-

Difference between revisions of "BOSC 2014 Schedule"

From Open Bioinformatics Foundation
Jump to: navigation, search
(BOSC Day 1: Friday, 11 July 2014)
(Only need OBF Update on one day - thanks Hilmar!)
Line 56: Line 56:
 
|-
 
|-
 
| 12:15-12:30
 
| 12:15-12:30
| Open Bioinformatics Foundation (OBF) Update
+
| [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation (OBF) update]
 
| Hilmar Lapp (OBF President)
 
| Hilmar Lapp (OBF President)
 
|-
 
|-
Line 164: Line 164:
 
! Speaker or Moderator
 
! Speaker or Moderator
 
|-  
 
|-  
| 8:45-8:50
+
| 8:55-9:00
 
| Announcements
 
| Announcements
 
| Peter Cock and/or Nomi Harris (Chairs, BOSC 2014)
 
| Peter Cock and/or Nomi Harris (Chairs, BOSC 2014)
 
|-
 
|-
| 8:50-9:00
+
| 9:00-9:15
 
| [[Codefest_2014 | Codefest 2014 Report]]
 
| [[Codefest_2014 | Codefest 2014 Report]]
 
| Brad Chapman
 
| Brad Chapman
|-
 
| 9:00-9:15
 
| [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation (OBF) update]
 
| Hilmar Lapp (President, Open Bioinformatics Foundation)
 
 
|-
 
|-
 
| 9:15-10:15
 
| 9:15-10:15

Revision as of 19:44, 14 June 2014

BOSC logo

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 [Poster], 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 [P1]
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 [P2]
11:39-11:57 [Genome-Scale] SigSeeker: An Ensemble for Analysis of Epigenetic Data Jens Lichtenberg [P3]
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 [P4]
14:18-14:36 [Visualization] BioJS: an open source standard for biological visualisation Manuel Corpas [P5]
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 [P6]
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 [P7]
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. Markie [P8]
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 logo

BOSC Day 2: Saturday, 12 July 2014

Time Topic Speaker or Moderator
8:55-9:00 Announcements Peter Cock and/or Nomi Harris (Chairs, BOSC 2014)
9:00-9:15 Codefest 2014 Report Brad Chapman
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 [P9]
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 [P10]
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 [P11]
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 will be above (posters 1 to 11). This table lists poster-only presentations.

Poster Title Presenter
P12 Using open source technology to extract biochemical data from big data repositories: the NCBI PubChem experience. Lewis Y. Geer
P13 Connecting computational steps for NGS, and beyond. Laurent Gautier
P14 Updates to MISO, the open-source NGS LIMS project Xingdong Bian
P15 Running Taverna Workflows within IPython Notebook Alan Williams / Aleksandra Pawlik (TBC)
P16 Reconstruction of ancestral genomes in presence of gene gain and loss Shuai Jiang
P17 Firehose in The Cancer Genome Atlas: Rigorous Open Science, At Scale Michael Noble
P18 GEPETTO Update: An Open Source Framework for Gene Prioritization Hoan Nguyen
P19 NeoPipe: An Open Source Framework for Protein sequence analysis Hoan Nguyen
P20 MyGene.info updates: scalable gene-centric web services with user contributions Chunlei Wu
P21 Aiding the journey from data to publication in the plant sciences Robert Davey
P22 Bio2RDF mobile: an app for biological semantic web databases Maxime Déraspe
... ... ...



Eagle Genomics logo
            
GigaScieece
        
Curoverse logo
Arvados logo
        
Google

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.


Return to BOSC 2014 main page