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Difference between revisions of "BOSC 2013 Schedule"

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m (→‎Day 2: Saturday, July 20)
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|-  
 
|-  
 
| 9:00-9:15
 
| 9:00-9:15
−
| Introduction and welcome ([http://www.open-bio.org/bosc2013/day1/BOSC2013_Intro_Nomi_Harris.pdf PDF])
+
| Introduction and welcome ([http://www.open-bio.org/bosc2013/day1/BOSC2013_Intro_Nomi_Harris.pdf PDF], [http://www.youtube.com/watch?v=eODK9lcniK8 YouTube])
 
| Nomi Harris (Chair, BOSC 2013)
 
| Nomi Harris (Chair, BOSC 2013)
 
|-
 
|-
 
| 9:15-10:15
 
| 9:15-10:15
−
| [Keynote] Network ready research: The role of open source and open thinking ([http://www.slideshare.net/CameronNeylon/network-enabled-research-the-role-of-open-source-and-open-thinking SlideShare])
+
| [Keynote] Network ready research: The role of open source and open thinking ([http://www.slideshare.net/CameronNeylon/network-enabled-research-the-role-of-open-source-and-open-thinking SlideShare] [http://www.youtube.com/watch?v=zZKc7V4ZHOU YouTube])
 
| Cameron Neylon (Public Library of Science)
 
| Cameron Neylon (Public Library of Science)
 
|-
 
|-
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|-
 
|-
 
| 11:15
 
| 11:15
−
| [Open Science] Empowering Cancer Research Through Open Development: The National Cancer Informatics Program
+
| [Open Science] Empowering Cancer Research Through Open Development: The National Cancer Informatics Program Open Development Initiative ([http://www.open-bio.org/bosc2013/day1/BOSC2013_NCIP_-_Juli_Klemm.pdf PDF])
−
Open Development Initiative ([http://www.open-bio.org/bosc2013/day1/BOSC2013_NCIP_-_Juli_Klemm.pdf PDF])
 
 
| Juli Klemm
 
| Juli Klemm
 
|-
 
|-
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|-
 
|-
 
| 2:00
 
| 2:00
−
| [Visualization] Refinery Platform - Integrating Visualization and Analysis of Large-Scale Biological Data
+
| [Visualization] Refinery Platform - Integrating Visualization and Analysis of Large-Scale Biological Data ([http://www.open-bio.org/bosc2013/day1/BOSC2013_Refinery_-_Nils_Gehlenborg.pdf PDF])
 
| Nils Gehlenborg
 
| Nils Gehlenborg
 
|-
 
|-
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| [Visualization] MetaSee: An interactive visualization toolbox for metagenomic sample analysis and comparison ([http://www.open-bio.org/bosc2013/day2/BOSC2013_MetaSee_-_Xiaoquan_Su.pdf PDF])
 
| [Visualization] MetaSee: An interactive visualization toolbox for metagenomic sample analysis and comparison ([http://www.open-bio.org/bosc2013/day2/BOSC2013_MetaSee_-_Xiaoquan_Su.pdf PDF])
 
| Xiaoquan Su (delayed to Day 2)
 
| Xiaoquan Su (delayed to Day 2)
 +
|-
 +
| 2:25
 +
| [Substitute Talk] Genomics applications in the cloud with the DNAnexus Platform ([http://www.open-bio.org/bosc2013/day1/BOSC2013-DNAnexus_Andrew_Kislyuk.pdf PDF])
 +
| Andrey Kislyuk
 
|-
 
|-
 
| 2:40
 
| 2:40
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|-
 
|-
 
| 2:55
 
| 2:55
−
| [Visualization] Genomic Visualization Everywhere with Dalliance
+
| [Visualization] Genomic Visualization Everywhere with Dalliance ([http://www.biodalliance.org/people/thomas/dalliance-talk-201307 Slides])
 
