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Revision as of 00:25, 15 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
| Day 1 (Saturday, July 22) | Day 2 (Sunday, July 23) | |||
| Time | Session | Time | Session | |
| 8:30-9:30 | (ISMB announcements & ISMB keynote) | 8:30-9:30 | (ISMB announcements & ISMB keynote) | |
| 10:00-10:10 | BOSC announcements | 10:00-10:05 | BOSC announcements | |
| 10:10-10:35 | Introduction to the Open Bioinformatics Foundation; OBF in the Google Summer of Code; Codefest 2017 Report | 10:05-11:30 | Session: Community Building and Citizen Science | |
| 10:35-12:20 | Session: Workflows | 11:30-12:20 | Late-Breaking Lightning Talks | |
| 12:30-14:00 | Lunch, BoFs, Posters | 12:30-14:00 | Lunch, BoFs, Posters | |
| 14:00-15:00 | Session: Data Science & Visualization | 14:00-15:00 | Session: Open Data | |
| 15:00-16:00 | Keynote (Dawn Field) | 15:00-16:00 | Panel: Open Data--Standards, Opportunities and Challenges | |
| 16:30-17:30 | Session: Developer tools and libraries for open science and reproducibility | 16:30-17:30 | Keynote (Nick Loman) and closing remarks | |
| 17:30-18:30 | BoFs | 17:30-18:30 | BoFs | |
Complete schedule of talks (subject to change)
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 | 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 | BioThings Explorer: Utilizing JSON-LD for Linking Biological APIs to Facilitate Knowledge Discovery | Jiwen Xin | 12:00 | 12:05 |
| Workflows | Discovery and visualisation of homologous genes and gene families using Galaxy | Anil S. Thanki | 12:05 | 12:10 |
| Workflows | YAMP : Yet Another Metagenomic Pipeline | Alessia Visconti | 12:10 | 12:15 |
| Birds of a Feather (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 | 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 |
| Developer tools / reproducibility | An ensemble approach for gene set testing analysis with reporting capabilities | Monther Alhamdoosh | 14:33 | 14:38 |
| Developer tools / reproducibility | OpenMS 2.0: a flexible open-source software platform for mass spectrometry data analysis | Timo Sachsenberg | 14:38 | 14:43 |
| Developer tools / reproducibility | Interoperable, collaborative multi-platform variant calling with bcbio | Brad Chapman | 14:43 | 14:48 |
| Developer tools / reproducibility | Gene Set Variation Analysis in cBioPortal | Kees van Bochove | 14:48 | 14:53 |
| Session: Data Science & Visualization | 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 |
| Data Science & Visualization | Revitalizing a classic bioinformatics tool using modern technologies: the case of the Cytoscape Project | Keiichiro Ono | 15:33 | 15:38 |
| Data Science & Visualization | The SPOT ontology toolkit : semantics as a service | Olga Vrousgou | 15:38 | 15:43 |
| Data Science & Visualization | Biopython Project Update 2017 | Sourav Singh | 15:43 | 15:48 |
| Coffee Break | 16:00 | 16:30 | ||
| Keynote | Understanding the Biocode: Global Sharing of Data | Dawn Field | 16:30 | 17:30 |
| Birds of a Feather (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 | 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 | Software and social strategies for community sourced biological networks and ontologies | Dexter Pratt | 10:59 | 11:04 |
| Community Building and Citizen Science | Building an open, collaborative, online infrastructure for bioinformatics training | Bérénice Batut | 11:04 | 11:22 |
| Community Building and Citizen Science | Distance-based, online bioinformatics training in Africa: the H3ABioNet experience | Kim Gurwitz | 11:22 | 11:27 |
| Session: Late-Breaking Lightning Talks | 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 | 12:00 |
| LBLTs | (Q&A for first 5 LBLTs) | 12:00 | 12:05 | |
| LBLTs | Integrating cloud storage providers for genomic analyses | Ted Liefeld | 12:05 | 12:10 |
| LBLTs | Open Humans: Opening human health data | Madeleine Ball | 12:10 | 12:15 |
| LBLTs | Fighting Superbugs with Open Source Software | Kai Blin | 12:15 | 12:20 |
| LBLTs | Users, Communication, and a Light Application-Level API: A Request for Comments | Seth Carbon | 12:20 | 12:25 |
| LBLTs | (Q&A for last 4 LBLTs) | 12:25 | 12:30 | |
| Birds of a Feather (BoFs) | Feel free to organize one! | 12:30 | 13:40 | |
| Lunch | 12:30 | 14:00 | ||
| Session: Open Data | ||||
| 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 |
| Panel | Panel: Open Data--Standards, Opportunities and Challenges | Moderator: Mónica Muñoz-Torres
Panelists: |
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 (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/)
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) 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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