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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
 

8:10pm

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 →



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

9:01am

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 →



Wednesday June 27, 2018 9:01am - 10:00am
Vollum Lecture Hall Vollum College Center, Reed Campus

10:00am

The journey of a team of engineers in learning packaging technology
→ Slides
Video (YouTubeVimeo)

Authors
Laure Quintric 1, Patrick Durand 1, Olivier Inizan 2, Valentin Marcon 2, Caroline Dussart 1, Valentin Loux 2, Maria Bernard 3, Géraldine Pascal 4

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



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

4:01pm

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 →



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

4:20pm

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

Moderators
avatar for Brad Chapman

Brad Chapman

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

Speakers
avatar for Bérénice Batut

Bérénice Batut

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

Fernando Pérez

Assistant Professor, Berkeley Institute for Data Science, University of California Berkeley
Dr. Pérez is an assistant professor in Statistics at UC Berkeley and a Faculty Scientist in the Department of Data Science and Technology at Lawrence Berkeley National Laboratory. After completing a PhD in particle physics at the University of Colorado at Boulder, his postdoctoral research in applied mathematics centered on the development of... Read More →
avatar for Tracy K. Teal

Tracy K. Teal

Executive Director, The Carpentries
Dr. Teal is the Executive Director of The Carpentries and a co-founder of Data Carpentry. After completing her PhD in Computation and Neural Systems at California Institute of Technology, her work as an NSF Postdoctoral Fellow focused on bioinformatics approaches to metagenomics and microbial community analysis. Then as an Assistant Professor of Microbiology and Molecular... Read More →
avatar for Jason Williams

Jason Williams

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


Wednesday June 27, 2018 4:20pm - 5:20pm
Vollum Lecture Hall Vollum College Center, Reed Campus
 
Thursday, June 28
 

4:01pm

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 →



Thursday June 28, 2018 4:01pm - 5:00pm
Vollum Lecture Hall Vollum College Center, Reed Campus

5:00pm

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

Speakers
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg
avatar for Nomi Harris

Nomi Harris

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

Nicole Vasilevsky

Lead Biocurator, 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 →



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