| Session
|
Title
|
Speaker (or Session Chair)
|
Start Time
|
End Time
|
| BOSC opening
|
Introduction and welcome
|
Nomi Harris (Chair, BOSC 2017)
|
10:00
|
10:10
|
| BOSC opening
|
The Open Bioinformatics Foundation
|
Hilmar Lapp
|
10:10
|
10:20
|
| BOSC opening
|
OBF in the Google Summer of Code. Wrapping up 2016 and presenting the 2017 projects (slides)
|
Kai Blin
|
10:20
|
10:30
|
| BOSC opening
|
Codefest 2017 summary (slides)
|
Brad Chapman
|
10:30
|
10:45
|
|
|
Session: Workflows
|
Chair: Brad Chapman
|
10:45
|
12:20
|
| Workflows
|
Rabix Executor: an open-source executor supporting recomputability and interoperability of workflow descriptions
|
Janko Simonovic
|
10:45
|
10:56
|
| Workflows
|
Rabix Composer: an open-source integrated development environment for the Common Workflow Language
|
Ivan Batic
|
10:56
|
11:05
|
| Workflows
|
CWL-svg: an open-source workflow visualization library for the Common Workflow Language
|
Maja Nedeljkovic
|
11:05
|
11:07
|
| Workflows
|
CWL-ts: an open-source TypeScript library for building developer tools for the Common Workflow Language
|
Maja Nedeljkovic
|
11:07
|
11:11
|
| Workflows
|
(Q&A for previous 4 talks)
|
|
11:11
|
11:15
|
| Workflows
|
The GA4GH Tool Registry Service (TRS) and Dockstore - Year One
|
Denis Yuen
|
11:15
|
11:22
|
| Workflows
|
The GA4GH Task Execution System (TES) and Funnel Server
|
Brian O'Connor
|
11:22
|
11:28
|
| Workflows
|
The GA4GH Workflow Execution Schema (WES)
|
Peter Amstutz
|
11:28
|
11:34
|
| Workflows
|
The GA4GH/DREAM Infrastructure Challenges
|
Brian D. O'Connor
|
11:34
|
11:41
|
| Workflows
|
(Q&A for previous 4 talks)
|
|
11:41
|
11:45
|
| Workflows
|
Workflows interoperability with Nextflow and Common WL
|
Kevin Sayers
|
11:45
|
11:50
|
| Workflows
|
CWL Viewer: The Common Workflow Language Viewer (slides, slides.com, poster)
|
Stian Soiland-Reyes
|
11:50
|
11:55
|
| Workflows
|
Screw: tools for building reproducible single-cell epigenomics workflows
|
Kieran O'Neill
|
11:55
|
12:00
|
| Workflows
|
(Q&A for previous 3 lightning talks)
|
|
12:00
|
12:03
|
| Workflows
|
BioThings Explorer: Utilizing JSON-LD for Linking Biological APIs to Facilitate Knowledge Discovery (slides)
|
Jiwen Xin
|
12:03
|
12:08
|
| Workflows
|
Discovery and visualisation of homologous genes and gene families using Galaxy (slides)
|
Anil S. Thanki
|
12:08
|
12:13
|
| Workflows
|
YAMP : Yet Another Metagenomic Pipeline (slides)
|
Alessia Visconti
|
12:13
|
12:18
|
| Workflows
|
(Q&A for previous 3 lightning talks)
|
|
12:18
|
12:20
|
| Birds of a Feather discussions (BoFs)
|
Feel free to organize one!
