| Please visit our ***NEW*** OBF/BOSC website: https://www.open-bio.org/ |
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Difference between revisions of "BOSC 2016 Schedule"
From Open Bioinformatics Foundation
(→BOSC Day 2 (Saturday, July 9, 2016)) |
(→BOSC Day 1 (Friday, July 8, 2016)) |
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|Chair: TBA | |Chair: TBA | ||
|- | |- | ||
| − | |10:45-11: | + | |10:45-11:03 |
|GenomeSpace: Open source interoperability platform with crowd-sourced analysis recipes | |GenomeSpace: Open source interoperability platform with crowd-sourced analysis recipes | ||
|Ted Liefeld | |Ted Liefeld | ||
|- | |- | ||
| − | |11: | + | |11:03-11:21 |
|This is Why We Can Have Nice Things: Getting to 1.0 of the Common Workflow Language | |This is Why We Can Have Nice Things: Getting to 1.0 of the Common Workflow Language | ||
|Michael R. Crusoe | |Michael R. Crusoe | ||
|- | |- | ||
| − | |11: | + | |11:21-11:39 |
|CWL in Practice: Experiences, challenges, and results from adopting Common Workflow Language | |CWL in Practice: Experiences, challenges, and results from adopting Common Workflow Language | ||
|Dan Leehr | |Dan Leehr | ||
|- | |- | ||
| − | |11: | + | |11:39-11:57 |
|Using the Common Workflow Language (CWL) to run portable workflows with Arvados and Toil | |Using the Common Workflow Language (CWL) to run portable workflows with Arvados and Toil | ||
|Peter Amstutz | |Peter Amstutz | ||
|- | |- | ||
| − | | | + | |11:57-12:03 |
|Planemo – A Scientific Workflow SDK | |Planemo – A Scientific Workflow SDK | ||
|John Chilton | |John Chilton | ||
|- | |- | ||
| − | |12: | + | |12:04-12:09 |
|Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics | |Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics | ||
|Daniel Blankenberg | |Daniel Blankenberg | ||
|- | |- | ||
| − | |12: | + | |12:10-12:15 |
|NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts | |NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts | ||
|Fabien Campagne | |Fabien Campagne | ||
|- | |- | ||
| − | |12: | + | |12:16-12:21 |
|Promoting platform interoperability with portable bcbio workflows | |Promoting platform interoperability with portable bcbio workflows | ||
|Brad Chapman | |Brad Chapman | ||
|- | |- | ||
| − | |12: | + | |12:21-12:26 |
|Questions for lightning talk speakers in this session | |Questions for lightning talk speakers in this session | ||
| | | | ||
| Line 84: | Line 84: | ||
|Chair: | |Chair: | ||
|- | |- | ||
| − | |14:00-14: | + | |14:00-14:18 |
|Enhancements to MISO: An open-source community-driven LIMS | |Enhancements to MISO: An open-source community-driven LIMS | ||
|Andre Masella | |Andre Masella | ||
|- | |- | ||
| − | |14: | + | |14:18-14:36 |
|Biothings APIs: high-performance bioentity-centric web services | |Biothings APIs: high-performance bioentity-centric web services | ||
|Chunlei Wu | |Chunlei Wu | ||
|- | |- | ||
| − | |14: | + | |14:36-14:54 |
|The Noctua Modeling Tool | |The Noctua Modeling Tool | ||
|Seth Carbon | |Seth Carbon | ||
|- | |- | ||
| − | | | + | |14:54-15:12 |
|Processing phenotype data using Phenopackets-API and PXFTools | |Processing phenotype data using Phenopackets-API and PXFTools | ||
|Chris Mungall | |Chris Mungall | ||
|- | |- | ||
| − | |15: | + | |15:12-15:17 |
|The EDAM Ontology | |The EDAM Ontology | ||
|Jon Ison | |Jon Ison | ||
|- | |- | ||
| − | |15: | + | |15:18-15:23 |
|Towards traceable, scriptable, and efficient data distribution for next-generation genomics | |Towards traceable, scriptable, and efficient data distribution for next-generation genomics | ||
|Hilmar Lapp | |Hilmar Lapp | ||
| Line 127: | Line 127: | ||
|Nomi Harris | |Nomi Harris | ||
|- | |- | ||
| − | |17: | + | |17:15-18:30 |
|'''BOFs''': Feel free to organize one! | |'''BOFs''': Feel free to organize one! | ||
| | | | ||
Revision as of 04:30, 31 May 2016
The full program including abstracts will be available soon.