| Thomas Down
 
| Thomas Down
 
|-
 
|-
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|-
 
|-
 
| 4:15
 
| 4:15
−
| [Project Updates] Biopython project update ([http://www.open-bio.org/bosc2013/day1/BOSC2013_Biopython_Update_-_Peter_Cock.pdf PDF])
+
| [Project Updates] Biopython project update 2013 ([http://www.open-bio.org/bosc2013/day1/BOSC2013_Biopython_Update_-_Peter_Cock.pdf PDF], [http://www.slideshare.net/pjacock/biopython-update-bosc2013/ SlideShare])
 
| Peter Cock
 
| Peter Cock
 
|-
 
|-
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|-
 
|-
 
| 8:50
 
| 8:50
−
| Codefest 2013 Report ([http://chapmanb.github.io/bcbb/talks/codefest2013_report/codefest2013_report.html SlideShare])
+
| Codefest 2013 Report ([http://chapmanb.github.io/bcbb/talks/codefest2013_report/codefest2013_report.html SlideShare] [http://www.youtube.com/watch?v=dtw4fKTSrUs YouTube])
 
| Brad Chapman
 
| Brad Chapman
 
|-
 
|-
 
| 9:00
 
| 9:00
−
| [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation:]  A Community For, By, and Of You
+
| [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation:]  A Community For, By, and Of You ([http://www.slideshare.net/hlapp/obf-address-bosc2013 SlideShare] [http://www.youtube.com/watch?v=DiReTX3FoLM YouTube])
 
| Hilmar Lapp (President, Open Bioinformatics Foundation)
 
| Hilmar Lapp (President, Open Bioinformatics Foundation)
 
|-
 
|-
 
| 9:15
 
| 9:15
−
| [Keynote] Biological sequence analysis in the post-data era
+
| [Keynote] Biological sequence analysis in the post-data era ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Keynote_-_Sean_Eddy.pdf PDF], [http://www.youtube.com/watch?v=nUwQqwl_VlI YouTube])
 
| Sean Eddy (Janelia Farm)
 
| Sean Eddy (Janelia Farm)
 
|-
 
|-
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|-
 
|-
 
| 11:10
 
| 11:10
−
| [Interoperability] Taverna Components: Semantically annotated and shareable units of functionality ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Taverna_Components_-_Donal_Fellows.pdf PDF])
+
| [Interoperability] Taverna Components: Semantically annotated and shareable units of functionality ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Taverna_Components_-_Donal_Fellows.pdf PDF] [http://www.youtube.com/watch?v=9voXGYeEcyw YouTube])
 
| Donal Fellows
 
| Donal Fellows
 
|-
 
|-
 
| 11:35
 
| 11:35
−
| [Interoperability] UGENE Workflow Designer – flexible control and extension of pipelines with scripts ([http://www.open-bio.org/bosc2013/day2/BOSC2013_UGENE_-_Yuriy_Vaskin.pdf PDF])
+
| [Interoperability] UGENE Workflow Designer – flexible control and extension of pipelines with scripts ([http://www.open-bio.org/bosc2013/day2/BOSC2013_UGENE_-_Yuriy_Vaskin.pdf PDF] [http://www.youtube.com/watch?v=eiqNcgsdDik YouTube])
 
| Yuriy Vaskin
 
| Yuriy Vaskin
 
|-
 
|-
 
| 11:50
 
| 11:50
−
| [Interoperability] Reproducible Quantitative Transcriptome Analysis with Oqtans ([http://www.open-bio.org/bosc2013/day2/BOSC2013_oqtans_-_Vipin_Sreedharan.pdf PDF])
+
| [Interoperability] Reproducible Quantitative Transcriptome Analysis with Oqtans ([http://www.open-bio.org/bosc2013/day2/BOSC2013_oqtans_-_Vipin_Sreedharan.pdf PDF] [http://www.youtube.com/watch?v=Q3nmrvS-Z8o YouTube])
 
| Vipin T. Sreedharan
 
| Vipin T. Sreedharan
 
|-
 
|-
 
| 12:05
 
| 12:05
−
| [Visualization] MetaSee: An interactive visualization toolbox for metagenomic sample analysis and comparison ([http://www.open-bio.org/bosc2013/day2/BOSC2013_MetaSee_-_Xiaoquan_Su.pdf PDF])
+
| [Visualization] MetaSee: An interactive visualization toolbox for metagenomic sample analysis and comparison ([http://www.open-bio.org/bosc2013/day2/BOSC2013_MetaSee_-_Xiaoquan_Su.pdf PDF] [http://www.youtube.com/watch?v=_ZNGm-cZACk YouTube])
 