|
|
12:20
|
13:40
|
| Lunch
|
12:30
|
14:00
|
|
|
Session: Developer tools and libraries for open science and reproducibility
|
Chair: Hilmar Lapp
|
14:00
|
15:00
|
| Developer tools / reproducibility
|
MultiQC: Visualising results from common bioinformatics tools (slides)
|
Phil Ewels
|
14:00
|
14:18
|
| Developer tools / reproducibility
|
NGL – a molecular graphics library for the web
|
Alexander S Rose
|
14:18
|
14:23
|
| Developer tools / reproducibility
|
GRAPHSPACE: Stimulating interdisciplinary collaborations in network biology
|
Aditya Bharadwaj
|
14:23
|
14:28
|
| Developer tools / reproducibility
|
Efficient detection of well-hopping duplicate reads on Illumina patterned flowcells
|
Timothy Booth
|
14:28
|
14:33
|
| Developer tools / reproducibility
|
(Q&A for first 3 lightning talks)
|
|
14:33
|
14:36
|
| Developer tools / reproducibility
|
An ensemble approach for gene set testing analysis with reporting capabilities
|
Monther Alhamdoosh
|
14:36
|
14:41
|
| Developer tools / reproducibility
|
OpenMS 2.0: a flexible open-source software platform for mass spectrometry data analysis
|
Timo Sachsenberg
|
14:41
|
14:46
|
| Developer tools / reproducibility
|
Interoperable, collaborative multi-platform variant calling with bcbio slides
|
Brad Chapman
|
14:46
|
14:51
|
| Developer tools / reproducibility
|
Gene Set Variation Analysis in cBioPortal
|
Kees van Bochove
|
14:51
|
14:56
|
| Developer tools / reproducibility
|
(Q&A for last 4 lightning talks)
|
|
14:56
|
15:00
|
|
|
Session: Data Science & Visualization
|
Chair: Karsten Hokamp
|
15:00
|
16:00
|
| Data Science & Visualization
|
The backbone of research reproducibility: sustainable and flexible tool deployment (slides)
|
Björn Grüning
|
15:00
|
15:18
|
| Data Science & Visualization
|
Reproducible bioinformatics software with GNU Guix
|
Pjotr Prins
|
15:18
|
15:23
|
| Data Science & Visualization
|
Reproducible and user-controlled software management in HPC with GNU Guix
|
Ricardo Wurmus
|
15:23
|
15:28
|
| Data Science & Visualization
|
A Ubiquitous Approach to Reproducible Bioinformatics across Computational Platforms (slides)
|
John Chilton
|
15:28
|
15:33
|
| Data Science & Visualization
|
(Q&A for first 3 lightning talks)
|
|
15:33
|
15:36
|
| Data Science & Visualization
|
Revitalizing a classic bioinformatics tool using modern technologies: the case of the Cytoscape Project (slides, poster)
|
Keiichiro Ono
|
15:36
|
15:41
|
| Data Science & Visualization
|
The SPOT ontology toolkit : semantics as a service
|
Olga Vrousgou
|
15:41
|
15:46
|
| Data Science & Visualization
|
Biopython Project Update 2017 (slides)
|
Sourav Singh
|
15:46
|
15:51
|
| Data Science & Visualization
|
(Q&A for last 3 lightning talks)
|
|
15:51
|
15:54
|
| Coffee Break
|
16:00
|
16:30
|
| Keynote
|
Open Sourcing Ourselves (slides)
|
Madeleine Ball
|
16:30
|
17:30
|
| Birds of a Feather discussions (BoFs)
|
Feel free to organize one!
