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Difference between revisions of "BOSC 2017 Schedule"

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(→‎Schedule at a glance: Split days into 2 tables. Should be easier to maintain. Feel free to revert if you don't like the look.)
(Added list of posters with links to F1000)
 
(74 intermediate revisions by 3 users not shown)
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__NOTOC__
 
__NOTOC__
 
[[File:Pear.png|120px|right|BOSC logo|link=BOSC_2017]]
 
[[File:Pear.png|120px|right|BOSC logo|link=BOSC_2017]]
 +
 +
== Complete Program  ==
 +
 +
This page has links to all the publicly available talk slides, videos and posters. Most of the slides and posters are on our [http://f1000research.com/collections/BOSC BOSC F1000 Research Collection] (others are on SlideShare and FigShare), while the videos are on the [https://www.youtube.com/watch?v=tV6hAWreTSY&list=PLir-OOQiOhXZX_2zmUJz0fx8RLALi3tkK BOSC 2017 YouTube playlist].
 +
 +
* [https://www.open-bio.org/w/images/4/42/BOSC2017-complete-program-compressed.pdf Download the complete program (including all talk and poster abstracts) as a PDF]
 +
 +
* [https://www.iscb.org/cms_addon/conferences/ismbeccb2017/bosc.php ISMB/ECCB schedule for BOSC, including brief descriptions of each talk topic]
  
 
== Pre-BOSC: Codefest 2017  ==
 
== Pre-BOSC: Codefest 2017  ==
Line 20: Line 28:
 
| 10:00-10:10 || BOSC announcements  
 
| 10:00-10:10 || BOSC announcements  
 
|-
 
|-
−
| 10:10-10:35 || Introduction to the Open Bioinformatics Foundation; OBF in the Google Summer of Code; Codefest 2017 Report
+
| 10:10-10:45 || Introduction to the Open Bioinformatics Foundation; OBF in the Google Summer of Code; Codefest 2017 Report
 
|-
 
|-
−
| 10:35-12:20 || Session: Workflows  
+
| 10:45-12:20 || Session: Workflows  
 
|-
 
|-
 
| 12:30-14:00 || Lunch, Posters, [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]
 
| 12:30-14:00 || Lunch, Posters, [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]
 
|-
 
|-
−
| 14:00-15:00 || Session: Data Science & Visualization
+
| 14:00-15:00 || Session: Developer tools and libraries for open science and reproducibility
 
|-
 
|-
−
| 15:00-16:00 || [[BOSC_2017_Keynote_Speakers| Keynote (Dawn Field)]]
+
| 15:00-16:00 || Session: Data Science & Visualization
 
|-
 
|-
−
| 16:30-17:30 || Session: Developer tools and libraries for open science and reproducibility
+
| 16:30-17:30 || [[BOSC_2017_Keynote_Speakers| Keynote: Madeleine Ball]]
 
|-
 
|-
 
| 17:30-18:30 || [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]
 
| 17:30-18:30 || [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]
 +
|-
 +
| 18:00-19:00 || [https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=B Posters]
 
|}
 
|}
 
| style="border: none" |
 
| style="border: none" |
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|-
 
|-
 
|  17:30-18:30 || [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]  
 
|  17:30-18:30 || [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]  
 +
|-
 +
| 18:00-19:00 || [https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=B Posters]
 
|}
 
|}
 
|}
 
|}
  
−
== Complete schedule of talks (subject to change) ==
+
= Complete schedule of talks =
  
−
==== Day 1 (Saturday, July 22, 2017) ====
+
== Day 1 (Saturday, July 22, 2017) ==
 
{| border="1" cellspacing="0" cellpadding="7"
 
{| border="1" cellspacing="0" cellpadding="7"
 
|- style="background:#D0F781"
 
|- style="background:#D0F781"
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|-
 
|-
 
|BOSC opening
 
|BOSC opening
−
|Introduction and welcome
+
|Introduction and welcome ([https://youtu.be/tV6hAWreTSY video])
 
|Nomi Harris (Chair, BOSC 2017)
 
|Nomi Harris (Chair, BOSC 2017)
 
|10:00
 
|10:00
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|-
 
|-
 
|BOSC opening
 
|BOSC opening
−
|The Open Bioinformatics Foundation
+
|The Open Bioinformatics Foundation ([https://youtu.be/DeDRLIpuWJg video])
 
|Hilmar Lapp
 
|Hilmar Lapp
 
|10:10
 
|10:10
Line 86: Line 98:
 
|-
 
|-
 
|BOSC opening
 
|BOSC opening
−
|OBF in the Google Summer of Code. Wrapping up 2016 and presenting the 2017 projects
+
|OBF in the Google Summer of Code. Wrapping up 2016 and presenting the 2017 projects ([https://f1000research.com/slides/6-1232 slides], [https://youtu.be/CKlF0eSbRjQ video])
 
|Kai Blin
 
|Kai Blin
 
|10:20
 
|10:20
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|-
 
|-
 
|BOSC opening
 
|BOSC opening
−
|Codefest 2017 summary
+
|[[Codefest 2017]] summary ([https://f1000research.com/slides/6-1187 slides], [https://youtu.be/CoSQwExrF8M video])
 
|Brad Chapman
 
|Brad Chapman
 
|10:30
 
|10:30
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|-
 
|-
 
|Workflows
 
|Workflows
−
|Rabix Executor: an open-source executor supporting recomputability and interoperability of workflow descriptions
+
|Rabix Executor: an open-source executor supporting recomputability and interoperability of workflow descriptions ([https://youtu.be/iTgZZnT0D6A video])
 
|Janko Simonovic
 
|Janko Simonovic
 
|10:45
 
|10:45
−
|10:57
+
|10:56
 
|-
 
|-
 
|Workflows
 
|Workflows
−
|Rabix Composer: an open-source integrated development environment for the Common Workflow Language
+
|Rabix Composer: an open-source integrated development environment for the Common Workflow Language ([https://youtu.be/xXaKZl1334M video])
 
|Ivan Batic
 
|Ivan Batic
−
|10:57
+
|10:56
 +
|11:05
 +
|-
 +
|Workflows
 +
|CWL-svg: an open-source workflow visualization library for the Common Workflow Language ([https://youtu.be/wAkagL8PWc0 video with next talk])
 +
|Maja Nedeljkovic
 +
|11:05
 
|11:07
 
|11:07
 
|-
 
|-
 
|Workflows
 
|Workflows
−
|CWL-svg: an open-source workflow visualization library for the Common Workflow Language
+
|CWL-ts: an open-source TypeScript library for building developer tools for the Common Workflow Language ([https://youtu.be/wAkagL8PWc0 video with previous talk])
 
|Maja Nedeljkovic
 
|Maja Nedeljkovic
 
|11:07
 
|11:07
−
|11:10
+
|11:11
 
|-
 
|-
 
|Workflows
 
|Workflows
−
|CWL-ts: an open-source TypeScript library for building developer tools for the Common Workflow Language
+
|(Q&A for previous 4 talks)
−
|Maja Nedeljkovic
+
|
−
|11:10
+
|11:11
 
|11:15
 
|11:15
 
|-
 
|-
 
|Workflows
 
|Workflows
−
|The GA4GH Tool Registry Service (TRS) and Dockstore - Year One
+
|The GA4GH Tool Registry Service (TRS) and Dockstore - Year One ([https://youtu.be/SuwONuO8LoA video])
 
|Denis Yuen
 
|Denis Yuen
 
|11:15
 
|11:15
−
|11:23
+
|11:22
 
|-
 
|-
 
|Workflows
 
|Workflows
−
|The GA4GH Task Execution System (TES) and Funnel Server
+
|The GA4GH Task Execution System (TES) and Funnel Server ([https://youtu.be/tTCyhxyFZfo video])
 
|Brian O'Connor
 
|Brian O'Connor
−
|11:23
+
|11:22
−
|11:30
+
|11:28
 
|-
 
|-
 
|Workflows
 
|Workflows
−
|The GA4GH Workflow Execution Schema (WES)
+
|The GA4GH Workflow Execution Schema (WES) ([https://youtu.be/VFpNBcA_y5g video])
 
