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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

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.

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Moderators
avatar for Tim Griffin

Tim Griffin

Professor, 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
 
Wednesday, June 27
 

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.

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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.

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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.

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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

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.

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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.

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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

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.

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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
 

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 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
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.

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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 data... 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
avatar for Nuwan Goonasekera

Nuwan Goonasekera

University of Melbourne

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

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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.

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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.

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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.

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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