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Difference between revisions of "BOSC 2014 Schedule"

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__NOTOC__
 
__NOTOC__
 
[[File:Pear.png|100px|right|BOSC logo|link=BOSC_2014]]
 
[[File:Pear.png|100px|right|BOSC logo|link=BOSC_2014]]
−
This is a working draft. Once finalised, you will also be able to:
 
  
−
- Download schedule as PDF
+
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.
  
−
- Download the complete program.
+
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.
 +
 
 +
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 11: Line 12:
 
See [[Codefest_2014 | Codefest 2014]] for details.
 
See [[Codefest_2014 | Codefest 2014]] for details.
  
−
== BOSC ==
+
== BOSC Day 1: Friday, 11 July 2014 ==
−
 
 
−
=== BOSC Day 1: Friday 11 July 2014 ===
 
  
 
{| border="1" cellspacing="0" cellpadding="7"
 
{| border="1" cellspacing="0" cellpadding="7"
 
! Time
 
! Time
 
! Topic
 
! Topic
−
! Speaker, Moderator, or notes
+
! Speaker [Poster], Moderator, or notes
 
|-  
 
|-  
−
| 7:30-9:00
+
| '''7:30-9:00'''
 
| '''Registration'''
 
| '''Registration'''
 
| Early arrival is recommended as there are usually long lines
 
| Early arrival is recommended as there are usually long lines
 
|-  
 
|-  
 
| 9:00-9:15
 
| 9:00-9:15
−
| Introduction and welcome
+
| Introduction and Welcome
−
| Peter Cock and/or Nomi Harris (Chairs, BOSC 2014)
+
|Nomi Harris and/or Peter Cock (Chairs, BOSC 2014)
 
|-
 
|-
 
| 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 36: Line 35:
 
|
 
|
 
|-
 
|-
−
| 10:45-12:30
+
| ''10:45-12:30''
−
| ''Session: Genome-scale Data and Beyond''
+
| '''''Session: Genome-scale Data and Beyond'''''
−
| Chair: TBC
+
| Chair: Chris Fields
 +
|--
 +
| 10:45-11:03
 +
| [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]
 +
|-
 +
| 11:03-11:21
 +
| [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
 +
|-
 +
| 11:21-11:39
 +
| [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]
 
|-
 
|-
−
| '''12:30-1:30'''
+
| 11:39-11:57
 +
| [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]
 +
|-
 +
| 11:57-12:15
 +
| [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
 +
|-
 +
| 12:15-12:30
 +
| [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation (OBF) update] ([https://youtu.be/1oSTb8ZAxec video])
 +
| Hilmar Lapp (OBF President)
 +
|-
 +
| '''12:30-13:30'''
 
| '''Lunch'''
 
| '''Lunch'''
−
| (And posters)
+
| (and poster session)
 
|-
 
|-
−
| 1:00-2:00
+
| '''13:00-14:00'''
−
| '''Poster Session and Birds of a Feather'''
+
| '''Poster Session and Birds of a Feather''' (overlapping with lunch)
−
| (Overlapping with Lunch)
+
| Suggest a BOF topic [[BOSC_2014/BOFs|here!]]
 
|-
 
|-
−
| 14:00-15:30
+
| ''14:00-15:30''
−
| ''Session: Visualization''
+
| '''''Session: Visualization'''''
−
| Chair: Chris Fields
+
| Chair: Rob Davey
 +
|-
 +
| 14:00-14:18
 +
| [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]
 +
|-
 +
| 14:18-14:36
 +
| [Visualization] BioJS: an Open Source Standard for Biological Visualisation ([https://youtu.be/aHtXNW-I2U0 video])
 +
| Manuel Corpas [P5]
 +
|-
 +
| 14:36-14:54
 +
| [Visualization] Biodalliance: a Fast, Extensible Genome Browser ([https://youtu.be/l4Z7wsppCaM video])
 +
| Thomas Down
 +
|-
 +
| 14:54-15:12
 +
| [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]
 +
|-
 +
| 15:12-15:30
 +
| [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
 
|-
 
|-
 
| '''15:30-16:00'''
 
| '''15:30-16:00'''
Line 56: Line 99:
 
