-

Difference between revisions of "BOSC 2014 Schedule"

From Open Bioinformatics Foundation
Jump to: navigation, search
(→‎BOSC Day 1: Friday, 11 July 2014: title case)
(→‎BOSC Day 2: Saturday, 12 July 2014: Direct YouTube links for day two)
 
(77 intermediate revisions by 9 users not shown)
Line 2: Line 2:
 
[[File:Pear.png|100px|right|BOSC logo|link=BOSC_2014]]
 
[[File:Pear.png|100px|right|BOSC logo|link=BOSC_2014]]
  
−
You can download the [http://www.open-bio.org/bosc2014/BOSC2014_program.pdf full program with abstracts (PDF)], however this wiki page is considered the definitive schedule and will be updated with any last minute changes.
+
This page has links to all the publicly available talk slides, videos and posters. The videos are all on the [https://www.youtube.com/playlist?list=PLir-OOQiOhXYxkgAqov3J8rwTPUxC0soJ BOSC 2014 YouTube playlist], with thanks to Google for sponsorship.
  
−
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 people who are interested in the topic will find the
+
You can download the [http://www.open-bio.org/bosc2014/BOSC2014_program.pdf full program with abstracts (PDF)]; however, this wiki page is considered the definitive schedule and was updated with any last minute changes.
−
speaker during a break or poster session to talk with them.
+
 
 +
There was lots of activity under Twitter - our hashtag was #BOSC2014 and there are Storify Tweet archives for [https://storify.com/pjacock/bosc-2014-day-one Day One], [https://storify.com/pjacock/bosc-2014-day-two/ Day Two] and [https://storify.com/pjacock/bosc-during-ismb-2014/ during ISMB].
  
 
== Pre-BOSC Codefest: July 9-10, 2014 ==
 
== Pre-BOSC Codefest: July 9-10, 2014 ==
Line 27: Line 28:
 
|-
 
|-
 
| 9:15-10:15
 
| 9:15-10:15
−
| [[BOSC_2014_Keynote_Speakers|Keynote: A History of Bioinformatics (in the Year 2039)]]
+
| [[BOSC_2014_Keynote_Speakers|Keynote: A History of Bioinformatics (in the Year 2039)]] ([https://youtu.be/uwsjwMO-TEA video], [http://www.slideshare.net/c.titus.brown/2014-bosckeynote slideshare], [http://ivory.idyll.org/blog/2014-bosc-keynote.html notes])
 
| C. Titus Brown
 
| C. Titus Brown
 
|-
 
|-
Line 39: Line 40:
 
|--
 
|--
 
| 10:45-11:03
 
| 10:45-11:03
−
| [Genome-Scale] ADAM: Fast, Scalable Genomic Analysis
+
| [Genome-Scale] ADAM: Fast, Scalable Genomic Analysis ([https://youtu.be/EtAWRuvuwr8 video], [http://www.open-bio.org/bosc2014/BOSC2014-Genome-01-ADAM-Nothaft.pdf slides])
 
| Frank Austin Nothaft [P1]
 
| Frank Austin Nothaft [P1]
 
|-
 
|-
 
| 11:03-11:21
 
| 11:03-11:21
−
| [Genome-Scale] A Framework for Benchmarking RNA-seq Pipelines
+
| [Genome-Scale] A Framework for Benchmarking RNA-seq Pipelines ([https://youtu.be/_LTaNFY9IjM video], [http://www.open-bio.org/bosc2014/BOSC2014-Genome-02-Rory.pdf slides])
 
| Rory Kirchner
 
| Rory Kirchner
 
|-
 
|-
 
| 11:21-11:39
 
| 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 ([https://youtu.be/vFA7BGzNMss video], [http://www.open-bio.org/bosc2014/BOSC2014-Genome-03-SPAdes-Prjibelski.pdf slides])
 
| Andrey Prjibelski [P2]
 
| Andrey Prjibelski [P2]
 
