:10pm - 2:16pm
Eliot Chapel Eliot Hall, 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
Eliot Chapel Eliot Hall, Reed Campus

2:16pm

A Galaxy Implementation of Next-Generation Clustered Heat Maps for Interactive Exploration of Large-Scale Molecular Profiling Data
Slides @ F1000

Authors:
Bradley M. Broom 1, Michael Ryan 2, Robert Brown 2 ,Chris Wakefield 1, Rehan Akbani 1, and John N. Weinstein 1,3

  1. Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
  2. In Silico Solutions, Falls Church, Virginia.
  3. Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.

Speakers
avatar for Bob Brown

Bob Brown

Scientist, In Silico Solutions
Viewing and analyzing complex datasets with our Next Generation Clustered Heat Map (NG-CHM) tool in Partnership with MD Anderson.Solving difficult biological problems with our bioinformatic expertise.Addressing significance in very large multivariate studies.



Thursday June 28, 2018 2:16pm - 2:22pm
Eliot Chapel Eliot Hall, Reed Campus

2:22pm

Candidate Gene Methylation quantification (CandiMeth) Within the Galaxy Bioinformatics Interface
Slides @ F1000

Authors:
Sara-Jayne Thursby, Sarah-Jayne Mackin, Rachelle Irwin and Colum P Walsh.

Centre for Molecular Biosciences, School of Biomedical Sciences, University of Ulster,Cromore Road, Coleraine BT52 1SA, UK.

Speakers
ST

Sara-Jayne Thursby

University of Ulster



Thursday June 28, 2018 2:22pm - 2:28pm
Eliot Chapel Eliot Hall, Reed Campus

2:27pm

Late-Breaking Lightning Talks ⚡
  • CWL Community Update: Michael R. Crusoe
  • Code is Science: a manifesto for open source code in science: Yo Yehudi
  • FAIRsharing: Working with the community to map the landscape of standards, databases and data policies: Massimiliano Izzo
  • Scalable computing in Bioconductor: from cores to clusters: Nitesh Turaga
  • BioThings Hub: An API Gateway for Biomedical Knowledge: Sébastien Lelong
  • Bioinformatics in the age of AI and personalized medicine: an open source example: michael duncan


Thursday June 28, 2018 2:27pm - 2:52pm
Vollum Lecture Hall Vollum College Center, Reed Campus

2:28pm

Making Immune Repertoire Sequence Analysis Accessible to Anyone via Galaxy
Slides online

Authors:
Timothy Fennel 1, Chen Song 2, Pingfang Liu 2, Timur Shtatland 2, Eileen T. Dimalanta 2, Bradley W. Langhorst 2

  1. Fulcrum Genomics
  2. New England Biolabs

Speakers
avatar for Bradley W. Langhorst

Bradley W. Langhorst

New England Biolabs



Thursday June 28, 2018 2:28pm - 2:34pm
Eliot Chapel Eliot Hall, Reed Campus

2:34pm

Galaxy Genome Annotation project: integrating Galaxy and GMOD for genome annotation
Slides

Authors:
Anthony Bretaudeau 1, Nathan Dunn 2, Simon Gladman 3, Björn Grüning 4, Eric Rasche 4, Torsten Seemann 3

  1. INRA, UMR IGEPP, BIPAA/GenOuest, Campus Beaulieu, Rennes, France
  2. Lawrence Berkeley National Lab, Berkeley, CA, USA
  3. Melbourne Bioinformatics, University of Melbourne, Australia
  4. de.NBI, Albert Ludwigs Universität, Freiburg, Baden-Württemberg, Germany.

