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Difference between revisions of "BOSC 2017 Schedule"

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(→‎Schedule at a Glance (subject to change))
(→‎Complete schedule of talks (subject to change))
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|Endtime
 
|Endtime
 
|-
 
|-
 +
|BOSC opening
 +
|BOSC introductory remarks
 +
|Nomi Harris
 +
|10:00
 +
|10:10
 +
|-
 +
|BOSC opening
 +
|The Open Bioinformatics Foundation
 +
|Hilmar Lapp
 +
|10:10
 +
|10:20
 +
|-
 +
|BOSC opening
 +
|Codefest 2017 summary
 +
|Brad Chapman
 +
|10:20
 +
|10:35
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|Workflows
 +
|Rabix Composer: an open-source integrated development environment for the Common Workflow Language
 +
|Ivan Batic
 +
|10:35
 +
|10:43
 +
|-
 +
|Workflows
 +
|Workflows: Rabix Executor: an open-source executor supporting recomputability and interoperability of workflow descriptions
 +
|Gaurav Kaushik
 +
|10:43
 +
|10:51
 +
|-
 +
|Workflows
 +
|CWL-svg: an open-source workflow visualization library for the Common Workflow Language
 +
|Maja Nedeljkovic
 +
|10:51
 +
|10:58
 +
|-
 +
|Workflows
 +
|CWL-ts: an open-source TypeScript library for building developer tools for the Common Workflow Language
 +
|Maja Nedeljkovic
 +
|10:58
 +
|11:05
 +
|-
 +
|Workflows
 +
|The GA4GH Tool Registry Service (TRS) and Dockstore - Year One
 +
|Denis Yuen
 +
|11:05
 +
|11:13
 +
|-
 +
|Workflows
 +
|The GA4GH Task Execution System (TES) and Funnel Server
 +
|Brian O'Connor
 +
|11:13
 +
|11:20
 +
|-
 +
|Workflows
 +
|The GA4GH Workflow Execution Schema (WES)
 +
|Brian D. O'Connor or Peter Amstutz?
 +
|11:20
 +
|11:27
 +
|-
 +
|Workflows
 +
|The GA4GH/DREAM Infrastructure Challenges
 +
|Brian D. O'Connor
 +
|11:27
 +
|11:35
 +
|-
 +
|Workflows
 +
|Workflows interoperability with Nextflow and Common WL
 +
|Kevin Sayers
 +
|11:35
 +
|11:40
 +
|-
 +
|Workflows
 +
|CWL Viewer: The Common Workflow Language Viewer
 +
|Stian Soiland-Reyes
 +
|11:40
 +
|11:45
 +
|-
 +
|Workflows
 +
|Screw: tools for building reproducible single-cell epigenomics workflows
 +
|Kieran O'Neill
 +
|11:45
 +
|11:50
 +
|-
 +
|Workflows
 +
|BioThings Explorer: Utilizing JSON-LD for Linking Biological APIs to Facilitate Knowledge Discovery
 +
|Jiwen Xin
 +
|11:50
 +
|11:55
 +
|-
 +
|Workflows
 +
|Discovery and visualisation of homologous genes and gene families using Galaxy
 +
|Anil S. Thanki
 +
|11:55
 +
|12:00
 +
|-
 +
|Workflows
 +
|YAMP : Yet Another Metagenomic Pipeline
 +
|Alessia Visconti
 +
|12:00
 +
|12:05
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|BoFs
 +
|Birds of a Feather (BoFs)
 +
|
 +
|12:20
 +
|13:40
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|Developer tools and libraries for open science and reproducibility
 +
|MultiQC: Visualising results from common bioinformatics tools
 +
|Phil Ewels
 +
|14:00
 +
|14:18
 +
|-
 +
|Developer tools and libraries for open science and reproducibility
 +
|NGL – a molecular graphics library for the web
 +
|Alexander S Rose
 +
|14:18
 +
|14:23
 +
|-
 +
|Developer tools and libraries for open science and reproducibility
 +
|GRAPHSPACE: Stimulating interdisciplinary collaborations in network biology
 +
|Aditya Bharadwaj
 +
|14:23
 +
|14:28
 +
|-
 +
|Developer tools and libraries for open science and reproducibility
 +
|Efficient detection of well-hopping duplicate reads on Illumina patterned flowcells
 +
|Timothy Booth
 +
|14:28
 +
|14:33
 +
|-
 +
|Developer tools and libraries for open science and reproducibility
 +
|An ensemble approach for gene set testing analysis with reporting capabilities
 +
|Monther Alhamdoosh
 +
|14:33
 +
|14:38
 +
|-
 +
|Developer tools and libraries for open science and reproducibility
 +
|OpenMS 2.0: a flexible open-source software platform for mass spectrometry data analysis
 +
|Timo Sachsenberg
 +
|14:38
 +
|14:43
 +
|-
 +
|Developer tools and libraries for open science and reproducibility
 +
|Interoperable, collaborative multi-platform variant calling with bcbio
 +
|Brad Chapman
 +
|14:43
 +
|14:48
 +
|-
 +
|Developer tools and libraries for open science and reproducibility
 +
|Pieter Lukasse, Fedde Schaeffer, Oleguer Plantalech Casals, Sander Tan and Sjoerd van Hagen, Gene Set Variation Analysis in cBioPortal
 +
|Pieter Lukasse (probably)
 +
|14:48
 +
|14:53
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|Data Science & Visualization
 +
|The backbone of research reproducibility: sustainable and flexible tool deployment
 +
|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
 +
|John Chilton
 +
|15:28
 +
|15:33
 +
|-
 +
|Data Science & Visualization
 +
|Revitalizing a classic bioinformatics tool using modern technologies: the case of the Cytoscape Project
 +
|Keiichiro Ono
 +
|15:33
 +
|15:38
 +
|-
 +
|Data Science & Visualization
 +
|The SPOT ontology toolkit : semantics as a service
 +
|Olga Vrousgou
 +
|15:38
 +
|15:43
 +
|-
 +
|Data Science & Visualization
 +
|Biopython Project Update 2017
 +
|Sourav Singh
 +
|15:43
 +
|15:48
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|Keynote
 +
|
 +
|Dawn Field
 +
|16:30
 +
|17:30
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|BoFs
 +
|Birds of a Feather (BoFs)
 +
|
 +
|17:30
 +
|18:30
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|}
 +
==== Day 2 (Sunday, July 23, 2017) ====
  