|-
 
|-
 
| 11:39-11:57
 
| 11:39-11:57
−
| [Genome-Scale] SigSeeker: An Ensemble for Analysis of Epigenetic Data
+
| [Genome-Scale] SigSeeker: An Ensemble for Analysis of Epigenetic Data ([https://youtu.be/3gTEoyVNA6Q video], [http://www.open-bio.org/bosc2014/BOSC2014-Genome-04-SigSeeker-Lichtenberg.pdf slides])
 
| Jens Lichtenberg [P3]
 
| Jens Lichtenberg [P3]
 
|-
 
|-
 
| 11:57-12:15
 
| 11:57-12:15
−
| [Genome-Scale]  Galaxy as an Extensible Job Execution Platform
+
| [Genome-Scale]  Galaxy as an Extensible Job Execution Platform ([https://youtu.be/XLh_Q4Q0YBE video], [https://docs.google.com/presentation/d/1uQmmC2Cl5gpPe9cBwjl0cdKno1tsRKz2XNZg9NOMwdI/edit#slide=id.p slides])
 
| John Chilton
 
| John Chilton
 
|-
 
|-
 
| 12:15-12:30
 
| 12:15-12:30
−
| [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation (OBF) update]
+
| [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation (OBF) update] ([https://youtu.be/1oSTb8ZAxec video])
 
| Hilmar Lapp (OBF President)
 
| Hilmar Lapp (OBF President)
 
|-
 
|-
Line 75: Line 76:
 
|-
 
|-
 
| 14:00-14:18
 
| 14:00-14:18
−
| [Visualization] WormGUIDES: an Interactive Informatic Developmental Atlas at Subcellular Resolution
+
| [Visualization] WormGUIDES: an Interactive Informatic Developmental Atlas at Subcellular Resolution ([https://youtu.be/uxPnmyGydW4 video], [http://www.open-bio.org/bosc2014/BOSC2014-Viz-01-WormGUIDES-Santella.pdf slides])
 
| Anthony Santella [P4]
 
| Anthony Santella [P4]
 
|-
 
|-
 
| 14:18-14:36
 
| 14:18-14:36
−
| [Visualization] BioJS: an Open Source Standard for Biological Visualisation
+
| [Visualization] BioJS: an Open Source Standard for Biological Visualisation ([https://youtu.be/aHtXNW-I2U0 video])
 
| Manuel Corpas [P5]
 
| Manuel Corpas [P5]
 
|-
 
|-
 
| 14:36-14:54
 
| 14:36-14:54
−
| [Visualization] Biodalliance: a Fast, Extensible Genome Browser
+
| [Visualization] Biodalliance: a Fast, Extensible Genome Browser ([https://youtu.be/l4Z7wsppCaM video])
 
| Thomas Down
 
| Thomas Down
 
|-
 
|-
 
| 14:54-15:12
 
| 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 ([https://youtu.be/yKx8lE2WQzI video], [http://www.open-bio.org/bosc2014/BOSC2014-Viz-04-TGAC_Browser-Anil.pdf slides])
 
| Anil S. Thanki [P6]
 
| Anil S. Thanki [P6]
 
|-
 
|-
 
| 15:12-15:30
 
| 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 ([https://youtu.be/b7O9rN2i0GM video], [http://www.open-bio.org/bosc2014/BOSC2014-Viz-05-IGB-Ann_Loraine.pdf slides])
 
| Ann Loraine
 
| Ann Loraine
 
|-
 
|-
Line 103: Line 104:
 
|-
 
|-
 
| 16:00-16:12
 
| 16:00-16:12
−
| [Updates] BioMart 0.9 – ntroducing Tools for Data Analysis and Visualisation
+
| [Updates] BioMart 0.9 – Introducing Tools for Data Analysis and Visualisation ([https://youtu.be/XJmyC1sfFeg video], [http://www.open-bio.org/bosc2014/BOSC2014-Updates-01-BioMart.pdf slides])
−
| Luca Pandini
+
| Arek Kasprzyk
 
|-
 
|-
 
| 16:12-16:24
 
| 16:12-16:24
−
| [Updates] Biocaml: The OCaml Bioinformatics Library
+
| [Updates] Biocaml: The OCaml Bioinformatics Library ([https://youtu.be/0lDWzyhdyP8 video], [http://www.open-bio.org/bosc2014/BOSC2014-Updates-02-Biocaml-Agarwal.pdf slides])
 
