| Please visit our ***NEW*** OBF/BOSC website: https://www.open-bio.org/ |
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Difference between revisions of "BOSC 2017 Schedule"
From Open Bioinformatics Foundation
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|11:55 | |11:55 | ||
|12:00 | |12:00 | ||
| + | |- | ||
| + | |Workflows | ||
| + | | (Q&A for first 3 lightning talks) | ||
| + | | | ||
| + | |12:00 | ||
| + | |12:03 | ||
|- | |- | ||
|Workflows | |Workflows | ||
|BioThings Explorer: Utilizing JSON-LD for Linking Biological APIs to Facilitate Knowledge Discovery | |BioThings Explorer: Utilizing JSON-LD for Linking Biological APIs to Facilitate Knowledge Discovery | ||
|Jiwen Xin | |Jiwen Xin | ||
| − | |12: | + | |12:03 |
| − | |12: | + | |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 | ||
|Anil S. Thanki | |Anil S. Thanki | ||
| − | |12: | + | |12:08 |
| − | |12: | + | |12:13 |
|- | |- | ||
|Workflows | |Workflows | ||
|YAMP : Yet Another Metagenomic Pipeline | |YAMP : Yet Another Metagenomic Pipeline | ||
|Alessia Visconti | |Alessia Visconti | ||
| − | |12: | + | |12:13 |
| − | |12: | + | |12:18 |
|- | |- | ||
|Workflows | |Workflows | ||
| − | | (Q&A for | + | | (Q&A for last 3 lightning talks) |
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| − | |12: | + | |12:18 |
|12:20 | |12:20 | ||
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|14:28 | |14:28 | ||
|14:33 | |14:33 | ||
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| + | |Workflows | ||
| + | | (Q&A for first 3 lightning talks) | ||
| + | | | ||
| + | |14:33 | ||
| + | |14:36 | ||
|- | |- | ||
|Developer tools / reproducibility | |Developer tools / reproducibility | ||
|An ensemble approach for gene set testing analysis with reporting capabilities | |An ensemble approach for gene set testing analysis with reporting capabilities | ||
|Monther Alhamdoosh | |Monther Alhamdoosh | ||
| − | |14: | + | |14:36 |
| − | |14: | + | |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: | + | |14:41 |
| − | |14: | + | |14:46 |
|- | |- | ||
|Developer tools / reproducibility | |Developer tools / reproducibility | ||
|Interoperable, collaborative multi-platform variant calling with bcbio | |Interoperable, collaborative multi-platform variant calling with bcbio | ||
|Brad Chapman | |Brad Chapman | ||
| − | |14: | + | |14:46 |
| − | |14: | + | |14:51 |
|- | |- | ||
|Developer tools / reproducibility | |Developer tools / reproducibility | ||
|Gene Set Variation Analysis in cBioPortal | |Gene Set Variation Analysis in cBioPortal | ||
|Kees van Bochove | |Kees van Bochove | ||
| − | |14: | + | |14:51 |
| − | |14: | + | |14:56 |
|- | |- | ||
|Developer tools / reproducibility | |Developer tools / reproducibility | ||
| − | | (Q&A for | + | | (Q&A for last 4 lightning talks) |
| | | | ||
| − | |14: | + | |14:56 |
|15:00 | |15:00 | ||
|- style="background:#E6E6E6" | |- style="background:#E6E6E6" | ||
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|15:28 | |15:28 | ||
|15:33 | |15:33 | ||
| + | |- | ||
| + | |Workflows | ||
| + | | (Q&A for first 3 lightning talks) | ||
| + | | | ||
| + | |15:33 | ||
| + | |15:36 | ||
|- | |- | ||
|Data Science & Visualization | |Data Science & Visualization | ||
|Revitalizing a classic bioinformatics tool using modern technologies: the case of the Cytoscape Project | |Revitalizing a classic bioinformatics tool using modern technologies: the case of the Cytoscape Project | ||
|Keiichiro Ono | |Keiichiro Ono | ||
| − | |15: | + | |15:36 |
| − | |15: | + | |15:41 |
|- | |- | ||
|Data Science & Visualization | |Data Science & Visualization | ||
|The SPOT ontology toolkit : semantics as a service | |The SPOT ontology toolkit : semantics as a service | ||
|Olga Vrousgou | |Olga Vrousgou | ||
| − | |15: | + | |15:41 |
| − | |15: | + | |15:46 |
|- | |- | ||
|Data Science & Visualization | |Data Science & Visualization | ||
|Biopython Project Update 2017 | |Biopython Project Update 2017 | ||
|Sourav Singh | |Sourav Singh | ||
| − | |15: | + | |15:46 |
| − | |15: | + | |15:51 |
|- | |- | ||
|Data Science & Visualization | |Data Science & Visualization | ||
| − | | (Q&A for | + | | (Q&A for last 3 lightning talks) |
| | | | ||
| − | |15: | + | |15:51 |
|15:54 | |15:54 | ||
|- style="background:#FAF4EE" | |- style="background:#FAF4EE" | ||
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|10:41 | |10:41 | ||
|10:59 | |10:59 | ||
| + | |- | ||
| + | |Community Building and Citizen Science | ||
| + | |Building an open, collaborative, online infrastructure for bioinformatics training | ||
| + | |Bérénice Batut | ||
| + | |11:59 | ||
| + | |11:17 | ||
|- | |- | ||
|Community Building and Citizen Science | |Community Building and Citizen Science | ||
|Software and social strategies for community sourced biological networks and ontologies | |Software and social strategies for community sourced biological networks and ontologies | ||
|Dexter Pratt | |Dexter Pratt | ||
| − | + | |11:17 | |
| − | |||
| − | |||
| − | |||
| − | |||
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| − | |11: | ||
|11:22 | |11:22 | ||
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|Community Building and Citizen Science | |Community Building and Citizen Science | ||
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|Community Building and Citizen Science | |Community Building and Citizen Science | ||