| Xiaoquan Su (postponed from day 1)
 
| Xiaoquan Su (postponed from day 1)
 
|-
 
|-
 
| 12:15
 
| 12:15
−
| [Interoperability] PhyloCommons: community storage, annotation and reuse of phylogenies ([http://www.open-bio.org/bosc2013/day2/BOSC2013_PhyloCommons_-_Hilmar_Lapp.pdf PDF])
+
| [Interoperability] PhyloCommons: community storage, annotation and reuse of phylogenies ([http://www.open-bio.org/bosc2013/day2/BOSC2013_PhyloCommons_-_Hilmar_Lapp.pdf PDF], [http://www.slideshare.net/hlapp/phylo-commons-bosc2013 SlideShare] [http://www.youtube.com/watch?v=SalhhoE6X9s YouTube])
 
| Hilmar Lapp
 
| Hilmar Lapp
 
|-
 
|-
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|-
 
|-
 
| 12:25
 
| 12:25
−
| [Interoperability] Rubra - flexible distributed pipelines for bioinformatics ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Rubra_-_Claire_Sloggett.pdf PDF])
+
| [Interoperability] Rubra - flexible distributed pipelines for bioinformatics ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Rubra_-_Claire_Sloggett.pdf PDF], [http://www.youtube.com/watch?v=A9sdkEancJA YouTube])
 
| Clare Sloggett
 
| Clare Sloggett
 
|-
 
|-
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|-
 
|-
 
| 1:30
 
| 1:30
−
| [Cloud/Genome-Scale] Towards Enabling Big Data and Federated Computing in the Cloud
+
| [Cloud/Genome-Scale] Towards Enabling Big Data and Federated Computing in the Cloud ([http://www.open-bio.org/bosc2013/day2/BOSC2013_CloudMan_-_Enis_Afgan.pdf PDF])
 
| Enis Afgan
 
| Enis Afgan
 
|-
 
|-
 
| 1:45
 
| 1:45
−
| [Cloud/Genome-Scale] MyGene.info: Making Elastic and Extensible Gene­-centric Web Services
+
| [Cloud/Genome-Scale] MyGene.info: Making Elastic and Extensible Gene­-centric Web Services ([http://www.open-bio.org/bosc2013/day2/BOSC2013_MyGene_-_Chunlei_Wu.pdf PDF])
 
| Chunlei Wu
 
| Chunlei Wu
 
|-
 
|-
 
| 2:00
 
| 2:00
−
| [Cloud/Genome-Scale] An update on the Seal Hadoop-based sequence processing toolbox
+
| [Cloud/Genome-Scale] An update on the Seal Hadoop-based sequence processing toolbox ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Seal_Hadoop_-_Luca_Pireddu.pdf PDF] [http://www.youtube.com/watch?v=6QEPMj5AIs4 YouTube])
 
| Luca Pireddu
 
| Luca Pireddu
 
|-
 
|-
 
| 2:15
 
| 2:15
−
| [Cloud/Genome-Scale] Open Source Configuration of Bioinformatics Infrastructure
+
| [Cloud/Genome-Scale] Open Source Configuration of Bioinformatics Infrastructure ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Infrastructure_-_John_Chilton.pdf PDF] [http://www.youtube.com/watch?v=WoiNyaFVOeE YouTube])
 
| John Chilton
 
| John Chilton
 
|-
 
|-
 
| 2:30
 
| 2:30
−
| [Cloud/Genome-Scale] An Open Source Framework for Gene Prioritization
+
| [Cloud/Genome-Scale] GEPETTO: An Open Source Framework for Gene Prioritization ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Gepetto_-_Vincent_Walter.pdf PDF] [http://www.youtube.com/watch?v=J6E_xu_kRdA YouTube])
−
| Hoan Nguyen / Vincent Walter
+
| Vincent Walter
 