| Ashish Agarwal
 
| Ashish Agarwal
 
|-
 
|-
 
| 16:24-16:36
 
| 16:24-16:36
−
| [Updates] BioRuby and Distributed Development
+
| [Updates] BioRuby and Distributed Development ([https://youtu.be/tRpxLmu4w3w video], [https://github.com/pjotrp/biogems.info/blob/master/doc/abstracts/BOSC2014_BioRuby_dev.md abstract], [http://www.open-bio.org/bosc2014/BOSC2014-Updates-03-BioRuby-Pjotr.pdf slides])
 
| Pjotr Prins
 
| Pjotr Prins
 
|-
 
|-
 
| 16:36-16:48
 
| 16:36-16:48
−
| [Updates] Biopython Project Update
+
| [Updates] Biopython Project Update ([https://youtu.be/bJ5OcCYq-G4 video], [http://www.open-bio.org/bosc2014/BOSC2014-Updates-04-Biopython-Arindrarto.pdf slides])
 
| Wibowo Arindrarto
 
| Wibowo Arindrarto
 
|-
 
|-
 
| 16:48-17:00
 
| 16:48-17:00
−
| [Updates] Shared Bioinformatics Database Within Unipro UGENE
+
| [Updates] Shared Bioinformatics Databases Within Unipro UGENE ([https://youtu.be/tS57J2JeL-Y video], [http://www.open-bio.org/bosc2014/BOSC2014-Updates-05-UGENE-Protsyuk.pdf slides])
 
| Ivan Protsyuk [P7]
 
| Ivan Protsyuk [P7]
 
|-
 
|-
Line 127: Line 128:
 
|-
 
|-
 
| 17:00-17:05
 
| 17:00-17:05
−
| [Lightning] Fostering the Next Generation of Data-driven Open Science with R
+
| [Lightning] Fostering the Next Generation of Data-driven Open Science with R ([https://youtu.be/p4hbpb3d6v8 video], [http://karthik.github.io/BOSC/ slides])
 
| Karthik Ram
 
| Karthik Ram
 
|-
 
|-
 
| 17:07-17:12
 
| 17:07-17:12
−
| [Lightning] Tripal: an Open Source Toolkit for Building Genomic and Genetic Data Websites and Databases
+
| [Lightning] Tripal: an Open Source Toolkit for Building Genomic and Genetic Data Websites and Databases ([https://youtu.be/-IUr8Tghvsw video], [http://www.open-bio.org/bosc2014/BOSC2014-Lightning-2-Tripal-Staton.pdf slides])
 
| Margaret Staton
 
| Margaret Staton
 
|-
 
|-
 
| 17:14-17:19
 
| 17:14-17:19
−
| [Lightning] PLUTo: Phyloinformatic Literature Unlocking Tools
+
| [Lightning] PLUTo: Phyloinformatic Literature Unlocking Tools ([https://youtu.be/qX0ocTMc8MY video], [http://www.open-bio.org/bosc2014/BOSC2014-Lightning-3-PLUTo-Mounce.pdf slides])
 
| Ross Mounce
 
| Ross Mounce
 
|-
 
|-
 
| 17:21-17:26
 
| 17:21-17:26
−
| [Lightning] A Publication Model that Aligns with the Key Open Source Software Principles
+
| [Lightning] A Publication Model that Aligns with the Key Open Source Software Principles ([https://youtu.be/iWQXfyFtRUU video], [http://www.open-bio.org/bosc2014/BOSC2014-Lightning-4-F1000-Markie.pdf slides])
 
| Michael L. Markie [P8]
 
| Michael L. Markie [P8]
 
|-
 
|-
Line 151: Line 152:
 
|-
 
|-
 
| 19:00
 
| 19:00
−
| ''Pay-your-own-way BOSC dinner'':
+
| ''Pay-your-own-way Friday BOSC dinner'' (FULL)
 
[http://www.classicirish.com/asgard-home.php The Asgard Irish Pub and Restaurant], [https://maps.google.com/maps?ll=42.352697,-71.0733475&z=15&geocode=FXAthgId4UjD-ylJGc0sBXrjiTEgso4wQw9wIA;FT1nhgId6RvD-yn13UfwVHfjiTESJTW6VTsm6Q&saddr=Hynes+Convention+Center+Station&daddr=The+Asgard+Irish+Pub+and+Restaurant,+350+Massachusetts+Ave,+Cambridge,+MA+02139&dirflg=r&output=classic&dg=ntvb 350 Massachusetts Avenue, Cambridge, MA] (1.2 miles north of the convention center).
 
