Please visit our ***NEW*** OBF/BOSC website: https://www.open-bio.org/ |
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Difference between revisions of "BOSC 2017 Schedule"
(Galaxy video links) |
(added video links) |
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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 | ||
Line 122: | Line 122: | ||
|- | |- | ||
|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 | ||
|10:56 | |10:56 | ||
Line 128: | Line 128: | ||
|- | |- | ||
|Workflows | |Workflows | ||
− | |CWL-svg: an open-source workflow visualization library for the Common Workflow Language | + | |CWL-svg: an open-source workflow visualization library for the Common Workflow Language ([https://youtu.be/wAkagL8PWc0 video]) |
|Maja Nedeljkovic | |Maja Nedeljkovic | ||
|11:05 | |11:05 | ||
Line 146: | Line 146: | ||
|- | |- | ||
|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 | ||
Line 152: | Line 152: | ||
|- | |- | ||
|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 | ||
|11:22 | |11:22 | ||
Line 158: | Line 158: | ||
|- | |- | ||
|Workflows | |Workflows | ||
− | |The GA4GH Workflow Execution Schema (WES) | + | |The GA4GH Workflow Execution Schema (WES) ([https://youtu.be/VFpNBcA_y5g video]) |
|Peter Amstutz | |Peter Amstutz | ||
|11:28 | |11:28 | ||
Line 164: | Line 164: | ||
|- | |- | ||
|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 | ||
|11:34 | |11:34 | ||
Line 176: | Line 176: | ||
|- | |- | ||
|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 | ||
Line 182: | Line 182: | ||
|- | |- | ||
|Workflows | |Workflows | ||
− | |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]) | + | |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 | ||
Line 188: | Line 188: | ||
|- | |- | ||
|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 | ||
Line 200: | Line 200: | ||
|- | |- | ||
|Workflows | |Workflows | ||
− | |BioThings Explorer: Utilizing JSON-LD for Linking Biological APIs to Facilitate Knowledge Discovery ([https://f1000research.com/slides/6-1176 slides]) | + | |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 | ||
|12:03 | |12:03 | ||
Line 212: | Line 212: | ||
|- | |- | ||
|Workflows | |Workflows | ||
− | |YAMP : Yet Another Metagenomic Pipeline ([https://f1000research.com/slides/6-1185 slides]) | + | |YAMP : Yet Another Metagenomic Pipeline ([https://f1000research.com/slides/6-1185 slides], [https://youtu.be/boQA4RrHeUk video]) |
|Alessia Visconti | |Alessia Visconti | ||
|12:13 | |12:13 | ||
Line 240: | Line 240: | ||
|- | |- | ||
|Developer tools / reproducibility | |Developer tools / reproducibility | ||
− | |MultiQC: Visualising results from common bioinformatics tools ([https://f1000research.com/slides/6-1177 slides]) | + | |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 | ||
Line 246: | Line 246: | ||
|- | |- | ||
|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 | ||
Line 252: | Line 252: | ||
|- | |- | ||
|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 | ||
Line 258: | Line 258: | ||
|- | |- | ||
|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 | ||
Line 270: | Line 270: | ||
|- | |- | ||
|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 ([https://youtu.be/tCwKSAlyY3k video]) |
|Monther Alhamdoosh | |Monther Alhamdoosh | ||
|14:36 | |14:36 | ||
Line 282: | Line 282: | ||
|- | |- | ||
|Developer tools / reproducibility | |Developer tools / reproducibility | ||
− | |Interoperable, collaborative multi-platform variant calling with bcbio [https://f1000research.com/slides/6-1188 slides] | + | |Interoperable, collaborative multi-platform variant calling with bcbio ([https://f1000research.com/slides/6-1188 slides], [https://youtu.be/S7bu17GQHqk video]) |
|Brad Chapman | |Brad Chapman | ||
|14:46 | |14:46 | ||
Line 288: | Line 288: | ||
|- | |- | ||
|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 | ||
|14:51 | |14:51 | ||
Line 312: | Line 312: | ||
|- | |- | ||
|Data Science & Visualization | |Data Science & Visualization | ||
− | |Reproducible bioinformatics software with GNU Guix | + | |Reproducible bioinformatics software with GNU Guix ([ video]) |
|Pjotr Prins | |Pjotr Prins | ||
|15:18 | |15:18 | ||
Line 318: | Line 318: | ||
|- | |- | ||
|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 | ||
Line 336: | Line 336: | ||
|- | |- | ||
|Data Science & Visualization | |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]) | + | |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 | ||
|15:36 | |15:36 | ||
Line 342: | Line 342: | ||
|- | |- | ||
|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 | ||
|15:41 | |15:41 | ||
Line 348: | Line 348: | ||
|- | |- | ||
|Data Science & Visualization | |Data Science & Visualization | ||
