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

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B. Conference [clear filter]
Tuesday, June 26
 

6:20pm PDT

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 PDT
TBA
  B. Conference, Birds-of-a-Feather

6:20pm PDT

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 Timothy J. Griffin

Timothy J. Griffin

Professor, University of Minnesota
avatar for Pratik Jagtap

Pratik Jagtap

Research Assistant Professor, University of Minnesota
Metaproteomics . DIA . Proteogenomics

Tuesday June 26, 2018 6:20pm - 7:40pm PDT
Reed Commons Cafe Reed College Commons, Reed Campus
  B. Conference, Birds-of-a-Feather

8:00pm PDT

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 Chair, LBNL
This is my 10th year chairing or co-chairing BOSC, the Bioinformatics Open Source Conference.In 2020, BOSC is part of the online Bioinformatics Community Conference, BCC2020.

S0 T1 Harris IntroductionSlideDeck pdf
Tuesday June 26, 2018 8:00pm - 8:10pm PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Session

8:00pm PDT

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, Oregon Health & Science University
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 PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Session

8:10pm PDT

Opening Keynote: Tracy K. Teal--"Democratizing Data"
→ Slides
→ Video (YouTube, Vimeo)

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 →

S0 T2 Teal 2018 06 26 pdf
Tuesday June 26, 2018 8:10pm - 9:10pm PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Talk
 
Wednesday, June 27
 

8:00am PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Help

9:00am PDT

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 PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Session

9:01am PDT

Keynote: Fernando Pérez--"Sustainable development of scientific open source tools: a view from Jupyter"
→ Slides
→ Video (YouTube, Vimeo)

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 →

jupyter pérez pdf
Wednesday June 27, 2018 9:01am - 10:00am PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Talk

10:00am PDT

The journey of a team of engineers in learning packaging technology
→ Slides
→ Video (YouTube, Vimeo)

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.
Speakers
PD
VM
LQ

GCCBOSC 2018 1 2 packaging technology pdf
S1 T2 packaging pdf
Wednesday June 27, 2018 10:00am - 10:20am PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Talk

10:20am PDT

Break
Head over to the Performing Arts building for a stretch, refreshments, and conversation.
Wednesday June 27, 2018 10:20am - 10:50am PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Break / Social / Networking

10:20am PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Sponsor

12:10pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Break / Social / Networking

12:10pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Sponsor

12:30pm PDT

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 PDT
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA
  B. Conference, Birds-of-a-Feather

12:30pm PDT

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, University of Cambridge & Open Life Science
Integrated genomic data (InterMine)

Wednesday June 27, 2018 12:30pm - 1:30pm PDT
PAB 130 Performing Arts Building
  B. Conference, Birds-of-a-Feather

12:30pm PDT

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
RB

Rob Buels

University of California, Berkeley


Wednesday June 27, 2018 12:30pm - 1:30pm PDT
PAB 104 Performing Arts Building, Reed Campus
  B. Conference, Birds-of-a-Feather

12:30pm PDT

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

Director of Outreach and Communications, Broad Institute Data Sciences Platform
I direct outreach and communication efforts for the software and services developed by the Data Sciences Platform at the Broad Institute, which include GATK, the Broad's open source toolkit for variant discovery analysis; the Cromwell/WDL workflow management system; and Terra.bio... 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 PDT
PAB 332 Performing Arts Building, Reed Campus
  B. Conference, Birds-of-a-Feather

12:30pm PDT

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 PDT
PAB 131 Performing Arts Building, Reed Campus
  B. Conference, Birds-of-a-Feather

3:00pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:00pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Sponsor

3:01pm PDT

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.

f1000research 210825 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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.

f1000research 210737 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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.

f1000research 210767 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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.

f1000research 211349 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
Speakers
MI

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Authors
Luiz Irber
Speakers
LC

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
Speakers
avatar for Sveinung Gundersen

Gundersen GCCBOSC 2018 GTrack web pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

f1000research 210889 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

f1000research 210756 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 →

f1000research 211882 (1) pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 enthusiastWorking on Provenance of bioinformatics workflows

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 project
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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Nuwan Goonesekera

University of Melbourne

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
MC

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

D05: Open Humans - connecting, sharing and analyzing personal data that enables community-driven research
Authors
Speakers
avatar for Bastian Greshake Tzovaras

Bastian Greshake Tzovaras

Director of Research, Open Humans Foundation
Bastian Greshake Tzovaras is the Director of Research for the Open Humans Foundation which is dedicated to empowering individuals and communities around their personal data, to explore  and share for the purposes of education, health, and research.