Speakers
avatar for Anthony Bretaudeau

Anthony Bretaudeau

BIPAA/GenOuest



Thursday June 28, 2018 2:34pm - 2:40pm
Eliot Chapel Eliot Hall, Reed Campus

2:40pm

OrthoQuery: A Tripal Module to Assess Gene Family Evolution in Sequenced Gymnosperms
Authors: 
Sumaira Zaman 1, Emily Grau 2, Sean Buehler 2, Stephen Ficklin 3, Jill Wegrzyn 2

  1. Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.
  2. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
  3. Department of Horticulture, Washington State University, Pullman, WA, USA

Speakers
SZ

Sumaira Zaman

University of Connecticut



Thursday June 28, 2018 2:40pm - 2:46pm
Eliot Chapel Eliot Hall, Reed Campus

2:46pm

Galaxy-E, a first step towards collaborative data analysis by citizens
Authors:
Yvan Le Bras 1, Valentin Chambon 1, Alan Amossé 1, Julien Sananikone 2, Elise Brax 2, Marianne Linares 2, Marie Delannoy 2, Grégoire Loïs 2, Romain Julliard 2

  1. French National Museum of Natural History, Station de Biologie marine BP 225, 29182 Concarneau CEDEX - CESCO UMR 7204 43 rue Buffon 75005 PARIS.
  2. French National Museum of Natural History, CESCO UMR 7204 43 rue Buffon 75005 PARIS.

Speakers
avatar for Yvan Le Bras

Yvan Le Bras

French National Museum of Natural History



Thursday June 28, 2018 2:46pm - 2:52pm
Eliot Chapel Eliot Hall, Reed Campus

2:52pm

Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things)
Slides @ F1000

Authors:
Hans-Rudolf Hotz, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland

Speakers
avatar for Hans-Rudolf Hotz

Hans-Rudolf Hotz

Friedrich Miescher Institute for Biomedical Research, Basel



Thursday June 28, 2018 2:52pm - 2:58pm
Eliot Chapel Eliot Hall, Reed Campus

2:52pm

Q&A for lightning talks in this session⚡
Got questions for this session's lightning talk speakers?  Ask them now.

Thursday June 28, 2018 2:52pm - 3:00pm
Vollum Lecture Hall Vollum College Center, Reed Campus

3:00pm

Posters & Demos: Even Numbered
Posters and Demos will be presented on two days and concurrently with 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

3:01pm

B02: Tripal Sequence Similarity Search provides efficient protein sequence similarity search for Tripal sites
Authors
Sean Buehler, Jill Wegrzyn, Nic Herndon, Taylor Falk, Sumaira Zaman, Emily Grau, Doreen Main, Sook Jung, Stephen Ficklin and Margaret Staton

Speakers
avatar for Sean Buehler

Sean Buehler

University of Connecticut


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B04: TreeGenes: enabling visualization and analysis in forest tree genomics
Authors
Emily Grau, Peter Richter, Sean Buehler, Taylor Falk, Nic Herndon and Jill Wegrzyn

Speakers

Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B06: Bioinformatics in the age of AI and personalized medicine: an open source example
Authors
Michael Duncan

Speakers
avatar for Michael Duncan

Michael Duncan

bioinformatics R&D, SingularityNet
Michael Duncan has been working at the intersection of AI and bioinformatics for the past 5 years. He is researching automated hypothesis generation from NGS scale big data sets. Currently Chief Computational Biologist at MOZI AI Health, a partner organizaition of SingularityNet... Read More →



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B08: GRADitude: A computational tool for the analysis of Grad-seq data
Authors
Silvia Di Giorgio, Jens Hör, Jörg Vogel and Konrad Förstner

Speakers
SD

Silvia Di Giorgio

PhD-student, University of Würzburg


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B10: Debarcer2, De-Barcoding and Error Correction of sequencing data containing molecular barcodes designed to handle different library designs.
Authors
Lawrence Heisler, Theodore Bodak, Paul Krzyzanowski, Philip Zuzarte and Lars Jorgensen

Speakers
avatar for Lawrence Heisler

Lawrence Heisler

Manager, Bioinformatics Support, Ontario Institute for Cancer Research


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B12: Plugging Docker-based visualizations into Django with django_docker_engine
Poster @ F1000

Authors
Chuck McCallum, Scott Ouellette and Nils Gehlenborg

Speakers


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B14: Cirrus-NGS: Cloud-optimized compute infrastructure for next generation sequencing analysis
Authors
Guorong Xu, Mustafa Guler, Mengyi Liu, Roman Sasik, Amanda Birmingham and Kathleen Fisch

Speakers

Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B16: Infrastructure for coordinating multi-site clinical research projects via REDCap and Synapse
Poster @ F1000