|Peter Amstutz
 
|Peter Amstutz
−
|11:30
+
|11:28
−
|11:37
+
|11:34
 
|-
 
|-
 
|Workflows
 
|Workflows
−
|The GA4GH/DREAM Infrastructure Challenges
+
|The GA4GH/DREAM Infrastructure Challenges ([https://youtu.be/CFc7bG0vzpU video])
 
|Brian D. O'Connor
 
|Brian D. O'Connor
−
|11:37
+
|11:34
 +
|11:41
 +
|-
 +
|Workflows
 +
|(Q&A for previous 4 talks)
 +
|
 +
|11:41
 
|11:45
 
|11:45
 
|-
 
|-
 
|Workflows
 
|Workflows
−
|Workflows interoperability with Nextflow and Common WL
+
|Workflows interoperability with Nextflow and Common WL ([https://youtu.be/RlsLzMXmIfk video])
 
|Kevin Sayers
 
|Kevin Sayers
 
|11:45
 
|11:45
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|-
 
|-
 
|Workflows
 
|Workflows
−
|CWL Viewer: The Common Workflow Language Viewer
+
|CWL Viewer: The Common Workflow Language Viewer ([https://f1000research.com/slides/6-1175 slides], [http://slides.com/markrobinson/cwlviewer#/ slides.com], [https://f1000research.com/posters/6-1075 poster], [https://youtu.be/iB_0l-Bm4nA video])
 
|Stian Soiland-Reyes
 
|Stian Soiland-Reyes
 
|11:50
 
|11:50
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|-
 
|-
 
|Workflows
 
|Workflows
−
|Screw: tools for building reproducible single-cell epigenomics workflows
+
|Screw: tools for building reproducible single-cell epigenomics workflows ([https://youtu.be/L9ljkoOGGL4 video])
 
|Kieran O'Neill
 
|Kieran O'Neill
 
|11:55
 
|11:55
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|-
 
|-
 
|Workflows
 
|Workflows
−
|BioThings Explorer: Utilizing JSON-LD for Linking Biological APIs to Facilitate Knowledge Discovery
+
| (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 ([https://f1000research.com/slides/6-1176 slides], [https://youtu.be/u7r_EI5dIRI video])
 
|Jiwen Xin
 
|Jiwen Xin
−
|12:00
+
|12:03
−
|12:05
+
|12:08
 
|-
 
|-
 
|Workflows
 
|Workflows
−
|Discovery and visualisation of homologous genes and gene families using Galaxy
+
|Discovery and visualisation of homologous genes and gene families using Galaxy ([https://f1000research.com/slides/6-1189 slides], [https://youtu.be/xE8uIXE05I4 videos])
 
|Anil S. Thanki
 
|Anil S. Thanki
−
|12:05
+
|12:08
−
|12:10
+
|12:13
 
|-
 
|-
 
|Workflows
 
|Workflows
−
|YAMP : Yet Another Metagenomic Pipeline
+
|YAMP : Yet Another Metagenomic Pipeline ([https://f1000research.com/slides/6-1185 slides], [https://youtu.be/boQA4RrHeUk video])
 
|Alessia Visconti
 
|Alessia Visconti
−
|12:10
+
|12:13
−
|12:15
+
|12:18
 
|-
 
|-
 +
|Workflows
 +
| (Q&A for previous 3  lightning talks)
 
|
 
|
−
|
+
|12:18
−
|
+
|12:20
−
|
 
−
|
 
 
|-  style="background:#FFFFCC"
 
|-  style="background:#FFFFCC"
 
| [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]
 
| [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]
Line 210: Line 240:
 
|-  
 
|-  
 
|Developer tools / reproducibility
 
|Developer tools / reproducibility
−
|MultiQC: Visualising results from common bioinformatics tools
+
|MultiQC: Visualising results from common bioinformatics tools ([https://f1000research.com/slides/6-1177 slides], [https://youtu.be/JNklyA8KfpE video])
 
|Phil Ewels
 
|Phil Ewels
 
|14:00
 
|14:00
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|-
 
|-
 
|Developer tools / reproducibility
 
|Developer tools / reproducibility
−
|NGL – a molecular graphics library for the web
+
|NGL – a molecular graphics library for the web ([https://youtu.be/e-QQd7uyMNQ video])
 
|Alexander S Rose
 
|Alexander S Rose
 
|14:18
 
|14:18
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|-
 
|-
 
|Developer tools / reproducibility
 
|Developer tools / reproducibility
−
|GRAPHSPACE: Stimulating interdisciplinary collaborations in network biology
+
|GRAPHSPACE: Stimulating interdisciplinary collaborations in network biology ([https://youtu.be/knaG9MLn6NA video])
 
|Aditya Bharadwaj
 
|Aditya Bharadwaj
 
|14:23
 
|14:23
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|-
 
|-
 
|Developer tools / reproducibility
 
|Developer tools / reproducibility
−
|Efficient detection of well-hopping duplicate reads on Illumina patterned flowcells
+
|Efficient detection of well-hopping duplicate reads on Illumina patterned flowcells ([https://youtu.be/JKrzRM2viZ8 video])
 
|Timothy Booth
 
|Timothy Booth
 
|14:28
 
|14:28
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|-
 
|-
 
|Developer tools / reproducibility
 
|Developer tools / reproducibility
−
|An ensemble approach for gene set testing analysis with reporting capabilities
+
| (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 ([https://f1000research.com/slides/6-1320 slides], [https://youtu.be/tCwKSAlyY3k video])
 
|Monther Alhamdoosh
 
|Monther Alhamdoosh
−
|14:33
+
|14:36
−
|14:38
+
|14:41
 
|-
 
|-
 
|Developer tools / reproducibility
 
|Developer tools / reproducibility
 
|OpenMS 2.0: a flexible open-source software platform for mass spectrometry data analysis
 
|OpenMS 2.0: a flexible open-source software platform for mass spectrometry data analysis
 
|Timo Sachsenberg
 
|Timo Sachsenberg
−
|14:38
+
|14:41
−
|14:43
+
|14:46
 
|-
 
|-
 
|Developer tools / reproducibility
 
|Developer tools / reproducibility
−
|Interoperable, collaborative multi-platform variant calling with bcbio
+
|Interoperable, collaborative multi-platform variant calling with bcbio ([https://f1000research.com/slides/6-1188 slides], [https://youtu.be/S7bu17GQHqk video])
 
|Brad Chapman
 
|Brad Chapman
−
|14:43
+
|14:46
−
|14:48
+
|14:51
 
|-
 
|-
 
|Developer tools / reproducibility
 
|Developer tools / reproducibility
−
|Gene Set Variation Analysis in cBioPortal
+
|Gene Set Variation Analysis in cBioPortal ([https://youtu.be/uC6yCx8Ebig video])
 
|Kees van Bochove
 
|Kees van Bochove
−
|14:48
+
|14:51
−
|14:53
+
|14:56
 +
|-
 +
|Developer tools / reproducibility
 +
| (Q&A for last 4  lightning talks)
 +
|
 +
|14:56
 +
|15:00
 
|- style="background:#E6E6E6"
 
|- style="background:#E6E6E6"
 
|  
 
|  
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|-
 
|-
 
|Data Science & Visualization
 
|Data Science & Visualization
−
|The backbone of research reproducibility: sustainable and flexible tool deployment
+
|The backbone of research reproducibility: sustainable and flexible tool deployment ([https://f1000research.com/slides/6-1203 slides], [https://youtu.be/zTne29-GU_E video])
 
|Björn Grüning
 
|Björn Grüning
 
|15:00
 
|15:00
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|-
 
|-
 
|Data Science & Visualization
 
|Data Science & Visualization
−
|Reproducible and user-controlled software management in HPC with GNU Guix
+
|Reproducible and user-controlled software management in HPC with GNU Guix ([https://youtu.be/cH6wCL6GeOQ video])
 
|Ricardo Wurmus
 
|Ricardo Wurmus
 
|15:23
 
|15:23
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|-
 
|-
 
|Data Science & Visualization
 
|Data Science & Visualization
−
|A Ubiquitous Approach to Reproducible Bioinformatics across Computational Platforms
+
|A Ubiquitous Approach to Reproducible Bioinformatics across Computational Platforms ([http://jmchilton.github.io/writing/bosc2017slides/biocontainers.html#1 slides], [https://youtu.be/OqzS4I-HSzs video])
 