|
 
|
 
|-
 
|-
−
| 16:00-17:00
+
| ''16:00-17:00''
−
| ''Session: Bioinformatics Open Source Project Updates''
+
| '''''Session: Bioinformatics Open Source Project Updates'''''
 +
| Chair: Peter Cock
 +
|-
 +
| 16:00-16:12
 +
| [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])
 +
| Arek Kasprzyk
 +
|-
 +
| 16:12-16:24
 +
| [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
 +
|-
 +
| 16:24-16:36
 +
| [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
 +
|-
 +
| 16:36-16:48
 +
| [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
 +
|-
 +
| 16:48-17:00
 +
| [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]
 +
|-
 +
| ''17:00-17:30''
 +
| '''''Session: Lightning Talks'''''
 
| Chair: Peter Cock
 
| Chair: Peter Cock
 
|-
 
|-
−
| 17:00-18:00
+
| 17:00-17:05
−
| Lightning Talks followed by [[BOSC_2014/BOFs|BOFs]]
+
| [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
 +
|-
 +
| 17:07-17:12
 +
| [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
 +
|-
 +
| 17:14-17:19
 +
| [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
 +
|-
 +
| 17:21-17:26
 +
| [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]
 +
|-
 +
| 17:27-17:30
 +
| Announcements
 +
| Nomi Harris and/or Peter Cock
 +
|-
 +
| 17:30-18:30
 +
| '''[[BOSC_2014/BOFs|BOFs]]'''
 
| Suggest a BOF topic [[BOSC_2014/BOFs|here!]]
 
| Suggest a BOF topic [[BOSC_2014/BOFs|here!]]
 
|-
 
|-
 
| 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).
 +
| Only those who have already RSVPed will be admitted.
 
|-  
 
|-  
 
|}
 
|}
Line 73: Line 161:
 
[[File:Pear.png|100px|right|BOSC logo|link=BOSC_2014]]
 
[[File:Pear.png|100px|right|BOSC logo|link=BOSC_2014]]
  
−
=== BOSC Day 2: Saturday 12 July 2014 ===
+
== BOSC Day 2: Saturday, 12 July 2014 ==
  
 
{| border="1" cellspacing="0" cellpadding="7"
 
{| border="1" cellspacing="0" cellpadding="7"
Line 80: Line 168:
 
! 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]] ([https://youtu.be/EuWgm6V9DgI video], [https://docs.google.com/presentation/d/114yvrK0Veasc_ns_rg484j2xxRi1h7wNlU2XKONuUqY/edit?usp=sharing slides])
 
| Brad Chapman
 
| Brad Chapman
 
|-
 
|-
−
| 9:00 - 9:15
+
| 9:15-10:15
−
| [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation (OBF) update]
+
| | [[BOSC_2014_Keynote_Speakers|Keynote: Biomedical Research as an Open Digital Enterprise]] ([https://youtu.be/VmRNkdHKJgA video], [http://www.slideshare.net/pebourne/bosc2014 slidesshare])
−
| Hilmar Lapp (President, Open Bioinformatics Foundation)
 
−
|-
 
−
| 9:15 - 10:15
 
−
| | [[BOSC_2014_Keynote_Speakers|Keynote: Biomedical Research as an Open Digital Enterprise]]
 
 
| Philip Bourne  
 
| Philip Bourne  
 
|-
 
|-
Line 100: Line 184:
 
|
 
|
 
|-
 
|-
−
| 10:45-12:30
+
| ''10:45-12:30''
−
| ''Session: Open Science and Reproducible Research''
+
| '''''Session: Software Interoperability'''''
−
| Chair: Hilmar Lapp
+
| Chair: Raoul Bonnal
 +
|-
 +
| 10:45-11:03
 +
| [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]
 +
|-
 +
| 11:03-11:21
 +
| [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
 +
|-
 +
| 11:21-11:39
 +
| [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
 +
|-
 +
| 11:39-11:57
 +
| [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]
 +
|-
 +
| 11:57-12:15
 +
| [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
 
|-
 
|-
 
| '''12:30-13:30'''
 
| '''12:30-13:30'''
 
| '''Lunch'''
 
| '''Lunch'''
−
| (And posters)
+
| (and poster session)
 +
|-
 +
| '''13:00-14:00'''
 +
| '''Poster Session and Birds of a Feather''' (overlapping with lunch)
 +
| Suggest a BOF topic [[BOSC_2014/BOFs|here!]]
 