[http://www.classicirish.com/asgard-home.php The Asgard Irish Pub and Restaurant], [https://maps.google.com/maps?ll=42.352697,-71.0733475&z=15&geocode=FXAthgId4UjD-ylJGc0sBXrjiTEgso4wQw9wIA;FT1nhgId6RvD-yn13UfwVHfjiTESJTW6VTsm6Q&saddr=Hynes+Convention+Center+Station&daddr=The+Asgard+Irish+Pub+and+Restaurant,+350+Massachusetts+Ave,+Cambridge,+MA+02139&dirflg=r&output=classic&dg=ntvb 350 Massachusetts Avenue, Cambridge, MA] (1.2 miles north of the convention center).
−
| Only those who [http://doodle.com/iigm6756xas5p9hq RSVP] will be admitted.
+
| Only those who have already RSVPed will be admitted.
 
|-  
 
|-  
 
|}
 
|}
Line 172: Line 173:
 
|-
 
|-
 
| 9:00-9:15
 
| 9:00-9:15
−
| [[Codefest_2014 | Codefest 2014 Report]]
+
| [[Codefest_2014 | Codefest 2014 Report]] ([https://youtu.be/EuWgm6V9DgI video], [https://docs.google.com/presentation/d/114yvrK0Veasc_ns_rg484j2xxRi1h7wNlU2XKONuUqY/edit?usp=sharing slides])
 
| Brad Chapman
 
| Brad Chapman
 
|-
 
|-
 
| 9:15-10:15
 
| 9:15-10:15
−
| | [[BOSC_2014_Keynote_Speakers|Keynote: Biomedical Research as an Open Digital Enterprise]]
+
| | [[BOSC_2014_Keynote_Speakers|Keynote: Biomedical Research as an Open Digital Enterprise]] ([https://youtu.be/VmRNkdHKJgA video], [http://www.slideshare.net/pebourne/bosc2014 slidesshare])
 
| Philip Bourne  
 
| Philip Bourne  
 
|-
 
|-
Line 188: Line 189:
 
|-
 
|-
 
| 10:45-11:03
 
| 10:45-11:03
−
| [Interoperability] Pathview: an R/Bioconductor package for pathway-based data integration and visualization
+
| [Interoperability] Pathview: an R/Bioconductor Package for Pathway-based Data Integration and Visualization ([https://youtu.be/sne_Nb9au20 video], [http://www.open-bio.org/bosc2014/BOSC2014-InterOp-01-Pathview-Weijun.pdf slides])
 
| Weijun Luo [P9]
 
| Weijun Luo [P9]
 
|-
 
|-
 
| 11:03-11:21
 
| 11:03-11:21
−
| [Interoperability] Use of semantically annotated resources in the Mobyle2 Web Framework
+
| [Interoperability] Use of Semantically Annotated Resources in the Mobyle2 Web Framework ([https://youtu.be/5sYUuoXOBiE video], [http://www.open-bio.org/bosc2014/BOSC2014-InterOp-02-Mobyle2_EDAM-Ménager.pdf slides])
 
| Hervé Ménager
 
| Hervé Ménager
 
|-
 
|-
 
| 11:21-11:39
 
| 11:21-11:39
−
| [Interoperability] Towards ubiquitous OWL computing: Simplifying programmatic authoring of and querying with OWL axioms
+
| [Interoperability] Towards Ubiquitous OWL Computing: Simplifying Programmatic Authoring of and Querying with OWL Axioms ([https://youtu.be/K0SlYwMyn-A video], [http://www.open-bio.org/bosc2014/BOSC2014-InterOp-03-Ubiquitous_OWL-Hilmar.pdf slides])
 