 +
{| class="wikitable collapsible"
 +
|Session
 +
|Title
 +
|Speaker
 +
|Starttime
 +
|Endtime
 +
|-
 +
|-
 +
|Day 2
 +
|BOSC Announcements
 +
|Heather Wiencko
 +
|10:00
 +
|10:05
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|Community Building and Citizen Science
 +
|BeerDeCoded: exploring the beer metagenome
 +
|Jonathan Sobel
 +
|10:05
 +
|10:23
 +
|-
 +
|Community Building and Citizen Science
 +
|Supporting curation communities & collecting technical dividends
 +
|Monica Munoz-Torres
 +
|10:23
 +
|10:41
 +
|-
 +
|Community Building and Citizen Science
 +
|Journal of Open Source Software (JOSS)
 +
|Pjotr Prins
 +
|10:41
 +
|10:59
 +
|-
 +
|Community Building and Citizen Science
 +
|Software and social strategies for community sourced biological networks and ontologies
 +
|Dexter Pratt
 +
|10:59
 +
|11:04
 +
|-
 +
|Community Building and Citizen Science
 +
|Building an open, collaborative, online infrastructure for bioinformatics training
 +
|Bérénice Batut
 +
|11:04
 +
|11:22
 +
|-
 +
|Community Building and Citizen Science
 +
|Distance-based, online bioinformatics training in Africa: the H3ABioNet experience
 +
|Kim Gurwitz
 +
|11:22
 +
|11:27
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|Late-Breaking Lightning Talks--TBA
 +
|
 +
|
 +
|11:30
 +
|12:20
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|BoFs
 +
|Birds of a Feather (BoFs)
 +
|
 +
|12:20
 +
|13:40
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|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
 +
|Andrew Su
 +
|14:18
 +
|14:36
 +
|-
 +
|Open Data
 +
|Emerging public databases of clinical genetic test results: Implications for large scale deployment of precision medicine
 +
|Stephen Lincoln
 +
|14:36
 +
|14:41
 +
|-
 +
|Open Data
 +
|Discovering datasets with DATS in DataMed
 +
|Alejandra Gonzalez-Beltran (or colleague)
 +
|14:41
 +
|14:46
 +
|-
 +
|Open Data
 +
|Bioschemas for life science data
 +
|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
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|Panel
 +
|Panel: Open Data--Standards, Opportunities and Challenges
 +
|
 +
|15:00
 +
|16:00
 +
|-
 +
|Keynote
 +
|
 +
|Nick Loman
 +
|16:30
 +
|17:30
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|BoFs
 +
|Birds of a Feather (BoFs)
 +
|
 +
|17:30
 +
|18:30
 