|John Chilton
 
|John Chilton
 
|15:28
 
|15:28
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|-
 
|-
 
|Data Science & Visualization
 
|Data Science & Visualization
−
|Revitalizing a classic bioinformatics tool using modern technologies: the case of the Cytoscape Project
+
| (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 ([https://f1000research.com/slides/6-1172 slides], [https://f1000research.com/posters/6-1171 poster], [https://youtu.be/kYesuPFL6pQ video])
 
|Keiichiro Ono
 
|Keiichiro Ono
−
|15:33
+
|15:36
−
|15:38
+
|15:41
 
|-
 
|-
 
|Data Science & Visualization
 
|Data Science & Visualization
−
|The SPOT ontology toolkit : semantics as a service
+
|The SPOT ontology toolkit : semantics as a service ([https://youtu.be/Yf3z1TFqxDc video])
 
|Olga Vrousgou
 
|Olga Vrousgou
−
|15:38
+
|15:41
−
|15:43
+
|15:46
 +
|-
 +
|Data Science & Visualization
 +
|Biopython Project Update 2017 ([https://github.com/cbrueffer/talks/blob/master/2017_BOSC/presentation/presentation.pdf slides], [https://youtu.be/tYD9P0aE8tA video])
 +
|Christian Brueffer
 +
|15:46
 +
|15:51
 
|-
 
|-
 
|Data Science & Visualization
 
|Data Science & Visualization
−
|Biopython Project Update 2017
+
| (Q&A for last 3  lightning talks)
−
|Sourav Singh
+
|
−
|15:43
+
|15:51
−
|15:48
+
|15:54
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
 
| colspan="3" | Coffee Break
 
| colspan="3" | Coffee Break
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|- style="background:#EFFBFB"
 
|- style="background:#EFFBFB"
 
|Keynote
 
|Keynote
−
| Understanding the Biocode: Global Sharing of Data
+
| Open Sourcing Ourselves ([https://f1000research.com/slides/6-1255 slides], [https://youtu.be/PXBxZCfvMXI video], [http://www.madeleineball.net/open-sourcing-ourselves/ transcript])
−
| [[BOSC_2017_Keynote_Speakers| Dawn Field]]  
+
| [[BOSC_2017_Keynote_Speakers| Madeleine Ball]]  
 
|16:30
 
|16:30
 
|17:30
 
|17:30
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|17:30
 
|17:30
 
|18:30
 
|18:30
−
|-
+
|- style="background:#E6E6FF"
 +
| colspan="3" |[https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=B Posters] (odd-numbered posters present)
 +
| 18:00
 +
| 19:00
 +
|- style="background:#FFE6FF"
 
| Dinner
 
| Dinner
−
| Optional pay-your-own-way dinner (must RSVP in advance--space limited)
+
| Optional pay-your-own-way dinner (must [https://beta.doodle.com/poll/74kp3m6si5pne3mt RSVP] in advance--space limited)
−
|
+
|  
 
| 19:30
 
| 19:30
 
|
 
|
 
|}
 
|}
  
−
==== Day 2 (Sunday, July 23, 2017) ====
+
== Day 2 (Sunday, July 23, 2017) ==
  
 
{| border="1" cellspacing="0" cellpadding="7"
 
{| border="1" cellspacing="0" cellpadding="7"
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|-
 
|-
 
|Community Building and Citizen Science
 
|Community Building and Citizen Science
−
|BeerDeCoded: exploring the beer metagenome
+
|BeerDeCoded: exploring the beer metagenome ([https://www.slideshare.net/JonathanSobel/beer-decoded-boscpresentation slides], [https://youtu.be/aiIiFaocaxM video])
 
|Jonathan Sobel
 
|Jonathan Sobel
 
|10:05
 
|10:05
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|-
 
|-
 
|Community Building and Citizen Science
 
|Community Building and Citizen Science
−
|Supporting curation communities & collecting technical dividends
+
|Supporting curation communities & collecting technical dividends ([https://f1000research.com/slides/6-1240 slides], [https://youtu.be/SqUF5t1nGko video])
 
|Monica Munoz-Torres
 
|Monica Munoz-Torres
 
|10:23
 
|10:23
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|-
 
|-
 
|Community Building and Citizen Science
 
|Community Building and Citizen Science
−
|Journal of Open Source Software (JOSS)
+
|Journal of Open Source Software (JOSS) ([https://f1000research.com/slides/6-1206 slides], [https://youtu.be/orG9P0JtlSA video])
 
|Pjotr Prins
 
|Pjotr Prins
 
|10:41
 
|10:41
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|-
 
|-
 
|Community Building and Citizen Science
 
|Community Building and Citizen Science
−
|Software and social strategies for community sourced biological networks and ontologies
+
|Building an open, collaborative, online infrastructure for bioinformatics training ([https://bebatut-slides.github.io/bosc_07_17/#/1 slides], [https://youtu.be/ZL7xTqCaRsI video], [https://f1000research.com/posters/6-1218 poster])
−
|Dexter Pratt
+
|Bérénice Batut
 
|10:59
 
|10:59
−
|11:04
+
|11:17
 
|-
 
|-
 
|Community Building and Citizen Science
 
|Community Building and Citizen Science
−
|Building an open, collaborative, online infrastructure for bioinformatics training
+
|Software and social strategies for community sourced biological networks and ontologies ([https://youtu.be/Qsi09ZBIMwQ video])
−
|Bérénice Batut
+
|Dexter Pratt
−
|11:04
+
|11:17
 
|11:22
 
|11:22
 +
 
|-
 
|-
 
|Community Building and Citizen Science
 
|Community Building and Citizen Science
−
|Distance-based, online bioinformatics training in Africa: the H3ABioNet experience
+
|Distance-based, online bioinformatics training in Africa: the H3ABioNet experience ([https://youtu.be/1PTG-FJ288g video])
 
|Nicola Mulder
 
|Nicola Mulder
 
|11:22
 
|11:22
 
|11:27
 
|11:27
 +
|-
 +
|Community Building and Citizen Science
 +
| (Q&A for previous 2 lightning talks)
 +
|
 +
|11:27
 +
|11:30
 
|- style="background:#E6E6E6"
 
|- style="background:#E6E6E6"
 
|  
 
|  
Line 394: Line 459:
 
|-
 
|-
 
|LBLTs
 
|LBLTs
−
|Recent object formation in the core of Galaxy
+
|Recent object formation in the core of Galaxy ([https://f1000research.com/slides/6-1207 slides], [https://youtu.be/_EWWMAW0x1s video])
 
|Martin Cech
 
|Martin Cech
 
|11:30
 
|11:30
Line 400: Line 465:
 
|-
 
|-
 
|LBLTs
 
|LBLTs
−
|Reproducibility of computational workflows is automated using continuous analysis
+
|Reproducibility of computational workflows is automated using continuous analysis ([https://youtu.be/Cd3RfcWY8lU video])
 
|Brett Beaulieu-Jones
 
|Brett Beaulieu-Jones
 
|11:35
 
|11:35
Line 406: Line 471:
 
|-
 
|-
 
|LBLTs
 
|LBLTs
−
|Full-stack genomics pipelining with GATK4 + WDL + Cromwell
+
|Full-stack genomics pipelining with GATK4 + WDL + Cromwell ([https://f1000research.com/slides/6-1381 slides], [https://youtu.be/ng7LjJanVd8 video])
 
|Kate Voss
 
|Kate Voss
 
|11:40
 
|11:40
Line 412: Line 477:
 
|-
 
|-
 
|LBLTs
 
|LBLTs
−
|ToolDog - generating tool descriptors from the ELIXIR tool registry
+
|ToolDog - generating tool descriptors from the ELIXIR tool registry ([https://f1000research.com/slides/6-1194 slides], [https://youtu.be/_CXeyTsBfWg video], [https://f1000research.com/posters/6-1193 poster], [https://youtu.be/_CXeyTsBfWg video])
 