Pre-BOSC: Codefest 2016
See Codefest 2016 for details.
BOSC Day 1 (Friday, July 8, 2016)
| Time | Title | Speaker or Session Chair |
|---|---|---|
| 7:30-9:00 | Registration | |
| 9:00-9:15 | Introduction and Welcome | Nomi Harris and Peter Cock (Co-Chairs, BOSC 2016) |
| 9:15-10:15 | Keynote: The open-source outbreak: can data prevent the next pandemic? | Jennifer Gardy |
| 10:15-10:45 | Coffee Break | |
| 10:45-12:30 | Session: Workflows | Chair: TBA |
| 10:45-11:03 | GenomeSpace: Open source interoperability platform with crowd-sourced analysis recipes | Ted Liefeld |
| 11:03-11:21 | This is Why We Can Have Nice Things: Getting to 1.0 of the Common Workflow Language | Michael R. Crusoe |
| 11:21-11:39 | CWL in Practice: Experiences, challenges, and results from adopting Common Workflow Language | Dan Leehr |
| 11:39-11:57 | Using the Common Workflow Language (CWL) to run portable workflows with Arvados and Toil | Peter Amstutz |
| 11:57-12:03 | Planemo – A Scientific Workflow SDK | John Chilton |
| 12:04-12:09 | Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics | Daniel Blankenberg |
| 12:10-12:15 | NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts | Fabien Campagne |
| 12:16-12:21 | Promoting platform interoperability with portable bcbio workflows | Brad Chapman |
| 12:21-12:26 | Questions for lightning talk speakers in this session | |
| 12:30-13:30 | Lunch | |
| 13:00-14:00 | Poster Session and Birds of a Feather sessions (overlapping with lunch) | |
| 14:00-15:30 | Session: Standards and Interoperability | Chair: |
| 14:00-14:18 | Enhancements to MISO: An open-source community-driven LIMS | Andre Masella |
| 14:18-14:36 | Biothings APIs: high-performance bioentity-centric web services | Chunlei Wu |
| 14:36-14:54 | The Noctua Modeling Tool | Seth Carbon |
| 14:54-15:12 | Processing phenotype data using Phenopackets-API and PXFTools | Chris Mungall |
| 15:12-15:17 | The EDAM Ontology | Jon Ison |
| 15:18-15:23 | Towards traceable, scriptable, and efficient data distribution for next-generation genomics | Hilmar Lapp |
| 15:30-16:00 | Coffee Break | |
| 16:00-17:00 | Panel: Growing and sustaining open source communities | Moderator: Mónica Muñoz-Torres
Panelists: Abigail Cabunoc Mayes, Bastian Greshake, |
| 17:00-17:10 | Open Bioinformatics Foundation (OBF) Update (or do Sat. morning?) | |
| 17:10-17:15 | Announcements | Nomi Harris |
| 17:15-18:30 | BOFs: Feel free to organize one! | |
| 19:00 | Pay-your-own-way dinner (TBA) |
BOSC Day 2 (Saturday, July 9, 2016)
| Time | Title | Speaker or Session Chair |
|---|---|---|
| 9:00-9:05 | Announcements | Peter Cock and Nomi Harris |
| 9:05-9:15 | Codefest 2016 Report | Brad Chapman (Codefest Organizer) |
| 9:15-10:15 | Keynote: Open source, open access, and open data: why science moves faster in an open world | Steven Salzberg |
| 10:15-10:45 | Coffee Break | |
| 10:45-12:30 | Session: Data Science | |
| 10:45-11:03 | Mango: Data Exploration on Large Genomic Datasets | Alyssa Morrow |
| 11:03-11:21 | ADAM Enables Distributed Analyses Across Large Scale Genomic Datasets | Frank Nothaft |
| 11:21-11:39 | SUPERSMART - A Self-Updating platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa |
Hannes Hettling |