| Hilmar Lapp
 
| Hilmar Lapp
 
|-
 
|-
 
| 11:39-11:57
 
| 11:39-11:57
−
| [Interoperability] Integrating Taverna Player into Scratchpads
+
| [Interoperability] Integrating Taverna Player into Scratchpads ([https://youtu.be/iL-rMaFtYdM video], [http://www.slideshare.net/roberthaines/tp-scratchtalk-36957762 slideshare], [https://zenodo.org/record/10871 poster])
 
| Robert Haines [P10]
 
| Robert Haines [P10]
 
|-
 
|-
 
| 11:57-12:15
 
| 11:57-12:15
−
| [Interoperability] Small tools for Bioinformatics
+
| [Interoperability] Small Tools for Bioinformatics ([http://youtu.be/8jHbvClB1i8 video], [http://www.open-bio.org/bosc2014/BOSC2014-InterOp-05-small_tools_Pjotr.pdf slides], [https://github.com/pjotrp/bioinformatics abstract], [https://github.com/pjotrp/bioinformatics manifesto])
 
| Pjotr Prins
 
| Pjotr Prins
 
|-
 
|-
Line 221: Line 222:
  
 
| 14:00-14:18
 
| 14:00-14:18
−
| [Open Science] SEEK for Science: A Data Management Platform which Supports Open and Reproducible Science
+
| [Open Science] SEEK for Science: A Data Management Platform which Supports Open and Reproducible Science ([https://youtu.be/g8b98kJwT60 video], [http://www.slideshare.net/carolegoble/bosc-seek2014goble slideshare])
 
| Carole Goble [P11]
 
| Carole Goble [P11]
 
|-
 
|-
 
| 14:18-14:36
 
| 14:18-14:36
−
| [Open Science] Arvados: Achieving Computational Reproducibility and Data Provenance in Large-Scale Genomic Analyses
+
| [Open Science] Arvados: Achieving Computational Reproducibility and Data Provenance in Large-Scale Genomic Analyses ([https://youtu.be/ZFAaJfzwxW4 video], [http://www.open-bio.org/bosc2014/BOSC2014-OpenScience-02-Arvados-Brett_Smith.pdf slides])
 
| Brett Smith
 
| Brett Smith
 
|-
 
|-
 
| 14:36-14:54
 
| 14:36-14:54
−
| [Open Science] Enhancing the Galaxy Experience through Community Involvement
+
| [Open Science] Enhancing the Galaxy Experience through Community Involvement ([https://youtu.be/z-Z1cuOO4ts video], [http://www.open-bio.org/bosc2014/BOSC2014-OpenScience-03-Galaxy-Blankenberg.pdf slides])
 
| Daniel Blankenberg
 
| Daniel Blankenberg
 
|-
 
|-
 
| 14:54-15:12
 
| 14:54-15:12
−
| [Open Science] Supporting dynamic community developed biological pipelines
+
| [Open Science] Supporting Dynamic Community Developed Biological Pipelines ([https://github.com/chapmanb/bcbb/blob/master/talks/bosc2014_bcbio/chapman_bcbio.pdf?raw=true slides])
 
| Brad Chapman
 
| Brad Chapman
 
|-
 
|-
 
| 15:12-15:30
 
| 15:12-15:30
−
| [Open Science] Open as a strategy for durability, reproducibility and scalability
+
| [Open Science] 'Open' as a Strategy for Durability, Reproducibility and Scalability ([https://youtu.be/TMzWRQUbO4U video], [http://www.open-bio.org/bosc2014/BOSC2014-OpenScience-05-Open_as_a_strategy-Rees.pdf slides])
 
| Jonathan Rees
 
| Jonathan Rees
 
|-
 
|-
Line 245: Line 246:
 
|-
 
|-
 
| 16:00-17:00
 
| 16:00-17:00
−
| '''Panel''': Reproducibility: Rewards and Challenges
+
| '''Panel''': Reproducibility: Rewards and Challenges ([https://youtu.be/65Rx89eZWpU video])
 