Authors
Xindi Guo, Kristen Dang and Justin Guinney

Speakers
XG

Xindi Guo

Research Associate, Sage Bionetworks



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B18: NIH Data Commons Pilot Phase leverages the cloud to access, analyze, and share FAIR biomedical data
Authors
David Siedzik and Data Commons Pilot Phase Consortium

Speakers
DS

David Siedzik

Broad Institute


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B20: Reproducible data analysis with Snakemake
Poster @ F1000

Authors


Speakers
JK

Johannes Köster

Genome Informatics, Institute of Human Genetics, University of Duisburg-EssenDepartment of Medical Oncology, Harvard Medical Schoolhttps://koesterlab.github.io



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B22: Code is Science: a manifesto for open source code in science
Authors

Speakers
avatar for Yo Yehudi

Yo Yehudi

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



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B24: The Hypergraph Algorithms Package
Authors
Anna Ritz, Brendan Avent, Aditya Pratapa and T. M. Murali

Speakers

Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B26: Fast, sustainable, and secure bioinformatics with Rust-Bio and Rust-Htslib
Poster @ F1000

Authors
Johannes Köster

Speakers
JK

Johannes Köster

Genome Informatics, Institute of Human Genetics, University of Duisburg-EssenDepartment of Medical Oncology, Harvard Medical Schoolhttps://koesterlab.github.io



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B28: Community Annotation with Apollo: Engaging the Collective in a Genome Annotation Workflow
Authors
Nathan Dunn, Deepak Unni, Eric Yao, Robert Buels, Ian Holmes, Christine Elsik and Suzanna Lewis

Speakers

Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B30: The Funnel Task Execution Server
Authors
Alexander Buchanan, Adam Struck and Kyle Ellrott


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B32: iMADS: A sustainable software collaboration for predicting transcription factor binding specificity
Poster @ F1000

Authors
Dan Leehr, John Bradley, Raluca Gordan, Ning Shen and Hilmar Lapp

Speakers

Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B34: Implementation of Nextflow for the automated processing of NovaSeq data sets
Authors
Netsanet Gebremedhin and Bradley W. Langhorst


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B36: Understanding reproducibility of bioinformatics workflows
Poster @ F1000

Authors
Sehrish Kanwal

Speakers
avatar for Sehrish Kanwal

Sehrish Kanwal

Bioinformatician, The University of Melbourne
Sehrish Kanwal, is an enthusiastic life scientist and bioinformatician who aims to deliver better health outcomes using technologies in the health informatics and by taking genomics from research to clinical/practical settings. Sehrish, has recently completed PhD entitled "Understanding... Read More →



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B38: You can't spell Cromwell without CWL
Poster @ F1000

Authors

Speakers
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 bioinformatics... Read More →



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B40: Running portable workflow and container specifications at production scale in the cloud: strategy & best practices
Authors
Geet Duggal, Kurt Jensen, Mike Lin, Ohad Rodeh, Nihar Sheth and Aleksandra Zalcman

Speakers

Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B42: The GA4GH/DREAM Workflow Execution Challenge
Authors
James Eddy, Jeremiah Savage, Brad Chapman, J. Seth Strattan, Michael Kotliar, Milt Epstein, Abraham Chavez, Junjun Zhang, Brice Aminou, Beri Shifaw, Justin Guinney, Kevin Osborn, Denis Yuen and Brian O'Connor

Speakers
avatar for James Eddy

James Eddy

Senior Scientist, Sage Bionetworks
I'm a data scientist, systems biologist, and an advocate for reproducible, open source, open access science and software. In collaboration with colleagues at Sage Bionetworks and across genomics and health research networks, I'm focused on developing infrastructure, standards, and... Read More →


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B44: A composable container system for genomic analysis pipelines
Authors
Xu Yang and Masahiro Kasahara

Speakers

Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

B46: Bespin: An open source system to run reproducible computational workflows on cloud infrastructure
Poster @ F1000

Authors
Dan Leehr, John Bradley, Hilmar Lapp, and David Corcoran

Speakers
JB

John Bradley

Duke University


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

D02: Adding R shiny apps as Galaxy interactive environment. A Galaxy-E demo
Authors
Valentin Chambon, Alan Amossé and Yvan Le Bras