|Kenzo-Hugo Hillion
 
|Kenzo-Hugo Hillion
 
|11:45
 
|11:45
Line 418: Line 483:
 
|-
 
|-
 
|LBLTs
 
|LBLTs
−
|BioThings SDK: a toolkit for building high-performance data APIs in biology
+
|BioThings SDK: a toolkit for building high-performance data APIs in biology ([https://youtu.be/R1-qKZvXk-I video])
 
|Chunlei Wu
 
|Chunlei Wu
 
|11:50
 
|11:50
−
|12:00
+
|11:55
 
|-
 
|-
 
|LBLTs
 
|LBLTs
−
|(Q&A for first 5 LBLTs)
+
| (Q&A for first 5 LBLTs)
 
|
 
|
 +
|11:55
 
|12:00
 
|12:00
−
|12:05
 
 
|-
 
|-
 
|LBLTs
 
|LBLTs
−
|Integrating cloud storage providers for genomic analyses
+
|Integrating cloud storage providers for genomic analyses ([https://youtu.be/2gKYkxqk5AU video])
 
|Ted Liefeld
 
|Ted Liefeld
 +
|12:00
 
|12:05
 
|12:05
−
|12:10
 
 
|-
 
|-
 
|LBLTs
 
|LBLTs
−
|Open Humans: Opening human health data
+
|Fighting Superbugs with Open Source Software ([https://f1000research.com/slides/6-1233 slides], [https://youtu.be/ZWUnCJ3Qlsc video])
−
|Madeleine Ball
+
|Kai Blin
 
|12:10
 
|12:10
 
|12:15
 
|12:15
 
|-
 
|-
 
|LBLTs
 
|LBLTs
−
|Fighting Superbugs with Open Source Software
+
| (Q&A for last 2 LBLTs)
−
|Kai Blin
+
|
−
|12:15
 
−
|12:20
 
−
|-
 
−
|LBLTs
 
−
|Users, Communication, and a Light Application-Level API: A Request for Comments
 
−
|Seth Carbon
 
 
|12:20
 
|12:20
 
|12:25
 
|12:25
−
|-
 
−
|LBLTs
 
−
|(Q&A for last 4 LBLTs)
 
−
|
 
−
|12:25
 
−
|12:30
 
 
|- style="background:#FFFFCC"
 
|- style="background:#FFFFCC"
 
| [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]
 
| [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]
Line 476: Line 529:
 
|-
 
|-
 
|Open Data
 
|Open Data
−
|RADAR-CNS - Research Infrastructure for processing wearable data to improve health
+
|RADAR-CNS - Research Infrastructure for processing wearable data to improve health ([https://youtu.be/XeMdYeJfVUE video])
 
|Nivethika Mahasivam
 
|Nivethika Mahasivam
 
|14:00
 
|14:00
Line 482: Line 535:
 
|-
 
|-
 
|Open Data
 
|Open Data
−
|Using Wikidata as an open, community-maintained database of biomedical knowledge
+
|Using Wikidata as an open, community-maintained database of biomedical knowledge ([https://www.slideshare.net/andrewsu/bosc2017-using-wikidata-as-an-open-communitymaintained-database-of-biomedical-knowledge slides], [https://youtu.be/Q16Df78iFZc video])
 
|Andrew Su
 
|Andrew Su
 
|14:18
 
|14:18
Line 488: Line 541:
 
|-
 
|-
 
|Open Data
 
|Open Data
−
|Emerging public databases of clinical genetic test results: Implications for large scale deployment of precision medicine
+
|Emerging public databases of clinical genetic test results: Implications for large scale deployment of precision medicine ([https://f1000research.com/slides/6-1192 slides], [https://youtu.be/V1U874_DztM video])
 
|Stephen Lincoln
 
|Stephen Lincoln
 
|14:36
 
|14:36
Line 494: Line 547:
 
|-
 
|-
 
|Open Data
 
|Open Data
−
|Discovering datasets with DATS in DataMed
+
|Discovering datasets with DATS in DataMed ([https://youtu.be/ui_V-5dZEA0 video])
 
|Philippe Rocca-Serra
 
|Philippe Rocca-Serra
 
|14:41
 
|14:41
Line 500: Line 553:
 
|-
 
|-
 
|Open Data
 
|Open Data
−
|Bioschemas for life science data
+
|Bioschemas for life science data ([https://f1000research.com/slides/6-1227 slides], [https://f1000research.com/posters/6-1226 poster], [https://youtu.be/ag_wLjYQsfw video])
 
|Carole Goble
 
|Carole Goble
 
|14:46
 
|14:46
Line 506: Line 559:
 
|-
 
|-
 
|Open Data
 
|Open Data
−
|Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data
+
|Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data ([https://youtu.be/vexoknJ8LMs video])
 
|Annemarie Eckes
 
|Annemarie Eckes
 
|14:51
 
|14:51
 
|14:56
 
|14:56
 
|-
 
|-
 +
|Open Data
 +
| (Q&A for previous 4  lightning talks)
 
|
 
|
−
|
+
|14:56
−
|
+
|15:00
−
|
+
|- style="background:#CCF2FF"
−
|
 
−
|- style="background:#CCCCFF"
 
 
|Panel
 
|Panel
 
|[[BOSC_2017_Panel| Panel: Open Data--Standards, Opportunities and Challenges]]
 
|[[BOSC_2017_Panel| Panel: Open Data--Standards, Opportunities and Challenges]]
Line 524: Line 577:
 
|15:00
 
|15:00
 
|16:00
 
|16:00
−
|- style="background:#FAF4EE"
+
|- style="background:#F2E6D9"
 
| colspan="3" | Coffee Break
 
| colspan="3" | Coffee Break
 
| 16:00
 
| 16:00
 
| 16:30
 
| 16:30
−
|- style="background:#CCFFFF"
+
|- style="background:#CCFFCC"
 
|Keynote
 
|Keynote
−
| Why I Love Open Data
+
| Open data meets ubiquitous sequencing: challenges and opportunities ([https://f1000research.com/slides/6-1266 slides],  [https://youtu.be/6QmITGqDvjQ video])
 
|| [[BOSC_2017_Keynote_Speakers| Nick Loman]]  
 
|| [[BOSC_2017_Keynote_Speakers| Nick Loman]]  
 
|16:30
 
|16:30
 
|17:30
 
|17:30
−
|-
 
−
|
 
−
|
 
−
|
 
−
|
 
−
|
 
 
|- style="background:#FFFFCC"
 
|- style="background:#FFFFCC"
 
| [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]
 
| [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit?usp=sharing Birds of a Feather discussions (BoFs)]
Line 546: Line 593:
 
|17:30
 
|17:30
 
|18:30
 
|18:30
−
|-
+
|- style="background:#E6E6FF"
 +
| colspan="3" |[https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=B Posters] (even-numbered posters present)
 +
| 18:00
 +
| 19:00
 +
|- style="background:#FFE6FF"
 
| Dinner
 
| Dinner
−
| Optional pay-your-own-way dinner (must RSVP in advance--space limited)
+
| Optional pay-your-own-way dinner (must [https://beta.doodle.com/poll/zw2ti3z6dsgdy2sb RSVP] in advance--space limited)
 
|
 
|
 
| 19:30
 
| 19:30
 
|
 
|
 
|}
 
|}
 +
(Schedule converted from Google Sheets to mediawiki by http://marianogappa.github.io/mediawiki-table-utility/)
 +
 +
== Complete Program  ==
 +
 +
* [https://www.open-bio.org/w/images/4/42/BOSC2017-complete-program-compressed.pdf Download the complete program (including all talk and poster abstracts) as a PDF]
 +
 +
* [https://www.iscb.org/cms_addon/conferences/ismbeccb2017/bosc.php ISMB/ECCB schedule for BOSC, including brief descriptions of each talk topic]
  
−
(Schedule converted from Google Sheets to mediawiki by http://marianogappa.github.io/mediawiki-table-utility/)
+
== Posters ==
 +
* [https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=B BOSC posters at ISMB/ECCB 2017]
 +
 
 +
* [https://www.open-bio.org/w/images/8/82/BOSC2017-PosterOverview.pdf PDF poster list]
 +
 