| − | | (Q&A for previous | + | | (Q&A for previous 2 lightning talks) |
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|11:27 | |11:27 | ||
| Line 440: | Line 459: | ||
|Chunlei Wu | |Chunlei Wu | ||
|11:50 | |11:50 | ||
| − | | | + | |11:55 |
|- | |- | ||
|LBLTs | |LBLTs | ||
| (Q&A for first 5 LBLTs) | | (Q&A for first 5 LBLTs) | ||
| | | | ||
| + | |11:55 | ||
|12:00 | |12:00 | ||
| − | |||
|- | |- | ||
|LBLTs | |LBLTs | ||
|Integrating cloud storage providers for genomic analyses | |Integrating cloud storage providers for genomic analyses | ||
|Ted Liefeld | |Ted Liefeld | ||
| + | |12:00 | ||
|12:05 | |12:05 | ||
| − | |||
|- | |- | ||
|LBLTs | |LBLTs | ||
|Open Humans: Opening human health data | |Open Humans: Opening human health data | ||
|Madeleine Ball | |Madeleine Ball | ||
| + | |12:05 | ||
|12:10 | |12:10 | ||
| − | |||
|- | |- | ||
|LBLTs | |LBLTs | ||
|Fighting Superbugs with Open Source Software | |Fighting Superbugs with Open Source Software | ||
|Kai Blin | |Kai Blin | ||
| + | |12:10 | ||
|12:15 | |12:15 | ||
| − | |||
|- | |- | ||
|LBLTs | |LBLTs | ||
|Users, Communication, and a Light Application-Level API: A Request for Comments | |Users, Communication, and a Light Application-Level API: A Request for Comments | ||
|Seth Carbon | |Seth Carbon | ||
| + | |12:15 | ||
|12:20 | |12:20 | ||
| − | |||
|- | |- | ||
|LBLTs | |LBLTs | ||
| (Q&A for last 4 LBLTs) | | (Q&A for last 4 LBLTs) | ||
| | | | ||
| + | |12:20 | ||
|12:25 | |12:25 | ||
| − | |||
|- 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)] | ||
Revision as of 13:46, 21 June 2017
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
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Complete schedule of talks (subject to change)
Day 1 (Saturday, July 22, 2017)
| 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 | Kai Blin | 10:20 | 10:30 |
| BOSC opening | Codefest 2017 summary | 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 | 10:57 |
| Workflows | Rabix Composer: an open-source integrated development environment for the Common Workflow Language | Ivan Batic | 10:57 | 11:07 |
| Workflows | CWL-svg: an open-source workflow visualization library for the Common Workflow Language | Maja Nedeljkovic | 11:07 | 11:10 |
| Workflows | CWL-ts: an open-source TypeScript library for building developer tools for the Common Workflow Language | Maja Nedeljkovic | 11:10 | 11:15 |
| Workflows | The GA4GH Tool Registry Service (TRS) and Dockstore - Year One | Denis Yuen | 11:15 | 11:23 |
| Workflows | The GA4GH Task Execution System (TES) and Funnel Server | Brian O'Connor | 11:23 | 11:30 |
| Workflows | The GA4GH Workflow Execution Schema (WES) | Peter Amstutz | 11:30 | 11:37 |
| Workflows | The GA4GH/DREAM Infrastructure Challenges | Brian D. O'Connor | 11:37 | 11:45 |
| Workflows | Workflows interoperability with Nextflow and Common WL | Kevin Sayers | 11:45 | 11:50 |
| Workflows | CWL Viewer: The Common Workflow Language Viewer | 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 first 3 lightning talks) | 12:00 | 12:03 | |
| Workflows | BioThings Explorer: Utilizing JSON-LD for Linking Biological APIs to Facilitate Knowledge Discovery | Jiwen Xin | 12:03 | 12:08 |
| Workflows | Discovery and visualisation of homologous genes and gene families using Galaxy | Anil S. Thanki | 12:08 | 12:13 |
| Workflows | YAMP : Yet Another Metagenomic Pipeline | Alessia Visconti | 12:13 | 12:18 |
| Workflows | (Q&A for last 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 | 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 |
| Workflows | (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 | 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 | 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 |
| Workflows | (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 | 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 | 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 | Understanding the Biocode: Global Sharing of Data | Dawn Field | 16:30 | 17:30 |
| Birds of a Feather discussions (BoFs) | Feel free to organize one! | 17:30 | 18:30 | |
| 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 | 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 | Building an open, collaborative, online infrastructure for bioinformatics training | Bérénice Batut | 11:59 | 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 | 1 |
| 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 | 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 | 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 | Open Humans: Opening human health data | Madeleine Ball | 12:05 | 12:10 | |
| LBLTs | Fighting Superbugs with Open Source Software | Kai Blin | 12:10 | 12:15 | |
| LBLTs | Users, Communication, and a Light Application-Level API: A Request for Comments | Seth Carbon | 12:15 | 12:20 | |
| LBLTs | (Q&A for last 4 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 | 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 | Philippe Rocca-Serra | 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 | |
| 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 | Why I Love Open Data | Nick Loman | 16:30 | 17:30 | |
| Birds of a Feather discussions (BoFs) | Feel free to organize one! | 17:30 | 18:30 | ||
| 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/)
Posters
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.
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