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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.b Conference - BOSC [clear filter]
Wednesday, June 27
 

10:50am

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

Moderators
avatar for Hilmar Lapp

Hilmar Lapp

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

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

10:51am

Cloud-based data ingest for the Human Cell Atlas
Video​​​

Speakers
avatar for Daniel Vaughan

Daniel Vaughan

Tech Lead, EMBL-EBI



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

11:05am

11:20am

11:40am

Enabling Machine Learning at Scale with “Tiled” Human Genomes
Video​​​

Speakers
avatar for Sarah Wait Zaranek

Sarah Wait Zaranek

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



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

11:45am

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

Speakers
avatar for Hervé Ménager

Hervé Ménager

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



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

11:50am

Building a community menagerie of automated variant validations
Video​​​

Speakers
avatar for Brad Chapman

Brad Chapman

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



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

11:55am

12:00pm

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

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

1:40pm

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

Moderators
avatar for Bastian Greshake Tzovaras

Bastian Greshake Tzovaras

co-founder, openSNP

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

1:41pm

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

Speakers
avatar for Lorena Pantano Rubino

Lorena Pantano Rubino

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



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

2:00pm

2:20pm

InterMine 2.0: More than fifteen years of open biological data integration
Video​​​

Speakers
avatar for Yo Yehudi

Yo Yehudi

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



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

2:40pm

GRADitude: A computational tool for the analysis of Grad-seq data
Video​​​

Speakers
SD

Silvia Di Giorgio

PhD-student, University of Würzburg



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

2:45pm

2:50pm

Reproducible data analysis with Snakemake
Video​​​

Speakers
JK

Johannes Köster

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



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

2:55pm

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

Wednesday June 27, 2018 2:55pm - 2:59pm
Vollum Lecture Hall Vollum College Center, Reed Campus
 
Thursday, June 28
 

9:00am

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

Moderators
avatar for Peter Cock

Peter Cock

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

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

9:01am

9:20am

The Funnel Task Execution Server
Video​​​



Thursday June 28, 2018 9:20am - 9:40am
Vollum Lecture Hall Vollum College Center, Reed Campus

9:40am

9:45am

Extended Extraction Transform Load: A novel framework for batch jobs on cloud computing resources
Video​​​

Speakers
avatar for Hiromu Ochiai

Hiromu Ochiai

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



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

9:50am

9:55am

The Arachne Graph Database Server
Video​​​

Speakers

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

10:00am

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

Speakers
avatar for Hilmar Lapp

Hilmar Lapp

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



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

10:05am

taxa: taxonomic data standards and methods for R and Python
Video​​​


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

10:10am

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

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

10:50am

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

Moderators
avatar for Karsten Hokamp

Karsten Hokamp

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

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

10:51am

CWLProv - Interoperable retrospective provenance capture and its challenges
Video​​​

Speakers
avatar for Farah Zaib Khan

Farah Zaib Khan

The University of Melbourne
Bioinformatics Workflow developer CWL enthusiastWorking on Provenance of bioinformatics workflows


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

11:10am

11:30am

The GA4GH/DREAM Workflow Execution Challenge
Video​​​

Speakers
avatar for James Eddy

James Eddy

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



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

11:35am

11:40am

CWL-Airflow pipeline manager as a backend for BioWardrobe data analysis platform
Video​​​

Speakers
avatar for Andrey Kartashov

Andrey Kartashov

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



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

11:45am

Scaling bioinformatics analysis using Nextflow and AWS
Video​​​



Thursday June 28, 2018 11:45am - 11:50am
Vollum Lecture Hall Vollum College Center, Reed Campus

11:50am

11:55am

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

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

1:40pm

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

Moderators
avatar for Chris Fields

Chris Fields

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

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

1:41pm

OBF update
Video​​​

Speakers
avatar for Hilmar Lapp

Hilmar Lapp

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


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

1:50pm

GSOC update
Video​​​

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 →



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

2:00pm

Biopython Project Update 2018

Speakers
avatar for Peter Cock

Peter Cock

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



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

2:07pm

Community Annotation with Apollo: Engaging the Collective in a Genome Annotation Workflow
Video​​​

Speakers
avatar for Nathan Dunn

Nathan Dunn

Software Developer, UC Berkeley
I work on the Apollo project, but also have worked on various other projects such as the Monarch Initiative, the (cross-species ontology relations between phenotypes and genomics), the Alliance of Genome resources (major mods curating data), the Gene Ontology, and the Xena Variant... Read More →



Thursday June 28, 2018 2:07pm - 2:27pm
Vollum Lecture Hall Vollum College Center, Reed Campus

2:27pm

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


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

2:52pm

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

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