 +
{|  border="1" cellspacing="0" cellpadding="7"
 +
|- style="background:#D0F781"
 +
! Poster
 +
! Title
 +
! Authors
 +
|-
 +
| A-107
 +
| GeoDiver: Differential Gene Expression Analysis & Gene-Set Analysis for GEO Datasets
 +
| Ismail Moghul, Suresh Hewapathirana, Nazrath Nawaz, Anisatu Rashid, Marian Priebe, Bruno Vieira, Fabrizio Smeraldi and Conrad Bessant
 +
|-
 +
| A-108
 +
| DAMON, an open source framework for reliable and reproducible analysis pipelines ([https://f1000research.com/posters/6-1387 poster])
 +
| Alberto Riva, Richard L Bennett and Jonathan D Licht
 +
|-
 +
| A-109
 +
| Workflow for processing standard bioinformatics formats with SciClone to infer tumor heterogeneity
 +
| Uros Sipetic
 +
|-
 +
| A-110
 +
| Microsatellite instability profiling of TCGA colorectal adenocarcinomas using a Common Workflow Language pipeline
 +
| Nikola Tesic and Marko Kalinic
 +
|-
 +
| A-111
 +
| GeneValidator: identify problems with protein-coding gene predictions
 +
| Monica-Andreea Dr_gan, Ismail Moghul, Anurag Priyam, Claudio Bustos and Yannick Wurm
 +
|-
 +
| A-112
 +
| Somatic Variant Calling Benchmarking
 +
| Sanja Mijalkovic, Milan Domazet
 +
|-
 +
| A-114
 +
| Aztec: Automated Biomedical Tool Index with Improved Information Retrieval System ([https://f1000research.com/posters/6-1450 poster])
 +
| Wei Wang, Yichao Zhou, Patrick Tan, Vincent Kyi, Xinxin Huang, Chelsea Ju, Justin Wood and Peipei Ping
 +
|-
 +
| A-115
 +
| Building a local bioinformatics community: challenges and efforts
 +
| Malvika Sharan, Toby Hodges, Julia Ritzerfeld and Georg Zeller
 +
|-
 +
| A-116
 +
| CHARME - harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research ([https://f1000research.com/posters/6-1449 poster])
 +
| Aleksandra Gruca
 +
|-
 +
| A-117
 +
| High Content Screening data storage and analysis platform - An open source solution
 +
| Vincenzo Belcastro, Stephane Cano, Diego Marescotti, Carine Poussin, Ignacio Gonzales-Suarez, Florian Martin, Filipe Bonjour, Nikolai Ivanov, Julia Hoeng
 +
|-
 +
| A-118
 +
| Expression Atlas: exploring gene expression results across species under different biological conditions
 +
| Laura Huerta, Elisabet Barrera, Wojciech Bazant, Nuno A. Fonseca, Anja Fullgrabe, Maria Keays, Suhaib Mohammed, Alfonso Munoz-Pomer Fuentes, Amy Tang, Irene Papatheodorou, Robert Petryszak, Ugis Sarkans and Alvis Brazma
 +
|-
 +
| A-119
 +
| Microservices in data, code, and project management.
 +
| Jorge Miguel Martins Boucas
 +
|-
 +
| A-120
 +
| Gene Set Variation Analysis in cBioPortal
 +
| Pieter Lukasse, Fedde Schaeffer, Oleguer Plantalech Casals, Sander Tan and Sjoerd van Hagen
 +
|-
 +
| A-121
 +
| Databases to support reanalysis of public high-throughput DNA sequencing data ([https://f1000research.com/posters/6-1312 poster])
 +
| Tazro Ohta
 +
|-
 +
| A-122
 +
| BioThings SDK: a toolkit for building high-performance data APIs in biology ([https://f1000research.com/posters/6-1348 poster])
 +
| Chunlei Wu, Cyrus Afrasiabi, Sebastien Lelong, Jiwen Xin, Ginger Tsueng and Andrew I. Su
 +
|-
 +
| A-123
 +
| Reproducing computational experiments in situ as an interactive figure in a journal article
 +
| Evanthia Kaimaklioti, Robert P Davey and Ian Mulvany
 +
|-
 +
| A-124
 +
| CWL Viewer: The Common Workflow Language Viewer ([https://f1000research.com/posters/6-1075 poster])
 +
| Mark Robinson, Stian Soiland-Reyes, Michael Crusoe and Carole Goble
 +
|-
 +
| A-125
 +
| Sequanix: a standalone application to expose Snakemake pipelines to end-users ([https://f1000research.com/posters/6-1174 poster])
 +
| Thomas Cokelaer, Dimitri Desvillechabrol, Rachel Legendre and Mélissa Cardon
 +
|-
 +
| A-126
 +
| NGI-RNAseq - a best practice analysis pipeline in Nextflow
 +
| Rickard Hammarén, Philip Ewels and Max Käller
 +
|-
 +
| A-127
 +
| PhyloProfile: an interactive and dynamic visualization tool for multi-layered phylogenetic profiles
 +
| Ngoc-Vinh Tran, Bastian Greshake and Ingo Ebersberger
 +
|-
 +
| A-128
 +
| CueSea: quality control tool for Illumina genotyping microarray data, with correction on intensity, clusterization and biological specificity.
 +
| Nikita Moshkov, Daria Iakovishina and Dimitri Nikogosov
 +
|-
 +
| A-129
 +
| Bio::DB::HTS - accessing HTSlib from Perl
 +
| Rishi Nag
 +
|-
 +
| A-130
 +
| NGLESS: Perfectly understandable and reproducible metagenomics pipelines using a domain-specific language
 +
| Luis Pedro Coelho, Paulo Monteiro, Renato Alves, A.T. Freitas and Peer Bork
 +
|-
 +
| A-131
 +
| CGP as a Service (CGPaaS) - From data submission to results using your web-browser
 +
| Keiran Raine, Adam Butler, Peter Clapham, Jon Teague, Peter Campbell
 +
|-
 +
| A-132
 +
| Large-scale genotypic and phenotypic data support for Tripal: Chado optimization by utilizing modern PostgreSQL functionality
 +
| Lacey-Anne Sanderson, Reynold Tan, Carolyn Caron, Kirstin Bett
 +
|-
 +
| A-133
 +
| GenePattern Notebooks: An integrative analytical environment for genomics research ([https://f1000research.com/posters/5-1900 poster])
 +
| Michael Reich, Thorin Tabor, Helga Thorvaldsdóttir, Barbara Hill, Ted Liefeld, Jill Mesirov, Pablo Tamayo
 +
|-
 +
| A-134
 +
| BioContainers for supercomputers: 2,000+ accessible, discoverable Singularity apps
 +
| John Fonner, Rion Dooley, Jacquelyn Turcinovic and Matthew Vaughn
 +
|-
 +
| A-135
 +
| Collaborative Open Plant Omics: A platform for "FAIR" data for plant science
 +
| Felix Shaw, Anthony Etuk, Rob Davey, Alejandra Gonzalez-Beltran, David Johnson, Phillipe Rocca-Serra and Susanna Sansone
 +
|-
 +
| A-136
 +
| CWL+Research Object == Complete Provenance
 +
| Farah Khan, Andrew Lonie, Richard Sinnott and Stian Soiland-Reyes
 +
|-
 +
| A-137
 +
| Workflow-ready bioinformatics packages for Debian-based distributions and this Linux distribution's infrastructure for low-friction reproducible research ([https://f1000research.com/posters/6-1190 poster])
 +
| Steffen Moeller
 +
|-
 +
| A-138
 +
| Forever in BlueGenes: a next-generation genomic data interface powered by InterMine ([https://f1000research.com/posters/6-1289 poster])
 +
| Yo Yehudi, Daniela Butano, Matthew Chadwick, Justin Clark-Casey, Sergio Contrino, Josh Heimbach, Rachel Lyne, Julie Sullivan and Gos Micklem
 +
|-
 +
| A-139
 +
| GRADitude: A computational tool for the analysis of Grad-seq data
 +
| Silvia Di Giorgio and Konrad Förstner Dr.
 +
|-
 +
| A-140
 +
| Enabling the optimization of open-source biological computational tools with scripting languages
 +
| Stefan Popa and Radu Dobrescu
 +
|-
 +
| A-141
 +
| Protein Inpainter: a Message-Passing-based Predictor using Spark GraphX
 +
| Rabie Saidi, Hanna Papkova, Tunca Dogan and Maria Martin
 +
|-
 +
| A-142
 +
| Reproducible and user-controlled software management in HPC with GNU Guix
 +
| Ricardo Wurmus and Altuna Akalin
 +
|-
 +
| A-143
 +
| An ensemble approach for gene set testing analysis with reporting capabilities ([https://f1000research.com/posters/6-1310 poster])
 +
| Monther Alhamdoosh, Milica Ng and Matthew Ritchie
 +
|-
 +
| A-144
 +
| RADAR-CNS - Research Infrastructure for processing wearable data to improve health
 +
| Julia Kurps, Maxim Moinat, Joris Borgdorff, Fanscesco Nobilia, Maximilian Kerz, Nivethika Mahasivam, Irina Pulyakhina, Matthias Dümpelmann, Herculano Campos, Mark Begale, Richard Dobson and Amos Folarin
 +
|-
 +
| A-145
 +
| Workflows interoperability with Nextflow and Common WL
 +
| Kevin Sayers, Paolo Di Tommaso, Maria Chatzou, Evan Floden and Cedric Notredame
 +
|-
 +
| A-146
 +
| Bioschemas for life science data ([https://f1000research.com/posters/6-1226 poster])
 +
| Carole Goble, Rafael Jimenez, Alasdair Gray, Niall Beard, Giuseppe Profiti and Norman Morrison
 +
|-
 +
| A-147
 +
| The GA4GH Tool Registry Service (TRS) and Dockstore - Year One
 +
| Denis Yuen, Brian O'Connor, Andrew Duncan, Solomon Shorser, Vincent Chung, Xiang Kun Liu, Janice Patricia, Han Yuan Cao, Gary Luu, Vincent Ferretti and Lincoln Stein
 +
|-
 +
| A-148
 +
| Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data
 +
| Annemarie H. Eckes, Tomasz Guba_a, Piotr Nowakowski, Tomasz Szymczyszyn, Rachel Wells, Judith A. Irwin, Carlos Horro, John M. Hancock, Graham King, Sarah C. Dyer and Wiktor Jurkowski
 +
|-
 +
| A-149
 +
| Discovery and visualisation of homologous genes and gene families using Galaxy
 +
| Anil S. Thanki, Nicola Soranzo, Wilfried Haerty and Robert P. Davey
 +
|-
 +
| A-150
 +
| The SPOT ontology toolkit : semantics as a service
 +
| Olga Vrousgou, Simon Jupp, Thomas Liener, Tony Burdett and Helen Parkinson
 +
|-
 +
| A-151
 +
| GRAPHSPACE: Stimulating interdisciplinary collaborations in network biology ([https://f1000research.com/posters/6-1390 poster])
 +
| Aditya Bharadwaj, Divit P. Singh, Anna Ritz, Allison N. Tegge, Christopher L. Poirel, Pavel Kraikivski, Neil Adames, Kurt Luther, Shiv D. Kale, Jean Peccoud, John J. Tyson and T. M. Murali
 +
|-
 +
| A-152
 +
| Revitalizing a classic bioinformatics tool using modern technologies: the case of the Cytoscape Project ([https://f1000research.com/posters/6-1171 poster])
 +
| Keiichiro Ono, Eric Sage and Barry Demchak
 +
|-
 +
| A-153
 +
| Screw: tools for building reproducible single-cell epigenomics workflows ([https://f1000research.com/posters/6-1411 poster])
 +
| Kieran O'Neill, Benjamin Decato, Alexander Goncearenco, Azhar Khandekar, Benjamin Busby and Aly Karsan
 +
|-
 +
| A-154
 +
| Emerging public databases of clinical genetic test results: Implications for large scale deployment of precision medicine
 +
| Stephen Lincoln, Shan Yang, Benedict Paten, Melissa Cline, Yuya Kobayashi, Scott Topper, Can Zhang, David Haussler and Robert Nussbaum
 +
|-
 +
| A-155
 +
| NGL - a molecular graphics library for the web ([https://f1000research.com/posters/6-1409 poster])
 +
| Alexander S. Rose and Stephen K. Burley
 +
|-
 +
| A-156
 +
| ToolDog - generating tool descriptors from the ELIXIR tool registry ([https://f1000research.com/posters/6-1193 poster])
 +
| Kenzo-Hugo Hillion, Ivan Kuzmin, Hedi Peterson, Jon Ison and Hervé Ménager
 +
|-
 +
| A-157
 +
| Integrating cloud storage providers for genomic analyses
 +
| Ted Liefeld, Marco Ocana, Michael Reich, Helga Thorvaldsdottir and Jill P Mesirov
 +
|-
 +
| A-159
 +
| Full-stack genomics pipelining with GATK4 + WDL + Cromwell
 +
| Kate Voss, Jeff Gentry and Geraldine Van der Auwera
 +
|-
 +
| A-160
 +
| BioXSD | BioJSON | BioYAML - Towards unified formats for sequences, alignments, features, and annotations ([https://f1000research.com/posters/6-1179 poster])
 +
| Matúš Kalaš, Sveinung Gundersen, László Kaján, Hervé Ménager, Jon Ison, Steve Pettifer, Christophe Blanchet, Rodrigo Lopez, Kristoffer Rapacki and Inge Jonassen
 +
|-
 +
| A-161
 +
| EDAM - The ontology of bioinformatics operations, types of data, topics, and data formats (2017 lightning update) ([https://f1000research.com/posters/6-1181 poster])
 +
| Matúš Kalaš, Hervé Ménager, Veit Schwämmle, Jon Ison and Edam Contributors
 +
|-
 +
|}
  