| Moderator: Brad Chapman;
 
| Moderator: Brad Chapman;
−
Panelists: Phil Bourne, Titus Brown, Varsha Khodiyar, Kay Thaney
+
Panelists: Phil Bourne, Titus Brown, Varsha Khodiyar, Kaitlin Thaney
 
|-
 
|-
 
| 17:00-17:10
 
| 17:00-17:10
Line 256: Line 257:
 
| [[BOSC_2014/BOFs|BOFs]]
 
| [[BOSC_2014/BOFs|BOFs]]
 
| Suggest a BOF topic [[BOSC_2014/BOFs|here!]]
 
| Suggest a BOF topic [[BOSC_2014/BOFs|here!]]
 +
|-
 +
| 19:00
 +
| Pay-your-own-way BOSC Saturday dinner: [http://www.summershackrestaurant.com/locations/boston/ Summer Shack], 50 Dalton St., Boston
 +
| Dinner now FULL. If you RSVPed yes but can't attend, please [http://doodle.com/iqhmez2rz57trazg edit your RSVP]
 
|-
 
|-
 
|}
 
|}
  
−
Note the ISMB reception starts at 17:30...
+
Note: the ISMB reception starts at 17:30...
  
 
----
 
----
Line 273: Line 278:
 
|-
 
|-
 
| P12
 
| P12
−
| ''Withdrawn''
+
| Advantages and challenges of using the Galaxy API within an integrated data analysis and visualization platform
−
| ''Withdrawn''
+
| Ilya Sytchev
 
|-
 
|-
 
| P13
 
| P13
−
| Connecting computational steps for NGS, and beyond.
+
| Connecting computational steps for NGS, and beyond. ([https://github.com/Novartis/railroadtracks source code])
 
| Laurent Gautier
 
| Laurent Gautier
 
|-
 
|-
Line 293: Line 298:
 
|-
 
|-
 
| P17
 
| P17
−
| Firehose in The Cancer Genome Atlas: Rigorous Open Science, At Scale
+
| ''Withdrawn''
−
| Michael Noble
+
| ''Withdrawn''
 
|-
 
|-
 
| P18
 
| P18
Line 316: Line 321:
 
| Maxime Déraspe
 
| Maxime Déraspe
 
|-
 
|-
−
| ...
+
| P24
−
| ...
+
| BioBuilds: A Model for Long Term Sustainability of Open Source Bioinformatics
−
| ...
+
| Chris Mueller
 +
|-
 +
| P25
 +
| GigaGalaxy: A GigaSolution for reproducible and sustainable genomic data publication and analysis ([http://figshare.com/articles/GigaGalaxy_A_GigaSolution_for_reproducible_and_sustainable_genomic_data_publication_and_analysis/713512 poster])
 +
| Scott Edmunds
 
|-
 
|-
 
|}
 
|}

Latest revision as of 16:51, 18 April 2017

BOSC logo

This page has links to all the publicly available talk slides, videos and posters. The videos are all on the BOSC 2014 YouTube playlist, with thanks to Google for sponsorship.

You can download the full program with abstracts (PDF); however, this wiki page is considered the definitive schedule and was updated with any last minute changes.

There was lots of activity under Twitter - our hashtag was #BOSC2014 and there are Storify Tweet archives for Day One, Day Two and during ISMB.