− | |Biopython Project Update 2017 ([https://github.com/cbrueffer/talks/blob/master/2017_BOSC/presentation/presentation.pdf slides]) | + | |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 | |15:46 | ||
|15:51 | |15:51 | ||
Line 410: | Line 410: | ||
|- | |- | ||
|Community Building and Citizen Science | |Community Building and Citizen Science | ||
− | |BeerDeCoded: exploring the beer metagenome ([https://www.slideshare.net/JonathanSobel/beer-decoded-boscpresentation slides]) | + | |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 | ||
Line 416: | Line 416: | ||
|- | |- | ||
|Community Building and Citizen Science | |Community Building and Citizen Science | ||
− | |Supporting curation communities & collecting technical dividends ([https://f1000research.com/slides/6-1240 slides]) | + | |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 | ||
Line 422: | Line 422: | ||
|- | |- | ||
|Community Building and Citizen Science | |Community Building and Citizen Science | ||
− | |Journal of Open Source Software (JOSS) ([https://f1000research.com/slides/6-1206 slides]) | + | |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 | ||
Line 434: | Line 434: | ||
|- | |- | ||
|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 ([https://youtu.be/Qsi09ZBIMwQ video]) |
|Dexter Pratt | |Dexter Pratt | ||
|11:17 | |11:17 | ||
Line 441: | Line 441: | ||
|- | |- | ||
|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 | ||
Line 465: | 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 471: | Line 471: | ||
|- | |- | ||
|LBLTs | |LBLTs | ||
− | |Full-stack genomics pipelining with GATK4 + WDL + Cromwell | + | |Full-stack genomics pipelining with GATK4 + WDL + Cromwell ([https://youtu.be/ng7LjJanVd8 video]) |
|Kate Voss | |Kate Voss | ||
|11:40 | |11:40 | ||
Line 477: | Line 477: | ||
|- | |- | ||
|LBLTs | |LBLTs | ||
− | |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]) | + | |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 483: | 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 | ||
Line 495: | Line 495: | ||
|- | |- | ||
|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 | |12:00 | ||
Line 501: | Line 501: | ||
|- | |- | ||
|LBLTs | |LBLTs | ||
− | |Fighting Superbugs with Open Source Software ([https://f1000research.com/slides/6-1233 slides]) | + | |Fighting Superbugs with Open Source Software ([https://f1000research.com/slides/6-1233 slides], [https://youtu.be/ZWUnCJ3Qlsc video]) |
|Kai Blin | |Kai Blin | ||
|12:10 | |12:10 | ||
Line 529: | 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 535: | Line 535: | ||
|- | |- | ||
|Open Data | |Open Data | ||
− | |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]) | + | |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 541: | Line 541: | ||
|- | |- | ||
|Open Data | |Open Data | ||
− | |Emerging public databases of clinical genetic test results: Implications for large scale deployment of precision medicine ([https://f1000research.com/slides/6-1192 slides]) | + | |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 547: | 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 553: | Line 553: | ||
|- | |- | ||
|Open Data | |Open Data | ||
− | |Bioschemas for life science data ([https://f1000research.com/slides/6-1227 slides], [https://f1000research.com/posters/6-1226 poster]) | + | |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 559: | 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 | ||
Line 583: | Line 583: | ||
|- style="background:#CCFFCC" | |- style="background:#CCFFCC" | ||
|Keynote | |Keynote | ||
− | | Open data meets ubiquitous sequencing: challenges and opportunities ([https://f1000research.com/slides/6-1266 slides]) | + | | 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 |
Revision as of 19:26, 3 August 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 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
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|
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) | Maja Nedeljkovic | 11:05 | 11:07 |
Workflows | CWL-ts: an open-source TypeScript library for building developer tools for the Common Workflow Language | Maja Nedeljkovic | 11:07 | 11:11 |
Workflows | (Q&A for previous 4 talks) | 11:11 | 11:15 | |
Workflows | The GA4GH Tool Registry Service (TRS) and Dockstore - Year One (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 (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 ([ video]) | 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) | 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 (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
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.