 
== Sponsors ==
 
== Sponsors ==
−
We are grateful to and welcome [http://thehyve.nl/ The Hyve] (open source solutions for bioinformatics), [https://science.mozilla.org/ Mozilla Science Lab] (a community of researchers, developers, and librarians making research open and accessible), [https://repositive.io/ Repositive Limited] (connecting the genomics community with the data they need), [https://www.sevenbridges.com/ Seven Bridges] (the Biomedical Data Analysis Platform) and [https://elifesciences.org/ eLife Sciences Publications] as new sponsors for BOSC 2017, and [http://gigasciencejournal.com GigaScience] (an open access, open data, open peer-review journal) as a returning sponsor.
+
We are grateful to and welcome [http://thehyve.nl/ The Hyve] (open source solutions for bioinformatics), [https://science.mozilla.org/ Mozilla Science Lab] (a community of researchers, developers, and librarians making research open and accessible), [https://repositive.io/ Repositive Limited] (connecting the genomics community with the data they need), [https://www.sevenbridges.com/ Seven Bridges] (the Biomedical Data Analysis Platform) and [https://elifesciences.org/labs eLife] (cutting-edge technology for cutting-edge research) as new sponsors for BOSC 2017, and [http://gigasciencejournal.com GigaScience] (an open access, open data, open peer-review journal) as a returning sponsor.
  
 
If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.org.
 
If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.org.
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Latest revision as of 12:28, 22 August 2017

BOSC logo

Complete Program

This page has links to all the publicly available talk slides, videos and posters. Most of the slides and posters are on our BOSC F1000 Research Collection (others are on SlideShare and FigShare), while the videos are on the BOSC 2017 YouTube playlist.