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) (video, slideshare, notes) 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 (video, slides) Frank Austin Nothaft [P1]
11:03-11:21 [Genome-Scale] A Framework for Benchmarking RNA-seq Pipelines (video, slides) Rory Kirchner
11:21-11:39 [Genome-Scale] New Frontiers of Genome Assembly with SPAdes 3.1 (video, slides) Andrey Prjibelski [P2]
11:39-11:57 [Genome-Scale] SigSeeker: An Ensemble for Analysis of Epigenetic Data (video, slides) Jens Lichtenberg [P3]
11:57-12:15 [Genome-Scale] Galaxy as an Extensible Job Execution Platform (video, slides) John Chilton
12:15-12:30 Open Bioinformatics Foundation (OBF) update (video) 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 (video, slides) Anthony Santella [P4]
14:18-14:36 [Visualization] BioJS: an Open Source Standard for Biological Visualisation (video) Manuel Corpas [P5]
14:36-14:54 [Visualization] Biodalliance: a Fast, Extensible Genome Browser (video) Thomas Down
14:54-15:12 [Visualization] TGAC Browser: Visualisation Solutions for Big Data in the Genomic Era (video, slides) Anil S. Thanki [P6]
15:12-15:30 [Visualization] Explore, Analyze, and Share Genomic Data Using Integrated Genome Browser (video, slides) 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 (video, slides) Arek Kasprzyk
16:12-16:24 [Updates] Biocaml: The OCaml Bioinformatics Library (video, slides) Ashish Agarwal
16:24-16:36 [Updates] BioRuby and Distributed Development (video, abstract, slides) Pjotr Prins
16:36-16:48 [Updates] Biopython Project Update (video, slides) Wibowo Arindrarto
16:48-17:00 [Updates] Shared Bioinformatics Databases Within Unipro UGENE (video, slides) 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 (video, slides) Karthik Ram
17:07-17:12 [Lightning] Tripal: an Open Source Toolkit for Building Genomic and Genetic Data Websites and Databases (video, slides) Margaret Staton
17:14-17:19 [Lightning] PLUTo: Phyloinformatic Literature Unlocking Tools (video, slides) Ross Mounce
17:21-17:26 [Lightning] A Publication Model that Aligns with the Key Open Source Software Principles (video, slides) 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 Friday BOSC dinner (FULL)

The Asgard Irish Pub and Restaurant, 350 Massachusetts Avenue, Cambridge, MA (1.2 miles north of the convention center).

Only those who have already RSVPed 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 (video, slides) Brad Chapman
9:15-10:15 Keynote: Biomedical Research as an Open Digital Enterprise (video, slidesshare) 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 (video, slides) Weijun Luo [P9]
11:03-11:21 [Interoperability] Use of Semantically Annotated Resources in the Mobyle2 Web Framework (video, slides) Hervé Ménager
11:21-11:39 [Interoperability] Towards Ubiquitous OWL Computing: Simplifying Programmatic Authoring of and Querying with OWL Axioms (video, slides) Hilmar Lapp
11:39-11:57 [Interoperability] Integrating Taverna Player into Scratchpads (video, slideshare, poster) Robert Haines [P10]
11:57-12:15 [Interoperability] Small Tools for Bioinformatics (video, slides, abstract, manifesto) 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 (video, slideshare) Carole Goble [P11]
14:18-14:36 [Open Science] Arvados: Achieving Computational Reproducibility and Data Provenance in Large-Scale Genomic Analyses (video, slides) Brett Smith
14:36-14:54 [Open Science] Enhancing the Galaxy Experience through Community Involvement (video, slides) Daniel Blankenberg
14:54-15:12 [Open Science] Supporting Dynamic Community Developed Biological Pipelines (slides) Brad Chapman
15:12-15:30 [Open Science] 'Open' as a Strategy for Durability, Reproducibility and Scalability (video, slides) Jonathan Rees
15:30-16:00 Coffee Break
16:00-17:00 Panel: Reproducibility: Rewards and Challenges (video) Moderator: Brad Chapman;

Panelists: Phil Bourne, Titus Brown, Varsha Khodiyar, Kaitlin 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!
19:00 Pay-your-own-way BOSC Saturday dinner: Summer Shack, 50 Dalton St., Boston Dinner now FULL. If you RSVPed yes but can't attend, please edit your RSVP

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 Advantages and challenges of using the Galaxy API within an integrated data analysis and visualization platform Ilya Sytchev
P13 Connecting computational steps for NGS, and beyond. (source code) 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 Withdrawn Withdrawn
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
P24 BioBuilds: A Model for Long Term Sustainability of Open Source Bioinformatics Chris Mueller
P25 GigaGalaxy: A GigaSolution for reproducible and sustainable genomic data publication and analysis (poster) Scott Edmunds


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

Retrieved from "https://www.open-bio.org/w/index.php?title=BOSC_2014_Schedule&oldid=4738"