BOSC 2017 Schedule

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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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