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Research engineer, French National Museum of Natural History

GCCBOSC2018 Demo GIE Shiny linear regression mp4
Demo Shiny Wallace SDM mp4
poster Galaxy E GCC2018 fin pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Authors
Anastasia Tyryshkina and Anton Nekrutenko
Speakers
AT

Anastasia Tyryshkina

Penn State University

f1000research 210810 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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.

f1000research 215049 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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.

f1000research 212228 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

G09: EWAS-Galaxy: a tool suite for population epigenetics integrated into the Galaxy
→ Poster @ F1000

Authors
Katarzyna Murat and Krzysztof Poterlowicz
Speakers
avatar for Krzysztof Poterlowicz

Krzysztof Poterlowicz

University of Bradford

GCC2018v8 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

f1000research 210815 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

G13: Bacterial genomics in Galaxy
→ Poster 

Authors
Delphine Larivière, Han Mei, Mallory Freeberg, James Taylor and Anton Nekrutenko
Speakers
avatar for Delphine Lariviere

Delphine Lariviere

Penn State University
Post-doc in the Galaxy Team (Nekrutenko Lab). Works on bacterial genomics, assembly, RNA Seq, TnSeq. Also interested in evolution, metagenomics, epigenetics and visualisation.

GCC 2018 POSTER pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

G15: Galaxy in a proteomics core facility
→ Poster

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

See also
Speakers
JV

Volkening GCC 20180625 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

f1000research 210739 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

f1000research 210947 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

JochenB poster GCC 2018 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
Speakers
avatar for Oleksandr Moskalenko

Oleksandr Moskalenko

RCF, University of Florida
User services (including Galaxy), apps and support lead at UF Research Computing, long-term Galaxy admin, RSE (Research Software Engineer), and a research computing enthusiast in general.

f1000research 211042 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
ME

Mark VKMZ v02 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 Kalas

Matúš Kalas

Senior Engineer, University of Bergen
Attending GCC2022 virtually 🌌Working on open science|source|society|education, EDAM ontology, ELIXIR Norway, Bio.tools, ...

Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

poster png
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
SO

ScottOuelletteGCC2018 pdf
Wednesday June 27, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

4:00pm PDT

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 PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Session

4:01pm PDT

Improving the Bioinformatics Curriculum
​Video​​​
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 →

S4 T1 WILLIAMS Bioinformatics Curriculum gccbosc 2018 pdf
Wednesday June 27, 2018 4:01pm - 4:20pm PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Talk

4:20pm PDT

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
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 PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Talk

5:40pm PDT

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 PDT
TBA
  B. Conference, Birds-of-a-Feather

5:40pm PDT

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 PDT
TBA
  B. Conference, Birds-of-a-Feather

5:40pm PDT

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, University of Cambridge & Open Life Science
Integrated genomic data (InterMine)


Wednesday June 27, 2018 5:40pm - 7:40pm PDT
Reed Commons Cafe Reed College Commons, Reed Campus
  B. Conference, Birds-of-a-Feather

5:40pm PDT

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 and Trainer, free element
Galaxy Enthusiast
AT

Anastasia Tyryshkina

Penn State University

Wednesday June 27, 2018 5:40pm - 7:40pm PDT
TBA
  B. Conference, Birds-of-a-Feather

5:40pm PDT

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 PDT
Reed Commons Cafe Reed College Commons, Reed Campus
  B. Conference, Birds-of-a-Feather

5:40pm PDT

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 PDT
TBA
  B. Conference, Break / Social / Networking

6:00pm PDT

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 PDT
Woodstock Neighborhood
  B. Conference, Sponsor

8:00pm PDT

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 PDT
TBA
  B. Conference, Birds-of-a-Feather

8:00pm PDT

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
avatar for Evan Floden

Wednesday June 27, 2018 8:00pm - 10:00pm PDT
Sitka Dorm, Ground Floor Sitka Residence Hall
  B. Conference, Birds-of-a-Feather

8:00pm PDT

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 PDT
Woodstock Neighborhood
  B. Conference, Birds-of-a-Feather
 
Thursday, June 28
 

8:00am PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Help

10:20am PDT

Break
Head over to the Performing Arts building for a stretch, refreshments, and conversation.
Thursday June 28, 2018 10:20am - 10:50am PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Break / Social / Networking

10:20am PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Sponsor

12:10pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Break / Social / Networking

12:10pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Sponsor

12:30pm PDT

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 PDT
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA
  B. Conference, Birds-of-a-Feather

12:30pm PDT

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
PA
avatar for John Chilton
avatar for Michael R. Crusoe

Michael R. Crusoe

Project Lead & Co-founder, Common Workflow Language project
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 PDT
PAB 332 Performing Arts Building, Reed Campus
  B. Conference, Birds-of-a-Feather

12:30pm PDT

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

Thursday June 28, 2018 12:30pm - 1:30pm PDT
PAB 130 Performing Arts Building
  B. Conference, Birds-of-a-Feather

12:30pm PDT

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
KW

Thursday June 28, 2018 12:30pm - 1:30pm PDT
PAB 131 Performing Arts Building, Reed Campus
  B. Conference, Birds-of-a-Feather

12:30pm PDT

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 The Other Enis Afgan

The Other Enis Afgan

Research scientist, Johns Hopkins University
avatar for Nuwan Goonesekera

Nuwan Goonesekera

University of Melbourne

Thursday June 28, 2018 12:30pm - 1:30pm PDT
PAB 104 Performing Arts Building, Reed Campus
  B. Conference, Birds-of-a-Feather