Speakers

Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

D04: A Galaxy Implementation of Next-Generation Clustered Heat Maps for Interactive Exploration of Large-Scale Molecular Profiling Data
→ Poster @ F1000

Authors
John Weinstein, Bradley Broom, Rehan Akbani, Chris Wakefield, Mike Ryan and Bob Brown

Speakers
avatar for Bob Brown

Bob Brown

Scientist, In Silico Solutions
Viewing and analyzing complex datasets with our Next Generation Clustered Heat Map (NG-CHM) tool in Partnership with MD Anderson.Solving difficult biological problems with our bioinformatic expertise.Addressing significance in very large multivariate studies.



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

D06: Distributed execution of bioinformatics tools on Apache Spark with ADAM and Cannoli
Authors

Speakers
avatar for Michael Heuer

Michael Heuer

UC Berkeley


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

D08: Owlery: An easily deployable web service for making reasoning queries over OWL ontologies web-native
Authors

Speakers
avatar for Hilmar Lapp

Hilmar Lapp

Director of Informatics, Duke University, Center for Gemonic and Computational Biology


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G02: Testing Wide-Area Lustre File Systems for Sharing load in Galaxy
Authors
Carrie Ganote, Philip Blood, Bhavya Nalagampalli Papudeshi, Sheri Sanders and Thomas Doak

Speakers
avatar for Carrie Ganote

Carrie Ganote

Indiana University Bloomington


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G04: Galaxy for AnswerALS on Microsoft Azure and Kubernetes
Authors
RC Carter, Enis Afgan, Nuwan Goonasekera, Abhik Ghosh, Gaurav Hind and Alex Lenail

Speakers
RC

RC Carter

Microsoft


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G06: Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things)
Poster @ F1000

Authors
Hans-Rudolf Hotz

Speakers
avatar for Hans-Rudolf Hotz

Hans-Rudolf Hotz

Friedrich Miescher Institute for Biomedical Research, Basel



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G08: Collecting data for association genetics: Tripal Plant PopGen Submit pipeline
Poster @ F1000

Authors
Peter Richter, Emily Grau, Sean Buehler, Nic Herndon, Taylor Falk and Jill Wegrzyn

Speakers


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G10: Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
Poster

Authors
Boris Simovski 1, Chakravarthi Kanduri 1,2, Sveinung Gundersen 1,3, Dmytro Titov 1,3, Diana Domanska 1, Christoph Bock 4,5,6, Lara Bossini-Castillo 7, Maria Chikina 8, Alexander Favorov 9,10, Ryan M. Layer 11,12, Andrey A. Mironov 13,14,15, Aaron R. Quinlan 11,12,16, Nathan C. Sheffield 17, Gosia Trynka 7 and Geir K. Sandve 1,2

  1. Department of Informatics, University of Oslo, Gaustadalleen 23 B, N-0373 Oslo, Norway
  2. K. G. Jebsen Centre for Coeliac Disease Research, Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway
  3. Elixir Norway - Oslo node, Department of Informatics, University of Oslo, Gaustadalleen 23 B, N-0373 Oslo, Norway
  4. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
  5. Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
  6. Max Planck Institute for Informatics, 66123 Saarbrucken, Germany
  7. 7Cellular Genetics Programme, Wellcome Sanger Institute, CB10 1SA Hinxton, UK
  8. University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15213, USA, 
  9. Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, 550 N Broadway, Baltimore, MD 21205, USA
  10. Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Gubkina Street 3, Moscow 119333, Russia
  11. Department of Human Genetics, University of Utah, 15 N 2030 E, Salt Lake City, UT 84112, USA 
  12. USTAR Center for Genetic Discovery, University of Utah, 15 N 2030 E, Salt Lake City, UT 84112, USA
  13. Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Lab. Bldg B, Vorobiovy Gory 1-73, Moscow 119992, Russia
  14. Skolkovo Institute of Science and Technology, Nobelya ul. 3, Moscow 121205, Russia
  15. Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karenty per. 19, Moscow 127994, Russia
  16. Department of Biomedical Informatics, University of Utah, 421 Wakara Way, Salt Lake City, UT 84108, USA and 
  17. Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903 USA




Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G12: Canada's Integrated Rapid Infectious Disease Analysis Platform (IRIDA)
Poster

Authors
Thomas Matthews, Franklin Bristow, Aaron Petkau, Josh Adam, Peter Kruczkiewicz, Jen Cabral, Damion Dooley, Emma Griffiths, Dan Fornkia, Geoff Windsor, Morag Graham, Eduardo Taboada, Robert Bieko, William Hsiao, Fiona Brinkman and Gary Van Domselaar

Speakers
avatar for Thomas Matthews

Thomas Matthews

Public Health Agency of Canada



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G14: HIV transmission clustering in Galaxy
Authors
Dave Bouvier, Steven Weaver, Stephen Shank, Aysam Guerler, James Taylor, Sergei Pond and Anton Nekrutenko

Speakers
avatar for Dave Bouvier

Dave Bouvier

Galaxy Project, Penn State University



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G16: Integrative proteo-transcriptomics workflows within the Galaxy framework to explore the correlation between the expression of RNA and proteins
→  Poster @ F1000

Authors
Praveen Kumar, Priyabrata Panigrahi, James Johnson, Caleb Easterly, Subina Mehta, Andrew Rajczewski, Ray Sajulga, Mohammad Heydarian, Anamika Krishanpal, Timothy Griffin and Pratik Jagtap

Speakers
avatar for Praveen Kumar

Praveen Kumar

Graduate Student, University of Minnesota



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G18: CRAVAT (Cancer-Related Analysis of Variants Toolkit) integration into Galaxy-P and extension towards proteogenomic studies
Poster 

Authors
Ray Sajulga, Rachel Karchin, Michael Ryan, James Johnson, Thomas McGowan, Subina Mehta, Candace Guerrero, Pratik Jagtap and Timothy J. Griffin

Speakers


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G20: Using Galaxy to analyze TCGA data: the experience of a Brazilian center
Poster @ F1000

Authors
Thais Hosokawa, Murilo Machado, Luciane Da Silva, Jose Fregnani, Rui Reis and Adriane Evangelista

Speakers


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G22: ARIAWeb: a structural bioinformatics web interface linked to galaxy
Authors
Fabrice Allain, Fabien Mareuil, Hervé Ménager and Benjamin Bardiaux

Speakers

Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G24: New tools to enhance the Galaxy-based metabolomics workbench
Authors
Arthur Eschenlauer, Mark Esler, James Johnson, Timothy Griffin and Adrian Hegeman

Speakers
avatar for Arthur Eschenlauer

Arthur Eschenlauer

Postdoc, University of Minnesota
Poster Abstract: | Untargeted metabolomics contrasts metabolome-scale analyses of samples without first identifying individual metabolites. Workflow4Metabolomics (W4m) provides a suite of Galaxy tools for untargeted metabolomics including univariate and multivariate statistical... Read More →



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G26: ISAcreate: a Galaxy tool for Prospective Data Management with ISA format support - Application to Metabolomics Datasets
Poster @ F1000

Authors
Philippe Rocca-Serra, David Johnson, Ralf Weber, Pierrick Roger-Merle, Luca Pireddu, Massimiliano Izzo, Alejandra Gonzalez-Beltran and Susanna-Assunta Sansone

Speakers
avatar for Philippe Rocca-Serra

Philippe Rocca-Serra

Researcher/Scholar/Scientist, University of Oxford
We are using Galaxy to manage and analyse Metabolite profiling data generated by Mass Spectrometry and NMR spectroscopy. We develop a set of Galaxy Tool to create documents in ISA format (used by EMBL-EBI Metabolights, NPG Scientific Data and OUP Gigascience. All the set of ISA tools... Read More →


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G28: EDAM: the ontology of bioinformatics operations, types of data, topics, and data formats (2018 update)
Authors
Hervé Ménager, Matúš Kalaš, Veit Schwämmle, Jon Ison and Edam Contributors

Speakers
avatar for Hervé Ménager

Hervé Ménager

Research Engineer, Institut Pasteur
Bioinformatics and Biostatistics Hub of the C3BI, Institut Pasteur


Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G30: Compliance? We don’t need no stinking compliance!
Poster @ F1000

Authors
Jeffrey Miller

Speakers
avatar for Jeffrey Miller

Jeffrey Miller

Sr. Systems Administrator, The University of Iowa
As a systems administrator with The University of Iowa ITS Research Services group, I primarily support the storage and computational infrastructure for the Iowa Institute of Human Genetics. Talk to me about scaling infrastructures, virtualization and automation with Puppet.