|-
 
|-
−
| '''12:30-13:30'''
+
| ''14:00-15:30''
−
| '''Poster Session''
+
| '''''Session: Open Science and Reproducible Research'''''
−
| (Overlapping with Lunch)
+
| Chair: Hilmar Lapp
 +
|-
 +
 
 +
| 14:00-14:18
 +
| [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]
 +
|-
 +
| 14:18-14:36
 +
| [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
 +
|-
 +
| 14:36-14:54
 +
| [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
 +
|-
 +
| 14:54-15:12
 +
| [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
 
|-
 
|-
−
| 13:30-15:30
+
| 15:12-15:30
−
| ''Session: Software Interoperability''
+
| [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])
−
| Chair: TBA
+
| Jonathan Rees
 
|-
 
|-
 
| '''15:30-16:00'''
 
| '''15:30-16:00'''
Line 120: Line 245:
 
|
 
|
 
|-
 
|-
−
| 16:00-16:15
+
| 16:00-17:00
−
| ''Session: Software Interoperability (continued)''
+
| '''Panel''': Reproducibility: Rewards and Challenges ([https://youtu.be/65Rx89eZWpU video])
−
| Chair: TBA
+
| Moderator: Brad Chapman;
 +
Panelists: Phil Bourne, Titus Brown, Varsha Khodiyar, Kaitlin Thaney
 
|-
 
|-
−
| 16:15-17:05
+
| 17:00-17:10
−
| '''Panel''': Reproducibility: Rewards and Challenges
+
| Presentation of Student Travel Awards & Concluding Remarks
−
| Moderator: Brad Chapman; Panelists: Phil Bourne, Titus Brown, Varsha Khodiyar, Kay Thaney
+
| Nomi Harris (Co-Chair, BOSC 2014)
 
|-
 
|-
−
| 17:05-17:15
+
| 17:10-18:00
−
| Presentation of Student Travel Awards
 
−
| Peter Cock and/or Nomi Harris (Chairs, BOSC 2014)
 
−
|-
 
−
| 17:20-18:00
 
 
| [[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 144: Line 270:
 
=== Posters ===
 
=== Posters ===
  
−
Shared links to presented posters will be posted here:
+
If the speaker also gave a talk, any poster link will be above (posters 1 to 11). This table lists poster-only presentations.
  
 
{| border="1" cellspacing="0" cellpadding="7"
 
{| border="1" cellspacing="0" cellpadding="7"
 +
! Poster
 
! Title
 
! Title
 
! Presenter
 
! 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. ([https://github.com/Novartis/railroadtracks 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
−
| A.N. Other et al.
+
| 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 ([http://figshare.com/articles/GigaGalaxy_A_GigaSolution_for_reproducible_and_sustainable_genomic_data_publication_and_analysis/713512 poster])
 +
| Scott Edmunds
 
|-
 
|-
 
|}
 
|}
  
 +
 +
----
 +
{|
 +
|rowspan="2"| [[File:Eagle_logo_2013.jpg‎|120px|left|Eagle Genomics logo|link=http://www.eaglegenomics.com/]]
 +
|rowspan="2"|             
 +
|rowspan="2"| [[File:gigascience-07.png‎|175px|center|GigaScieece|link=http://www.gigasciencejournal.com/]]
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|rowspan="2"|         
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| [[File:Curoverse.png|175px|center|Curoverse logo|link=http://curoverse.com]]
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|-
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| [[File: Arvados.png|150px|center|Arvados logo|link=http://arvados.org]]
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|rowspan="2"|         
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|rowspan="2"| [[File:google-logo11w.png‎|205px|center|Google|link=http://www.google.com/]]
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|}
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We thank [http://www.eaglegenomics.com/ Eagle Genomics] for sponsoring the BOSC Student Travel Awards again this year, and welcome the open access journal [http://www.gigasciencejournal.com/ GigaScience], and [http://curoverse.com Curoverse] (the team behind the open source platform [http://arvados.org Arvados]) as new sponsors for BOSC 2014.
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We are grateful to [http://www.google.com/ Google] for their generous support for videorecording BOSC 2014.
  
 
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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

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