| Please visit our ***NEW*** OBF/BOSC website: https://www.open-bio.org/ |
-
Difference between revisions of "BOSC 2014 Schedule"
From Open Bioinformatics Foundation
(→BOSC Day 2: Saturday, 12 July 2014: Move "Integrating Taverna Player into Scratchpads" before lunch) |
(→BOSC Day 1: Friday, 11 July 2014: Insert OBF update before lunch on day one) |
||
| Line 33: | Line 33: | ||
| Chair: Chris Fields | | Chair: Chris Fields | ||
|-- | |-- | ||
| − | | 10:45 | + | | 10:45-11:03 |
| [Genome-Scale] ADAM: Fast, Scalable Genomic Analysis | | [Genome-Scale] ADAM: Fast, Scalable Genomic Analysis | ||
| Frank Austin Nothaft | | Frank Austin Nothaft | ||
|- | |- | ||
| − | | 11: | + | | 11:03-11:21 |
| [Genome-Scale] A framework for benchmarking RNA-seq pipelines | | [Genome-Scale] A framework for benchmarking RNA-seq pipelines | ||
| Rory Kirchner | | Rory Kirchner | ||
|- | |- | ||
| − | | 11: | + | | 11:21-11:39 |
| [Genome-Scale] New Frontiers of Genome Assembly with SPAdes 3.1 | | [Genome-Scale] New Frontiers of Genome Assembly with SPAdes 3.1 | ||
| Andrey Prjibelski | | Andrey Prjibelski | ||
|- | |- | ||
| − | | 11: | + | | 11:39-11:57 |
| [Genome-Scale] SigSeeker: An Ensemble for Analysis of Epigenetic Data | | [Genome-Scale] SigSeeker: An Ensemble for Analysis of Epigenetic Data | ||
| Jens Lichtenberg | | Jens Lichtenberg | ||
|- | |- | ||
| − | | 12: | + | | 11:57-12:15 |
| [Genome-Scale] Galaxy as an Extensible Job Execution Platform | | [Genome-Scale] Galaxy as an Extensible Job Execution Platform | ||
| John Chilton | | John Chilton | ||
| + | |- | ||
| + | | 12:15-12:30 | ||
| + | | Open Bioinformatics Foundation (OBF) Update | ||
| + | | Hilmar Lapp (OBF President) | ||
|- | |- | ||
| '''12:30-13:30''' | | '''12:30-13:30''' | ||
| Line 65: | Line 69: | ||
| Chair: Rob Davey | | Chair: Rob Davey | ||
|- | |- | ||
| − | | 14:00 | + | | 14:00-14:18 |
| [Visualization] WormGUIDES: an Interactive Informatic Developmental Atlas at Subcellular Resolution | | [Visualization] WormGUIDES: an Interactive Informatic Developmental Atlas at Subcellular Resolution | ||
| Anthony Santella | | Anthony Santella | ||
|- | |- | ||
| − | | 14:18 | + | | 14:18-14:36 |
| [Visualization] BioJS: an open source standard for biological visualisation | | [Visualization] BioJS: an open source standard for biological visualisation | ||
| Manuel Corpas | | Manuel Corpas | ||
|- | |- | ||
| − | | 14:36 | + | | 14:36-14:54 |
| [Visualization] Biodalliance: a fast, extensible genome browser | | [Visualization] Biodalliance: a fast, extensible genome browser | ||
| Thomas Down | | Thomas Down | ||
|- | |- | ||
| − | | 14:54 | + | | 14:54-15:12 |
| [Visualization] TGAC Browser: visualisation solutions for big data in the genomic era | | [Visualization] TGAC Browser: visualisation solutions for big data in the genomic era | ||
| Anil S. Thanki | | Anil S. Thanki | ||
|- | |- | ||
| − | | 15:12 | + | | 15:12-15:30 |
| [Visualization] Explore, analyze, and share genomic data using Integrated Genome Browser | | [Visualization] Explore, analyze, and share genomic data using Integrated Genome Browser | ||
| Ann Loraine | | Ann Loraine | ||