|}
 
|}

Revision as of 22:57, 29 May 2017

BOSC logo

Sponsors

We are grateful to BOSC 2017 sponsors The Hyve (open source solutions for bioinformatics), Mozilla Science Lab (a community of researchers, developers, and librarians making research open and accessible), Repositive Limited (connecting the genomics community with the data they need) and GigaScience (an open access, open data, open peer-review journal). If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.org.

The Hyve logo
    
Mozilla Science Lab logo
    
Repositive Limited logo
    
GigaScience

Pre-BOSC: Codefest 2017

Codefest 2017 (a pre-BOSC hackathon) will take place July 20-21 at Brmlab, Prague (a non-profit, community-run hackerspace). Codefest is FREE and open to all (even if you're not attending BOSC). See Codefest 2017 for details and to sign up.

Schedule at a glance (subject to change)

Day 1 (Saturday, July 22)   Day 2 (Sunday, July 23)
Time Session Time Session
8:30-9:30 ISMB announcements & ISMB keynote 8:30-9:30 ISMB announcements & ISMB keynote
10:00-10:10 BOSC announcements 10:00-10:05 BOSC announcements
10:10-10:35 Introduction to the Open Bioinformatics Foundation; Codefest 2017 Report 10:05-11:30 Session: Community Building and Citizen Science
10:35-12:20 Session: Workflows 11:30-12:20 Late-Breaking Lightning Talks
12:30-14:00 Lunch, BoFs, Posters 12:30-14:00 Lunch, BoFs, Posters
14:00-15:00 Session: Data Science & Visualization 14:00-15:00 Session: Open Data
15:00-16:00 Keynote (Dawn Field) 15:00-16:00 Panel: Open Data--Standards, Opportunities and Challenges
16:30-17:30 Session: Developer tools and libraries for open science and reproducibility 16:30-17:30 Keynote (Nick Loman) and closing remarks
17:30-18:30 BoFs 17:30-18:30 BoFs

Complete schedule of talks (subject to change)

(Converted from Google Sheets to mediawiki by http://marianogappa.github.io/mediawiki-table-utility/)