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

3:01pm

G32: Results of an Extended Developer Support consultation with the CloudLaunch project
Poster @ F1000

Authors
Marcus Christie, Enis Afgan and Nuwan Goonasekera

Speakers
avatar for Marcus Christie

Marcus Christie

Principal Science Gateway Research Consultant, Indiana University
Apache Airavata, scientific computing, high performance computing, React, Django, big data, cloud computing



Thursday June 28, 2018 3:01pm - 4:00pm
PAB Atrium Performing Arts Building, Reed College

4:00pm

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

Speakers
avatar for Pratik Jagtap

Pratik Jagtap

Research assistant Professor, University of Minnesota
University of Minnesota


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

4:01pm

Closing Keynote: Confound it! Reproducible biology from "omics" data analysis
Abstract:
High throughput sequencing (HTS) has become a preferred choice for the measurement of genome-wide biological phenomena at the molecular level, from genetics to gene expression regulation. Despite its widespread use, challenges remain in HTS data analysis. One often-overlooked aspect is normalization. Despite the fact that a variety of factors or “confounders” can contribute unwanted variation to the data, commonly used normalization methods often only correct for sequencing depth. The study of gene expression and gene expression regulation is particularly problematic when it is influenced simultaneously by a variety of biological factors in addition to the one of interest. Using examples from our lab and others, we show that confounders can dominate the signal of interest.  If the effect of confounders is not properly accounted for the power, reproducibility and biological insight of the results is compromised. I will focus on two methods aimed at correcting for confounding factors: RUVSeq (for RNA-seq) and DEScan (for epigenomic-seq). Our results show that removing confounding factors can make a dramatic difference on the biological conclusions of genome-wide studies of gene expression and epigenomic regulation.


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... Read More →



Thursday June 28, 2018 4:01pm - 5:00pm
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.

Speakers
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg
avatar for Nomi Harris

Nomi Harris

BOSC 2018 Chair, Lawrence Berkeley National Laboratory
Nomi Harris is a bioinformatics program manager at LBNL. She has chaired or co-chaired BOSC since 2011.
avatar for Nicole Vasilevsky

Nicole Vasilevsky

Lead Biocurator, OHSU
avatar for Heather Wiencko

Heather Wiencko

Software Engineer, Hosted Graphite
I'm a software engineer working for Hosted Graphite in the heart of Dublin, Ireland. As co-chair of BOSC, I'm excited about partnering with GCC to put on a conference the likes of which the world has never seen. I also serve as a member-at-large on the OBF Board of Directors. If you're... Read More →



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

5:40pm

Birds-of-a-Feather (BoFs), the Final Flight!
Organize/Submit a BoF!

Birds-of-a-feather are informal 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!

BoFs in the final flocking are:



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

5:40pm

BoF: Bioconda gathering
Let's discuss the (bright) future and current status of Bioconda. Everybody is welcome to join.

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

Organize/Submit a BoF!


Moderators
JK

Johannes Köster

Genome Informatics, Institute of Human Genetics, University of Duisburg-EssenDepartment of Medical Oncology, Harvard Medical Schoolhttps://koesterlab.github.io

Thursday June 28, 2018 5:40pm - 7:00pm
PAB 104 Performing Arts Building, Reed Campus

5:40pm

BoF: GA4GH/DREAM group writing session
Organizers and participants from the GA4GH/DREAM Workflow Execution Challenge have been piecing together a manuscript to report results, lessons, and a vision for ongoing infrastructure challenges. It's rare to have so many members of this group in the same place at the same time — so we'd like to take advantage of the opportunity for some focused writing! The paper and process are entirely open, so anyone else from the community is welcome to come and contribute ideas (and maybe even text). Here is the working draft of the manuscript.