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

Day 1 (Saturday, July 22)
Time Session
8:30-9:30 (ISMB announcements & ISMB keynote)
10:00-10:10 BOSC announcements
10:10-10:45 Introduction to the Open Bioinformatics Foundation; OBF in the Google Summer of Code; Codefest 2017 Report
10:45-12:20 Session: Workflows
12:30-14:00 Lunch, Posters, Birds of a Feather discussions (BoFs)
14:00-15:00 Session: Developer tools and libraries for open science and reproducibility
15:00-16:00 Session: Data Science & Visualization
16:30-17:30 Keynote: Madeleine Ball
17:30-18:30 Birds of a Feather discussions (BoFs)
18:00-19:00 Posters
Day 2 (Sunday, July 23)
Time Session
8:30-9:30 (ISMB announcements & ISMB keynote)
10:00-10:05 BOSC announcements
10:05-11:30 Session: Community Building and Citizen Science
11:30-12:20 Late-Breaking Lightning Talks
12:30-14:00 Lunch, Posters, Birds of a Feather discussions (BoFs)
14:00-15:00 Session: Open Data
15:00-16:00 Panel: Open Data--Standards, Opportunities and Challenges
16:30-17:30 Keynote (Nick Loman) and closing remarks
17:30-18:30 Birds of a Feather discussions (BoFs)
18:00-19:00 Posters

Complete schedule of talks

Day 1 (Saturday, July 22, 2017)

Session Title Speaker (or Session Chair) Start Time End Time
BOSC opening Introduction and welcome (video) Nomi Harris (Chair, BOSC 2017) 10:00 10:10
BOSC opening The Open Bioinformatics Foundation (video) Hilmar Lapp 10:10 10:20
BOSC opening OBF in the Google Summer of Code. Wrapping up 2016 and presenting the 2017 projects (slides, video) Kai Blin 10:20 10:30
BOSC opening Codefest 2017 summary (slides, video) 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 (video) Janko Simonovic 10:45 10:56
Workflows Rabix Composer: an open-source integrated development environment for the Common Workflow Language (video) Ivan Batic 10:56 11:05
Workflows CWL-svg: an open-source workflow visualization library for the Common Workflow Language (video with next talk) Maja Nedeljkovic 11:05 11:07
Workflows CWL-ts: an open-source TypeScript library for building developer tools for the Common Workflow Language (video with previous talk) 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 (video) Denis Yuen 11:15 11:22
Workflows The GA4GH Task Execution System (TES) and Funnel Server (video) Brian O'Connor 11:22 11:28
Workflows The GA4GH Workflow Execution Schema (WES) (video) Peter Amstutz 11:28 11:34
Workflows The GA4GH/DREAM Infrastructure Challenges (video) 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 (video) Kevin Sayers 11:45 11:50
Workflows CWL Viewer: The Common Workflow Language Viewer (slides, slides.com, poster, video) Stian Soiland-Reyes 11:50 11:55
Workflows Screw: tools for building reproducible single-cell epigenomics workflows (video) 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, video) Jiwen Xin 12:03 12:08
Workflows Discovery and visualisation of homologous genes and gene families using Galaxy (slides, videos) Anil S. Thanki 12:08 12:13
Workflows YAMP : Yet Another Metagenomic Pipeline (slides, video) 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, video) Phil Ewels 14:00 14:18
Developer tools / reproducibility NGL – a molecular graphics library for the web (video) Alexander S Rose 14:18 14:23
Developer tools / reproducibility GRAPHSPACE: Stimulating interdisciplinary collaborations in network biology (video) Aditya Bharadwaj 14:23 14:28
Developer tools / reproducibility Efficient detection of well-hopping duplicate reads on Illumina patterned flowcells (video) 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 (slides, video) 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, video) Brad Chapman 14:46 14:51
Developer tools / reproducibility Gene Set Variation Analysis in cBioPortal (video) 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, video) 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 (video) Ricardo Wurmus 15:23 15:28
Data Science & Visualization A Ubiquitous Approach to Reproducible Bioinformatics across Computational Platforms (slides, video) 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, video) Keiichiro Ono 15:36 15:41
Data Science & Visualization The SPOT ontology toolkit : semantics as a service (video) Olga Vrousgou 15:41 15:46
Data Science & Visualization Biopython Project Update 2017 (slides, video) Christian Brueffer 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, video, transcript) 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

Day 2 (Sunday, July 23, 2017)

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, video) Jonathan Sobel 10:05 10:23
Community Building and Citizen Science Supporting curation communities & collecting technical dividends (slides, video) Monica Munoz-Torres 10:23 10:41
Community Building and Citizen Science Journal of Open Source Software (JOSS) (slides, video) Pjotr Prins 10:41 10:59
Community Building and Citizen Science Building an open, collaborative, online infrastructure for bioinformatics training (slides, video, poster) Bérénice Batut 10:59 11:17
Community Building and Citizen Science Software and social strategies for community sourced biological networks and ontologies (video) Dexter Pratt 11:17 11:22
Community Building and Citizen Science Distance-based, online bioinformatics training in Africa: the H3ABioNet experience (video) 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, video) Martin Cech 11:30 11:35
LBLTs Reproducibility of computational workflows is automated using continuous analysis (video) Brett Beaulieu-Jones 11:35 11:40
LBLTs Full-stack genomics pipelining with GATK4 + WDL + Cromwell (slides, video) Kate Voss 11:40 11:45
LBLTs ToolDog - generating tool descriptors from the ELIXIR tool registry (slides, video, poster, video) Kenzo-Hugo Hillion 11:45 11:50
LBLTs BioThings SDK: a toolkit for building high-performance data APIs in biology (video) 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 (video) Ted Liefeld 12:00 12:05
LBLTs Fighting Superbugs with Open Source Software (slides, video) 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 (video) Nivethika Mahasivam 14:00 14:18
Open Data Using Wikidata as an open, community-maintained database of biomedical knowledge (slides, video) 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, video) Stephen Lincoln 14:36 14:41
Open Data Discovering datasets with DATS in DataMed (video) Philippe Rocca-Serra 14:41 14:46
Open Data Bioschemas for life science data (slides, poster, video) Carole Goble 14:46 14:51
Open Data Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data (video) 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 (slides, video) 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