Session Title Speaker Starttime Endtime
BOSC opening BOSC introductory remarks Nomi Harris 10:00 10:10
BOSC opening The Open Bioinformatics Foundation Hilmar Lapp 10:10 10:20
BOSC opening Codefest 2017 summary Brad Chapman 10:20 10:35
Workflows Rabix Composer: an open-source integrated development environment for the Common Workflow Language Ivan Batic 10:35 10:43
Workflows Workflows: Rabix Executor: an open-source executor supporting recomputability and interoperability of workflow descriptions Gaurav Kaushik 10:43 10:51
Workflows CWL-svg: an open-source workflow visualization library for the Common Workflow Language Maja Nedeljkovic 10:51 10:58
Workflows CWL-ts: an open-source TypeScript library for building developer tools for the Common Workflow Language Maja Nedeljkovic 10:58 11:05
Workflows The GA4GH Tool Registry Service (TRS) and Dockstore - Year One Denis Yuen 11:05 11:13
Workflows The GA4GH Task Execution System (TES) and Funnel Server Brian O'Connor 11:13 11:20
Workflows The GA4GH Workflow Execution Schema (WES) Brian D. O'Connor or Peter Amstutz? 11:20 11:27
Workflows The GA4GH/DREAM Infrastructure Challenges Brian D. O'Connor 11:27 11:35
Workflows Workflows interoperability with Nextflow and Common WL Kevin Sayers 11:35 11:40
Workflows CWL Viewer: The Common Workflow Language Viewer Stian Soiland-Reyes 11:40 11:45
Workflows Screw: tools for building reproducible single-cell epigenomics workflows Kieran O'Neill 11:45 11:50
Workflows BioThings Explorer: Utilizing JSON-LD for Linking Biological APIs to Facilitate Knowledge Discovery Jiwen Xin 11:50 11:55
Workflows Discovery and visualisation of homologous genes and gene families using Galaxy Anil S. Thanki 11:55 12:00
Workflows YAMP : Yet Another Metagenomic Pipeline Alessia Visconti 12:00 12:05
BoFs Birds of a Feather (BoFs) 12:20 13:40
Developer tools and libraries for open science and reproducibility MultiQC: Visualising results from common bioinformatics tools Phil Ewels 14:00 14:18
Developer tools and libraries for open science and reproducibility NGL – a molecular graphics library for the web Alexander S Rose 14:18 14:23
Developer tools and libraries for open science and reproducibility GRAPHSPACE: Stimulating interdisciplinary collaborations in network biology Aditya Bharadwaj 14:23 14:28
Developer tools and libraries for open science and reproducibility Efficient detection of well-hopping duplicate reads on Illumina patterned flowcells Timothy Booth 14:28 14:33
Developer tools and libraries for open science and reproducibility An ensemble approach for gene set testing analysis with reporting capabilities Monther Alhamdoosh 14:33 14:38
Developer tools and libraries for open science and reproducibility OpenMS 2.0: a flexible open-source software platform for mass spectrometry data analysis Timo Sachsenberg 14:38 14:43
Developer tools and libraries for open science and reproducibility Interoperable, collaborative multi-platform variant calling with bcbio Brad Chapman 14:43 14:48
Developer tools and libraries for open science and reproducibility Pieter Lukasse, Fedde Schaeffer, Oleguer Plantalech Casals, Sander Tan and Sjoerd van Hagen, Gene Set Variation Analysis in cBioPortal Pieter Lukasse (probably) 14:48 14:53
Data Science & Visualization The backbone of research reproducibility: sustainable and flexible tool deployment 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 John Chilton 15:28 15:33
Data Science & Visualization Revitalizing a classic bioinformatics tool using modern technologies: the case of the Cytoscape Project Keiichiro Ono 15:33 15:38
Data Science & Visualization The SPOT ontology toolkit : semantics as a service Olga Vrousgou 15:38 15:43
Data Science & Visualization Biopython Project Update 2017 Sourav Singh 15:43 15:48
Keynote Dawn Field 16:30 17:30
BoFs Birds of a Feather (BoFs) 17:30 18:30

Day 2 (Sunday, July 23, 2017)

Session Title Speaker Starttime Endtime
Day 2 BOSC Announcements Heather Wiencko 10:00 10:05
Community Building and Citizen Science BeerDeCoded: exploring the beer metagenome Jonathan Sobel 10:05 10:23
Community Building and Citizen Science Supporting curation communities & collecting technical dividends Monica Munoz-Torres 10:23 10:41
Community Building and Citizen Science Journal of Open Source Software (JOSS) Pjotr Prins 10:41 10:59
Community Building and Citizen Science Software and social strategies for community sourced biological networks and ontologies Dexter Pratt 10:59 11:04
Community Building and Citizen Science Building an open, collaborative, online infrastructure for bioinformatics training Bérénice Batut 11:04 11:22
Community Building and Citizen Science Distance-based, online bioinformatics training in Africa: the H3ABioNet experience Kim Gurwitz 11:22 11:27
Late-Breaking Lightning Talks--TBA 11:30 12:20
BoFs Birds of a Feather (BoFs) 12:20 13:40
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 Andrew Su 14:18 14:36
Open Data Emerging public databases of clinical genetic test results: Implications for large scale deployment of precision medicine Stephen Lincoln 14:36 14:41
Open Data Discovering datasets with DATS in DataMed Alejandra Gonzalez-Beltran (or colleague) 14:41 14:46
Open Data Bioschemas for life science data 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
Panel Panel: Open Data--Standards, Opportunities and Challenges 15:00 16:00
Keynote Nick Loman 16:30 17:30
BoFs Birds of a Feather (BoFs) 17:30 18:30
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