| Line 93: | Line 97: | ||
| Chair: Peter Cock | | Chair: Peter Cock | ||
|- | |- | ||
| − | | 16:00 | + | | 16:00-16:12 |
| [Updates] BioMart 0.9 – introducing tools for data analysis and visualisation | | [Updates] BioMart 0.9 – introducing tools for data analysis and visualisation | ||
| Luca Pandini | | Luca Pandini | ||
|- | |- | ||
| − | | 16:12 | + | | 16:12-16:24 |
| [Updates] Biocaml: The OCaml Bioinformatics Library | | [Updates] Biocaml: The OCaml Bioinformatics Library | ||
| Ashish Agarwal | | Ashish Agarwal | ||
|- | |- | ||
| − | | 16:24 | + | | 16:24-16:36 |
| [Updates] BioRuby and distributed development | | [Updates] BioRuby and distributed development | ||
| Pjotr Prins | | Pjotr Prins | ||
|- | |- | ||
| − | | 16:36 | + | | 16:36-16:48 |
| [Updates] Biopython Project Update | | [Updates] Biopython Project Update | ||
| Wibowo Arindrarto | | Wibowo Arindrarto | ||
|- | |- | ||
| − | | 16:48 | + | | 16:48-17:00 |
| [Updates] Shared bioinformatics database within Unipro UGENE | | [Updates] Shared bioinformatics database within Unipro UGENE | ||
| Ivan Protsyuk | | Ivan Protsyuk | ||
Revision as of 05:51, 6 June 2014
Pre-BOSC Codefest: July 9-10, 2014
See Codefest 2014 for details.
BOSC Day 1: Friday, 11 July 2014
| Time | Topic | Speaker, Moderator, or notes |
|---|---|---|
| 7:30-9:00 | Registration | Early arrival is recommended as there are usually long lines |
| 9:00-9:15 | Introduction and welcome | Nomi Harris and/or Peter Cock (Chairs, BOSC 2014) |
| 9:15-10:15 | Keynote: A History of Bioinformatics (in the year 2039) | C. Titus Brown |
| 10:15-10:45 | Coffee Break | |
| 10:45-12:30 | Session: Genome-scale Data and Beyond | Chair: Chris Fields |
| 10:45-11:03 | [Genome-Scale] ADAM: Fast, Scalable Genomic Analysis | Frank Austin Nothaft |
| 11:03-11:21 | [Genome-Scale] A framework for benchmarking RNA-seq pipelines | Rory Kirchner |
| 11:21-11:39 | [Genome-Scale] New Frontiers of Genome Assembly with SPAdes 3.1 | Andrey Prjibelski |
| 11:39-11:57 | [Genome-Scale] SigSeeker: An Ensemble for Analysis of Epigenetic Data | Jens Lichtenberg |
| 11:57-12:15 | [Genome-Scale] Galaxy as an Extensible Job Execution Platform | John Chilton |
| 12:15-12:30 | Open Bioinformatics Foundation (OBF) Update | Hilmar Lapp (OBF President) |
| 12:30-13:30 | Lunch | (and poster session) |
| 13:00-14:00 | Poster Session and Birds of a Feather (overlapping with lunch) | Suggest a BOF topic here! |
| 14:00-15:30 | Session: Visualization | Chair: Rob Davey |
| 14:00-14:18 | [Visualization] WormGUIDES: an Interactive Informatic Developmental Atlas at Subcellular Resolution | Anthony Santella |
| 14:18-14:36 | [Visualization] BioJS: an open source standard for biological visualisation | Manuel Corpas |
| 14:36-14:54 | [Visualization] Biodalliance: a fast, extensible genome browser | Thomas Down |
| 14:54-15:12 | [Visualization] TGAC Browser: visualisation solutions for big data in the genomic era | Anil S. Thanki |
| 15:12-15:30 | [Visualization] Explore, analyze, and share genomic data using Integrated Genome Browser | Ann Loraine |
| 15:30-16:00 | Coffee Break | |
| 16:00-17:00 | Session: Bioinformatics Open Source Project Updates | Chair: Peter Cock |