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

Organize/Submit a BoF!


Moderators
avatar for James Eddy

James Eddy

Senior Scientist, Sage Bionetworks
I'm a data scientist, systems biologist, and an advocate for reproducible, open source, open access science and software. In collaboration with colleagues at Sage Bionetworks and across genomics and health research networks, I'm focused on developing infrastructure, standards, and... Read More →

Thursday June 28, 2018 5:40pm - 7:00pm
PAB 332 Performing Arts Building, Reed Campus

5:40pm

BoF: Galaxy Dataset Collection: Defining Priorities
Dataset collections are a powerful mechanism for representing large complex datasets within the Galaxy user interface. This BoF will discuss existing limitations and usage scenarios to define implementation priorities.

We'll walk over to Gigantic Brewing immediately after Session 8 ends.

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

Organize/Submit a BoF!


Moderators
avatar for Anton Nekrutenko

Anton Nekrutenko

Galaxy Project, Penn State University
Penn State University

Thursday June 28, 2018 5:40pm - 7:00pm
Gigantic Brewing 5224 SE 26th Ave, Portland, OR 97202

5:40pm

BoF: GalaxyAdmins
The annual in-person meeting of Galaxy system administrators.

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

Organize/Submit a BoF!


Moderators
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University

Thursday June 28, 2018 5:40pm - 7:00pm
PAB 131 Performing Arts Building, Reed Campus

7:00pm

Conference Dinner Sponsored by Google Cloud
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.

And please thank Google Cloud for sponsoring the GCCBOSC 2018 Dinner!  This dinner would not have been possible without their generous, Platinum level sponsorship.  So go find Jonathan Sheffi and Asha Rostamianfar and give 'em a hug!


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

8:00am

Conference desk open
Need to checkin? Need help?  This is the place

Friday June 29, 2018 8:00am - 6:00pm
PAB Atrium Performing Arts Building, Reed College

9:00am

GCC OBF CollaborationFest: Core
OBF’s CodeFest, Galaxy’s Hack the Galaxy, and the NIH’s Data Commons Pilot Phase Consortium are all converging for CollaborationFest 2018.  CoFest starts at 9am on Friday morning, the day after the GCCBOSC meeting ends and features 2, 3, or 4 days of collaborative work on projects that matter to open source bioinformatics.

CoFest will be held in the Performing Arts Building (PAB) and will make extensive use of classrooms and PAB Atrium, an ideal space for collaboration.
CollaborationFest has four tracks:

  • OBF: Contribute to any open source bioinformatics project.
  • 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.
  • Data Commons

CoFest participants will coalesce around shared interests and address common challenges related to those interests. These clusters form before, at the beginning of, and throughout CollaborationFest. These clusters will be fluid and highly interactive with each other.  These groups and clusters will be fluid and highly interactive with each other. There will be a joint gathering of all communities at least once a day.

Prepare for CoFest

See the CollaborationFest page for more.

Moderators
avatar for Dannon Baker

Dannon Baker

Galaxy Project, Johns Hopkins University
Talk to me about Galaxy Development, especially the UI!
avatar for Brad Chapman

Brad Chapman

Bioinformatics Core, Harvard Chan School
Brad is a senior research scientist in the Bioinformatics Core at Harvard T.H. Chan School of Public Health. He develops open source community built infrastructure for analyzing biological data, focusing on multi platform interoperability and automated validation against heterogeneous... Read More →
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg

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

8:45am

Conference desk open
Checkin, checkout; lost, found; badges, stickers; ...

Saturday June 30, 2018 8:45am - 6:00pm
PAB Atrium Performing Arts Building, Reed College

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
 

8:45am

Conference desk open
Checkin, checkout; lost, found; badges, stickers; ...

Sunday July 1, 2018 8:45am - 6:00pm
PAB Atrium Performing Arts Building, Reed College

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
 

8:45am

Conference desk open
Checkin, checkout; lost, found; badges, stickers; ...

Monday July 2, 2018 8:45am - 6:00pm
PAB Atrium Performing Arts Building, Reed College

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