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

Complete Program

Posters

Poster Title Authors
A-107 GeoDiver: Differential Gene Expression Analysis & Gene-Set Analysis for GEO Datasets Ismail Moghul, Suresh Hewapathirana, Nazrath Nawaz, Anisatu Rashid, Marian Priebe, Bruno Vieira, Fabrizio Smeraldi and Conrad Bessant
A-108 DAMON, an open source framework for reliable and reproducible analysis pipelines (poster) Alberto Riva, Richard L Bennett and Jonathan D Licht
A-109 Workflow for processing standard bioinformatics formats with SciClone to infer tumor heterogeneity Uros Sipetic
A-110 Microsatellite instability profiling of TCGA colorectal adenocarcinomas using a Common Workflow Language pipeline Nikola Tesic and Marko Kalinic
A-111 GeneValidator: identify problems with protein-coding gene predictions Monica-Andreea Dr_gan, Ismail Moghul, Anurag Priyam, Claudio Bustos and Yannick Wurm
A-112 Somatic Variant Calling Benchmarking Sanja Mijalkovic, Milan Domazet
A-114 Aztec: Automated Biomedical Tool Index with Improved Information Retrieval System (poster) Wei Wang, Yichao Zhou, Patrick Tan, Vincent Kyi, Xinxin Huang, Chelsea Ju, Justin Wood and Peipei Ping
A-115 Building a local bioinformatics community: challenges and efforts Malvika Sharan, Toby Hodges, Julia Ritzerfeld and Georg Zeller
A-116 CHARME - harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research (poster) Aleksandra Gruca
A-117 High Content Screening data storage and analysis platform - An open source solution Vincenzo Belcastro, Stephane Cano, Diego Marescotti, Carine Poussin, Ignacio Gonzales-Suarez, Florian Martin, Filipe Bonjour, Nikolai Ivanov, Julia Hoeng
A-118 Expression Atlas: exploring gene expression results across species under different biological conditions Laura Huerta, Elisabet Barrera, Wojciech Bazant, Nuno A. Fonseca, Anja Fullgrabe, Maria Keays, Suhaib Mohammed, Alfonso Munoz-Pomer Fuentes, Amy Tang, Irene Papatheodorou, Robert Petryszak, Ugis Sarkans and Alvis Brazma
A-119 Microservices in data, code, and project management. Jorge Miguel Martins Boucas
A-120 Gene Set Variation Analysis in cBioPortal Pieter Lukasse, Fedde Schaeffer, Oleguer Plantalech Casals, Sander Tan and Sjoerd van Hagen
A-121 Databases to support reanalysis of public high-throughput DNA sequencing data (poster) Tazro Ohta
A-122 BioThings SDK: a toolkit for building high-performance data APIs in biology (poster) Chunlei Wu, Cyrus Afrasiabi, Sebastien Lelong, Jiwen Xin, Ginger Tsueng and Andrew I. Su
A-123 Reproducing computational experiments in situ as an interactive figure in a journal article Evanthia Kaimaklioti, Robert P Davey and Ian Mulvany
A-124 CWL Viewer: The Common Workflow Language Viewer (poster) Mark Robinson, Stian Soiland-Reyes, Michael Crusoe and Carole Goble
A-125 Sequanix: a standalone application to expose Snakemake pipelines to end-users (poster) Thomas Cokelaer, Dimitri Desvillechabrol, Rachel Legendre and Mélissa Cardon
A-126 NGI-RNAseq - a best practice analysis pipeline in Nextflow Rickard Hammarén, Philip Ewels and Max Käller
A-127 PhyloProfile: an interactive and dynamic visualization tool for multi-layered phylogenetic profiles Ngoc-Vinh Tran, Bastian Greshake and Ingo Ebersberger
A-128 CueSea: quality control tool for Illumina genotyping microarray data, with correction on intensity, clusterization and biological specificity. Nikita Moshkov, Daria Iakovishina and Dimitri Nikogosov
A-129 Bio::DB::HTS - accessing HTSlib from Perl Rishi Nag
A-130 NGLESS: Perfectly understandable and reproducible metagenomics pipelines using a domain-specific language Luis Pedro Coelho, Paulo Monteiro, Renato Alves, A.T. Freitas and Peer Bork
A-131 CGP as a Service (CGPaaS) - From data submission to results using your web-browser Keiran Raine, Adam Butler, Peter Clapham, Jon Teague, Peter Campbell
A-132 Large-scale genotypic and phenotypic data support for Tripal: Chado optimization by utilizing modern PostgreSQL functionality Lacey-Anne Sanderson, Reynold Tan, Carolyn Caron, Kirstin Bett
A-133 GenePattern Notebooks: An integrative analytical environment for genomics research (poster) Michael Reich, Thorin Tabor, Helga Thorvaldsdóttir, Barbara Hill, Ted Liefeld, Jill Mesirov, Pablo Tamayo
A-134 BioContainers for supercomputers: 2,000+ accessible, discoverable Singularity apps John Fonner, Rion Dooley, Jacquelyn Turcinovic and Matthew Vaughn
A-135 Collaborative Open Plant Omics: A platform for "FAIR" data for plant science Felix Shaw, Anthony Etuk, Rob Davey, Alejandra Gonzalez-Beltran, David Johnson, Phillipe Rocca-Serra and Susanna Sansone
A-136 CWL+Research Object == Complete Provenance Farah Khan, Andrew Lonie, Richard Sinnott and Stian Soiland-Reyes
A-137 Workflow-ready bioinformatics packages for Debian-based distributions and this Linux distribution's infrastructure for low-friction reproducible research (poster) Steffen Moeller
A-138 Forever in BlueGenes: a next-generation genomic data interface powered by InterMine (poster) Yo Yehudi, Daniela Butano, Matthew Chadwick, Justin Clark-Casey, Sergio Contrino, Josh Heimbach, Rachel Lyne, Julie Sullivan and Gos Micklem
A-139 GRADitude: A computational tool for the analysis of Grad-seq data Silvia Di Giorgio and Konrad Förstner Dr.
A-140 Enabling the optimization of open-source biological computational tools with scripting languages Stefan Popa and Radu Dobrescu
A-141 Protein Inpainter: a Message-Passing-based Predictor using Spark GraphX Rabie Saidi, Hanna Papkova, Tunca Dogan and Maria Martin
A-142 Reproducible and user-controlled software management in HPC with GNU Guix Ricardo Wurmus and Altuna Akalin
A-143 An ensemble approach for gene set testing analysis with reporting capabilities (poster) Monther Alhamdoosh, Milica Ng and Matthew Ritchie
A-144 RADAR-CNS - Research Infrastructure for processing wearable data to improve health Julia Kurps, Maxim Moinat, Joris Borgdorff, Fanscesco Nobilia, Maximilian Kerz, Nivethika Mahasivam, Irina Pulyakhina, Matthias Dümpelmann, Herculano Campos, Mark Begale, Richard Dobson and Amos Folarin
A-145 Workflows interoperability with Nextflow and Common WL Kevin Sayers, Paolo Di Tommaso, Maria Chatzou, Evan Floden and Cedric Notredame
A-146 Bioschemas for life science data (poster) Carole Goble, Rafael Jimenez, Alasdair Gray, Niall Beard, Giuseppe Profiti and Norman Morrison
A-147 The GA4GH Tool Registry Service (TRS) and Dockstore - Year One Denis Yuen, Brian O'Connor, Andrew Duncan, Solomon Shorser, Vincent Chung, Xiang Kun Liu, Janice Patricia, Han Yuan Cao, Gary Luu, Vincent Ferretti and Lincoln Stein
A-148 Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data Annemarie H. Eckes, Tomasz Guba_a, Piotr Nowakowski, Tomasz Szymczyszyn, Rachel Wells, Judith A. Irwin, Carlos Horro, John M. Hancock, Graham King, Sarah C. Dyer and Wiktor Jurkowski
A-149 Discovery and visualisation of homologous genes and gene families using Galaxy Anil S. Thanki, Nicola Soranzo, Wilfried Haerty and Robert P. Davey
A-150 The SPOT ontology toolkit : semantics as a service Olga Vrousgou, Simon Jupp, Thomas Liener, Tony Burdett and Helen Parkinson
A-151 GRAPHSPACE: Stimulating interdisciplinary collaborations in network biology (poster) Aditya Bharadwaj, Divit P. Singh, Anna Ritz, Allison N. Tegge, Christopher L. Poirel, Pavel Kraikivski, Neil Adames, Kurt Luther, Shiv D. Kale, Jean Peccoud, John J. Tyson and T. M. Murali
A-152 Revitalizing a classic bioinformatics tool using modern technologies: the case of the Cytoscape Project (poster) Keiichiro Ono, Eric Sage and Barry Demchak
A-153 Screw: tools for building reproducible single-cell epigenomics workflows (poster) Kieran O'Neill, Benjamin Decato, Alexander Goncearenco, Azhar Khandekar, Benjamin Busby and Aly Karsan
A-154 Emerging public databases of clinical genetic test results: Implications for large scale deployment of precision medicine Stephen Lincoln, Shan Yang, Benedict Paten, Melissa Cline, Yuya Kobayashi, Scott Topper, Can Zhang, David Haussler and Robert Nussbaum
A-155 NGL - a molecular graphics library for the web (poster) Alexander S. Rose and Stephen K. Burley
A-156 ToolDog - generating tool descriptors from the ELIXIR tool registry (poster) Kenzo-Hugo Hillion, Ivan Kuzmin, Hedi Peterson, Jon Ison and Hervé Ménager
A-157 Integrating cloud storage providers for genomic analyses Ted Liefeld, Marco Ocana, Michael Reich, Helga Thorvaldsdottir and Jill P Mesirov
A-159 Full-stack genomics pipelining with GATK4 + WDL + Cromwell Kate Voss, Jeff Gentry and Geraldine Van der Auwera
A-160 BioJSON | BioYAML - Towards unified formats for sequences, alignments, features, and annotations (poster) Matúš Kalaš, Sveinung Gundersen, László Kaján, Hervé Ménager, Jon Ison, Steve Pettifer, Christophe Blanchet, Rodrigo Lopez, Kristoffer Rapacki and Inge Jonassen
A-161 EDAM - The ontology of bioinformatics operations, types of data, topics, and data formats (2017 lightning update) (poster) Matúš Kalaš, Hervé Ménager, Veit Schwämmle, Jon Ison and Edam Contributors

Sponsors

We are grateful to and welcome 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), Seven Bridges (the Biomedical Data Analysis Platform) and eLife (cutting-edge technology for cutting-edge research) as new sponsors for BOSC 2017, and GigaScience (an open access, open data, open peer-review journal) as a returning sponsor.

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
    
Seven Bridges
    
eLife

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