| 16:00-16:12 | [Updates] BioMart 0.9 – introducing tools for data analysis and visualisation | Luca Pandini |
| 16:12-16:24 | [Updates] Biocaml: The OCaml Bioinformatics Library | Ashish Agarwal |
| 16:24-16:36 | [Updates] BioRuby and distributed development | Pjotr Prins |
| 16:36-16:48 | [Updates] Biopython Project Update | Wibowo Arindrarto |
| 16:48-17:00 | [Updates] Shared bioinformatics database within Unipro UGENE | Ivan Protsyuk |
| 17:00-18:00 | Lightning Talks followed by BOFs | Suggest a BOF topic here! |
| 19:00 | Pay-your-own-way BOSC dinner |
BOSC Day 2: Saturday, 12 July 2014
| Time | Topic | Speaker or Moderator |
|---|---|---|
| 8:45 - 8:50 | Announcements | Peter Cock and/or Nomi Harris (Chairs, BOSC 2014) |
| 8:50 - 9:00 | Codefest 2014 Report | Brad Chapman |
| 9:00 - 9:15 | Open Bioinformatics Foundation (OBF) update | Hilmar Lapp (President, Open Bioinformatics Foundation) |
| 9:15 - 10:15 | Keynote: Biomedical Research as an Open Digital Enterprise | Philip Bourne |
| 10:15-10:45 | Coffee Break | |
| 10:45-12:30 | Session: Software Interoperability | Chair: Raoul Bonnal |
| 10:45 | [Interoperability] Pathview: an R/Bioconductor package for pathway-based data integration and visualization | Weijun Luo |
| 11:03 | [Interoperability] Use of semantically annotated resources in the Mobyle2 Web Framework | Hervé Ménager |
| 11:20 | [Interoperability] Towards ubiquitous OWL computing: Simplifying programmatic authoring of and querying with OWL axioms | Hilmar Lapp |
| 11:38 | [Interoperability] The coming of the age of the platform for bioinformatics? (And how to keep it open-source) | Konstantinos Krampis |
| 12:55 | [Interoperability] Integrating Taverna Player into Scratchpads | Robert Haines |
| 12:13 | [Interoperability] Small tools for Bioinformatics | Pjotr Prins |
| 12:30-13:30 | Lunch | (and poster session) |
| 13:00-14:00 | Poster Session and Birds of a Feather (overlapping with lunch) | Suggest a BOF topic here! |
| 14:00-15:30 | Session: Open Science and Reproducible Research | Chair: Hilmar Lapp |
| 14:00 | [Open Science] SEEK for Science: A Data Management Platform which Supports Open and Reproducible Science | Stuart Owen |
| 14:18 | [Open Science] Arvados: Achieving Computational Reproducibility and Data Provenance in Large-Scale Genomic Analyses | Brett Smith |
| 14:36 | [Open Science] Enhancing the Galaxy Experience through Community Involvement | Daniel Blankenberg |
| 14:54 | [Open Science] Supporting dynamic community developed biological pipelines | Brad Chapman |
| 15:12 | [Open Science] Open as a strategy for durability, reproducibility and scalability | Jonathan Rees |
| 15:30-16:00 | Coffee Break | |
| 16:00-17:00 | Panel: Reproducibility: Rewards and Challenges | Moderator: Brad Chapman; Panelists: Phil Bourne, Titus Brown, Varsha Khodiyar, Kay Thaney |
| 17:00-17:05 | Presentation of Student Travel Awards | Nomi Harris (Co-Chair, BOSC 2014) |
| 17:05-18:00 | BOFs | Suggest a BOF topic here! |
Note the ISMB reception starts at 17:30...
Posters
Shared links to presented posters will be posted here:
| Title | Presenter |
|---|---|
| ... | A.N. Other et al. |