|
|
17:30
|
18:30
|
| Posters (odd-numbered posters present)
|
18:00
|
19:00
|
| Dinner
|
Optional pay-your-own-way dinner (must RSVP in advance--space limited)
|
|
19:30
|
|
| Session
|
Title
|
Speaker (or Session Chair)
|
Start Time
|
End Time
|
| Day 2
|
BOSC Announcements
|
Heather Wiencko (Co-Chair, BOSC 2017)
|
10:00
|
10:05
|
|
|
Session: Community Building and Citizen Science
|
Chair: Peter Cock
|
10:05
|
11:30
|
| Community Building and Citizen Science
|
BeerDeCoded: exploring the beer metagenome (slides)
|
Jonathan Sobel
|
10:05
|
10:23
|
| Community Building and Citizen Science
|
Supporting curation communities & collecting technical dividends (slides)
|
Monica Munoz-Torres
|
10:23
|
10:41
|
| Community Building and Citizen Science
|
Journal of Open Source Software (JOSS) (slides)
|
Pjotr Prins
|
10:41
|
10:59
|
| Community Building and Citizen Science
|
Building an open, collaborative, online infrastructure for bioinformatics training (slides, poster)
|
Bérénice Batut
|
10:59
|
11:17
|
| Community Building and Citizen Science
|
Software and social strategies for community sourced biological networks and ontologies
|
Dexter Pratt
|
11:17
|
11:22
|
| Community Building and Citizen Science
|
Distance-based, online bioinformatics training in Africa: the H3ABioNet experience
|
Nicola Mulder
|
11:22
|
11:27
|
| Community Building and Citizen Science
|
(Q&A for previous 2 lightning talks)
|
|
11:27
|
11:30
|
|
|
Session: Late-Breaking Lightning Talks
|
Chair: Nomi Harris
|
11:30
|
12:30
|
| LBLTs
|
Recent object formation in the core of Galaxy (slides)
|
Martin Cech
|
11:30
|
11:35
|
| LBLTs
|
Reproducibility of computational workflows is automated using continuous analysis
|
Brett Beaulieu-Jones
|
11:35
|
11:40
|
| LBLTs
|
Full-stack genomics pipelining with GATK4 + WDL + Cromwell
|
Kate Voss
|
11:40
|
11:45
|
| LBLTs
|
ToolDog - generating tool descriptors from the ELIXIR tool registry (slides, poster)
|
Kenzo-Hugo Hillion
|
11:45
|
11:50
|
| LBLTs
|
BioThings SDK: a toolkit for building high-performance data APIs in biology
|
Chunlei Wu
|
11:50
|
11:55
|
| LBLTs
|
(Q&A for first 5 LBLTs)
|
|
11:55
|
12:00
|
| LBLTs
|
Integrating cloud storage providers for genomic analyses
|
Ted Liefeld
|
12:00
|
12:05
|
| LBLTs
|
Fighting Superbugs with Open Source Software (slides)
|
Kai Blin
|
12:10
|
12:15
|
| LBLTs
|
(Q&A for last 2 LBLTs)
|
|
12:20
|
12:25
|
| Birds of a Feather discussions (BoFs)
|
Feel free to organize one!
|
|
12:30
|
13:40
|
| Lunch
|
12:30
|
14:00
|
|
|
Session: Open Data
|
Chair: Bastian Greshake
|
14:00
|
15:00
|
| Open Data
|
RADAR-CNS - Research Infrastructure for processing wearable data to improve health
|
Nivethika Mahasivam
|
14:00
|
14:18
|
| Open Data
|
Using Wikidata as an open, community-maintained database of biomedical knowledge (slides)
|
Andrew Su
|
14:18
|
14:36
|
| Open Data
|
Emerging public databases of clinical genetic test results: Implications for large scale deployment of precision medicine (slides)
|
Stephen Lincoln
|
14:36
|
14:41
|
| Open Data
|
Discovering datasets with DATS in DataMed
|
Philippe Rocca-Serra
|
14:41
|
14:46
|
| Open Data
|
Bioschemas for life science data (slides, poster)
|
Carole Goble
|
14:46
|
14:51
|
| Open Data
|
Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data
|
Annemarie Eckes
|
14:51
|
14:56
|
| Open Data
|
(Q&A for previous 4 lightning talks)
|
|
14:56
|
15:00
|
| Panel
|
Panel: Open Data--Standards, Opportunities and Challenges
|
Moderator: Mónica Muñoz-Torres.
Panelists: Madeleine Ball, Carole Goble, Nick Loman, Andrew Su
|
15:00
|
16:00
|
| Coffee Break
|
16:00
|
16:30
|
| Keynote
|
Open data meets ubiquitous sequencing: challenges and opportunities
|
Nick Loman
|
16:30
|
17:30
|
| Birds of a Feather discussions (BoFs)
|
Feel free to organize one!
|
|
17:30
|
18:30
|
| Posters (even-numbered posters present)
|
18:00
|
19:00
|
| Dinner
|
Optional pay-your-own-way dinner (must RSVP in advance--space limited)
|
|
19:30
|
|
If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.org.
