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Difference between revisions of "BOSC 2014 Schedule"
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| Running Taverna Workflows within IPython Notebook | | Running Taverna Workflows within IPython Notebook | ||
| Alan Williams / Aleksandra Pawlik (TBC) | | Alan Williams / Aleksandra Pawlik (TBC) | ||
| + | |- | ||
| + | | Driver Mutation Pipeline and Visualization in Galaxy | ||
| + | | Saket Choudhary | ||
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| Reconstruction of ancestral genomes in presence of gene gain and loss | | Reconstruction of ancestral genomes in presence of gene gain and loss | ||
Revision as of 10:32, 14 June 2014
This year we have allocated all the talks an equal slot, 15 minutes plus 3 minutes for questions (making 18 minutes), except for the project update session where this is reduced to 10 minutes plus 2 minutes for questions (making 12 minutes in all). Lightning talks are 5 minutes only (no questions), and are intended for a brief introduction with the expectation that interested people will talk in the evening or next day.
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 |
| 17:00-17:30 | Session: Lightning Talks | Chair: Peter Cock |
| 17:00-17:05 | [Lightning] Fostering the next generation of data-driven open science with R | Karthik Ram |
| 17:07-17:12 | [Lightning] Tripal: an open source toolkit for building genomic and genetic data websites and databases | Margaret Staton |
| 17:14-17:19 | [Lightning] PLUTo: Phyloinformatic Literature Unlocking Tools | Ross Mounce |
| 17:21-17:26 | [Lightning] A publication model that aligns with the key Open Source Software principles | Michael L. Markle |
| 17:27-17:30 | Announcements | Nomi Harris and/or Peter Cock |
| 17:30-18:30 | BOFs | Suggest a BOF topic here! |
| 19:00 | Pay-your-own-way BOSC dinner:
The Asgard Irish Pub and Restaurant, 350 Massachusetts Avenue, Cambridge, MA (1.2 miles north of the convention center). |
Only those who RSVP will be admitted. |
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 |
| 10:45-11:03 | [Interoperability] Pathview: an R/Bioconductor package for pathway-based data integration and visualization | Weijun Luo |
| 11:03-11:21 | [Interoperability] Use of semantically annotated resources in the Mobyle2 Web Framework | Hervé Ménager |
| 11:21-11:39 | [Interoperability] Towards ubiquitous OWL computing: Simplifying programmatic authoring of and querying with OWL axioms | Hilmar Lapp |
| 11:39-11:57 | [Interoperability] Integrating Taverna Player into Scratchpads | Robert Haines |
| 11:57-12:15 | [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 |
| 14:00-14:18 | [Open Science] SEEK for Science: A Data Management Platform which Supports Open and Reproducible Science | Carole Goble |
| 14:18-14:36 | [Open Science] Arvados: Achieving Computational Reproducibility and Data Provenance in Large-Scale Genomic Analyses | Brett Smith |
| 14:36-14:54 | [Open Science] Enhancing the Galaxy Experience through Community Involvement | Daniel Blankenberg |
| 14:54-15:12 | [Open Science] Supporting dynamic community developed biological pipelines | Brad Chapman |
| 15:12-15:30 | [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 |
| 17:00-17:10 | Presentation of Student Travel Awards & Concluding Remarks | Nomi Harris (Co-Chair, BOSC 2014) |
| 17:10-18:00 | BOFs | Suggest a BOF topic here! |
Note the ISMB reception starts at 17:30...
Posters
If the speaker also gave a talk, any poster link with be above. This table lists poster-only presentations.
| Title | Presenter |
|---|---|
| Using open source technology to extract biochemical data from big data repositories: the NCBI PubChem experience. | Lewis Y. Geer |
| Connecting computational steps for NGS, and beyond. | Laurent Gautier |
| Updates to MISO, the open-source NGS LIMS project | Xingdong Bian |
| Running Taverna Workflows within IPython Notebook | Alan Williams / Aleksandra Pawlik (TBC) |
| Driver Mutation Pipeline and Visualization in Galaxy | Saket Choudhary |
| Reconstruction of ancestral genomes in presence of gene gain and loss | Shuai Jiang |
| Firehose in The Cancer Genome Atlas: Rigorous Open Science, At Scale | Michael Noble |
| MyGene.info updates: scalable gene-centric web services with user contributions | Chunlei Wu |
| Aiding the journey from data to publication in the plant sciences | Robert Davey |
| Bio2RDF mobile: an app for biological semantic web databases | Maxime Déraspe |
| ... | ... |
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We thank Eagle Genomics for sponsoring the BOSC Student Travel Awards again this year, and welcome the open access journal GigaScience, and Curoverse (the team behind the open source platform Arvados) as new sponsors for BOSC 2014.
We are grateful to Google for their generous support for videorecording BOSC 2014.