| 11:39-11:57 | Characterization of the small RNA transcriptome using the bcbio-nextgen python framework | Lorena Pantano Rubino |
| 11:57-12:15 | MetaR: simple, high-level languages for data analysis with the R ecosystem | Fabien Campagne |
| 12:15-12:20 | Development of NGSEP as an open-source comprehensive solution for analysis of high throughput sequencing data | Jorge Duitama |
| 12:21-12:26 | GRNmap and GRNsight: open source software for dynamical systems modeling and visualization of medium-scale gene regulatory networks |
Kam D. Dahlquist |
| 12:30-13:30 | Lunch | |
| 13:00-14:00 | Poster Session and BOFs (overlapping with lunch) | |
| 14:00-14:40 | Session: Developer tools and libraries | Chair: Chris Fields |
| TIME | Biopython Project Update 2016 | Christian Brueffer |
| TIME | Sequenceserver: a modern graphical user interface for custom BLAST databases | Anurag Priyam |
| TIME | Linuxbrew and Homebrew-Science to Navigate the Software Dependency Labyrinth | Shaun Jackman |
| TIME | SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata | Benjamin Hitz |
| 14:40-15:30 | Session: Open Science and Reproducibility | Chair: |
| TIME | State of the openSNP.org Union: Dockerizing, Crowdfunding & Opening for Contributors | Bastian Greshake |
| TIME | The GenePattern Notebook Environment | Michael Reich |
| TIME | Reproducibility in computationally intensive workflows with continuous analysis | Brett K Beaulieu-Jones |
| TIME | ReportMD: Writing complex scientific reports in R | Peter Humburg |
| TIME | Reproducible Research in the Cloud with the Refinery Platform | Nils Gehlenborg |
| 15:30-16:00 | Coffee Break | |
| 16:00-17:00 | Session: Late-Breaking Lightning Talks | |
| 16:00-16:05 | ||
| 16:06-16:11 | ||
| 16:12-16:17 | ||
| 16:18-16:23 | ||
| 16:24-16:29 | ||
| 16:30-16:35 | ||
| 16:35-16:40 | Questions for lightning talk presenters | |
| 16:40-16:50 | Concluding remarks | Nomi Harris and Peter Cock |
| 17:00-18:30 | BOFs: Feel free to organize one! | |
| 19:00 | Pay-your-own-way dinner (TBA) |
Posters
If a poster presenter also is giving a talk, the poster link will be above. The table below lists poster-only presentations.
| Poster | Title | Presenter |
|---|---|---|
| P30 |
BOSC 2016 Organizing Committee
Nomi Harris and Peter Cock (Co-Chairs)
Brad Chapman, Chris Fields, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres, Heather Wiencko
BOSC 2016 Program Committee
Nomi Harris, Michael Heuer, Karen Cranston, Gianluca Della Vedova, George Githinji, Christopher Fields, Hilmar Lapp, Scott Markel, Frank Nothaft, Lorena Pantano, Michael Reich, Morgan Taschuk, Heather Wiencko, Kai Blin, Spencer Bliven, Brad Chapman, Michael Crusoe, Bastian Greshake, Hans-Rudolf Hotz, Herve Menager, Fiona Nielsen, Konstantin Okonechnikov, João Rodrigues, Eric Talevich, Jason Williams, Melissa Wilson Sayres, Peter Cock, Björn Grüning, Karsten Hokamp, Amye Kenall, John Chilton, Konrad Förstner, Jens Lichtenberg, Monica C Munoz-Torres
BOSC is a community effort—we thank all those who made it possible, including the organizing committee, the program committee, the session chairs, our sponsors, and the ISMB SIG chair, Steven Leard.
If you are interested in helping to organize BOSC 2017, please email bosc@open-bio.org