3:00pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:00pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Sponsor

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
EG

Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 →

mduncan bosc2018 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Authors
Chuck McCallum, Scott Ouellette and Nils Gehlenborg
Speakers
CM

f1000research 211129 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
GX

Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

f1000research 210746 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

f1000research 210878 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

B22: Code is Science: a manifesto for open source code in science
Authors
Speakers
avatar for Yo Yehudi

Yo Yehudi

Software Developer, University of Cambridge & Open Life Science
Integrated genomic data (InterMine)

Code is Science Manifesto GCCBOSC pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

f1000research 210781 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
avatar for Nathan Dunn

Nathan Dunn

Software Developer, Lawrence Berkeley National Lab

Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
DL

Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 →

f1000research 209678 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 →

f1000research 211127 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
avatar for Geet Duggal

Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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.

f1000research 211700 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

f1000research 210906 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
PR

f1000research 211272 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Speakers
avatar for Sveinung Gundersen

Gundersen GCCBOSC 2018 Coloc stats web pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

GCC2018 Matthews pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Computational Scientist, Galaxy Project, Penn State University

G14: HIV transmission clustering in Galaxy pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

f1000research 212355 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
avatar for Ray Sajulga

Ray Sajulga

University of Minnesota

rsajulga GCC Poster 2018 CRAVAT pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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
TH

f1000research 211392 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Fabien Mareuil

Research Engineer, Institut Pasteur

Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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

Researcher 5, University of Minnesota
https://experts.umn.edu/en/persons/art-eschenlauerhttps://orcid.org/0000-0002-2882-0508Art has a Ph.D. in Biochemistry and twenty years experience in the business community supporting Windows and Linux systems and software. Since his return to academia, Art has created tools and developed... Read More →

2018 GCC ArtEschenlauer pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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 PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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.

G30 Compiance pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

3:01pm PDT

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, Vue.js, Django, big data, cloud computing

f1000research 210742 pdf
Thursday June 28, 2018 3:01pm - 4:00pm PDT
PAB Atrium Performing Arts Building, Reed College
  B. Conference, Posters + Demos

4:00pm PDT

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
Metaproteomics . DIA . Proteogenomics

Thursday June 28, 2018 4:00pm - 5:20pm PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Session

4:01pm PDT

Closing Keynote: Confound it! Reproducible biology from "omics" data analysis
→ Slides
→ Video (YouTube, Vimeo)

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 →

S8 T1 Peixoto GCCBOSC June2018 pdf
Thursday June 28, 2018 4:01pm - 5:00pm PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Talk

5:00pm PDT

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 Bjorn Gruning

Bjorn Gruning

University of Freiburg
avatar for Nomi Harris

Nomi Harris

BOSC Chair, LBNL
This is my 10th year chairing or co-chairing BOSC, the Bioinformatics Open Source Conference.In 2020, BOSC is part of the online Bioinformatics Community Conference, BCC2020.
avatar for Nicole Vasilevsky

Nicole Vasilevsky

Lead Biocurator, Oregon Health & Science University
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 →

S8 T2 Closing for GCCBOSC2018 pdf
Thursday June 28, 2018 5:00pm - 5:20pm PDT
Vollum Lecture Hall Vollum College Center, Reed Campus
  B. Conference, Talk

5:40pm PDT

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 PDT
Performing Arts Building 3017 SE Woodstock Blvd, Portland, OR 97202, USA
  B. Conference, Birds-of-a-Feather

5:40pm PDT

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 PDT
PAB 104 Performing Arts Building, Reed Campus
  B. Conference, Birds-of-a-Feather

5:40pm PDT

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 →
BO

Thursday June 28, 2018 5:40pm - 7:00pm PDT
PAB 332 Performing Arts Building, Reed Campus
  B. Conference, Birds-of-a-Feather

5:40pm PDT

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

Penn State University
Penn State University

Thursday June 28, 2018 5:40pm - 7:00pm PDT
Gigantic Brewing 5224 SE 26th Ave, Portland, OR 97202
  B. Conference, Birds-of-a-Feather

5:40pm PDT

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

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avatar for Nate Coraor

Nate Coraor

System Administrator, Galaxy Project, Penn State University

Thursday June 28, 2018 5:40pm - 7:00pm PDT
PAB 131 Performing Arts Building, Reed Campus
  B. Conference, Birds-of-a-Feather

7:00pm PDT

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 PDT
TBA
  B. Conference, Break / Social / Networking
 
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Eliot Chapel
Gigantic Brewing
PAB 104
PAB 130
PAB 131
PAB 320
PAB 332
PAB Atrium
Performing Arts Building
Reed College Campus
Reed Commons Cafe
Sitka Dorm, Ground Floor
TBA
Vollum Lecture Hall
Vollum Lounge
Woodstock Neighborhood
  • A. Training
  • B. Conference
  • B.b Conference - BOSC
  • B.g Conference - GCC
  • C. CollaborationFest