|-
 
|-
 
| 2:55
 
| 2:55
−
| [Cloud/Genome-Scale] RAMPART: an automated de novo assembly pipeline
+
| [Cloud/Genome-Scale] RAMPART: an automated de novo assembly pipeline ([http://www.open-bio.org/bosc2013/day2/BOSC2013_RAMPART_-_Daniel_Mapleson.pdf PDF] [http://www.youtube.com/watch?v=mojcGfZWZtg YouTube])
 
| Daniel Mapleson
 
| Daniel Mapleson
 
|-
 
|-
 
| 3:10
 
| 3:10
−
| [Cloud/Genome-Scale] OmicsConnect: flexible multi-omics data capture and integration tools for high-throughput biology
+
| [Cloud/Genome-Scale] OmicsConnect: flexible multi-omics data capture and integration tools for high-throughput biology ([http://www.open-bio.org/bosc2013/day2/BOSC2013_OmicConnect_-_Joeri_van_der_Velde.pdf PDF])
 
| Joeri van der Velde
 
| Joeri van der Velde
 
|-
 
|-
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|-
 
|-
 
| 4:00
 
| 4:00
−
| [Translational] Community development of human variant calling and validation pipelines ([http://chapmanb.github.io/bcbb/talks/bosc2013_bcbio_nextgen/chapmanb_bosc2013_bcbio.html slides])
+
| [Translational] Community development of human variant calling and validation pipelines ([http://chapmanb.github.io/bcbb/talks/bosc2013_bcbio_nextgen/chapmanb_bosc2013_bcbio.html slides] [http://www.youtube.com/watch?v=dT5UEU0xF1Q YouTube])
 
| Brad Chapman
 
| Brad Chapman
 
|-
 
|-
 
| 4:25
 
| 4:25
−
| [Translational] Understanding Cancer Genomes Using Galaxy
+
| [Translational] Understanding Cancer Genomes Using Galaxy ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Galaxy_-_Jeremey_Goecks.pdf PDF] [http://www.youtube.com/watch?v=zoSYCLycpMk YouTube])
 
| Jeremy Goecks
 
| Jeremy Goecks
 
|-
 
|-
 
| 4:40-5:30
 
| 4:40-5:30
−
| '''Panel''': Strategies for Funding and Maintaining Open Source Software
+
| '''Panel''': Strategies for Funding and Maintaining Open Source Software ([http://www.youtube.com/watch?v=UDBOuuclDsQ YouTube])
 
| Moderator: Brad Chapman
 
| Moderator: Brad Chapman
 
Panelists: Peter Cock, Sean Eddy, Carole Goble,  Scott Markel, Jean Peccoud
 
Panelists: Peter Cock, Sean Eddy, Carole Goble,  Scott Markel, Jean Peccoud
 
|-
 
|-
 
| 5:30-5:40
 
| 5:30-5:40
−
| Presentation of Student Travel Awards
+
| Presentation of Student Travel Awards ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Student_travel_awards.pdf PDF])
 
| Nomi Harris
 
| Nomi Harris
 
|-
 
|-
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|-
 
|-
 
|}
 
|}
 +
 +
----
 +
 +
= Posters =
 +
 +
This table currently only lists presented posters for which the authors have shared the PDF.
 +
 +
{| border="1" cellspacing="0" cellpadding="7"
 +
! Title
 +
! Presenter
 +
|-
 +
| BIOINFO-C: C-based Bioinformatics Library and Web Application Framework ([http://bioinfoc.ch/doc/BioinfoC_lib_webfile_poster_BOSC_2013.pdf PDF])
 +
| Detlef Wolf
 +
|-
 +
| Reproducible Quantitative Transcriptome Analysis with ocqtans ([http://www.open-bio.org/bosc2013/posters/BOSC2013_oqtans_vipin.pdf PDF])
 +
| Vipin T. Sreedharan
 +
|}
 +
 +
 +
----
  
 
You can also:
 
You can also:

Latest revision as of 16:16, 10 September 2013


BOSC logo

You can also:

- Download schedule as PDF (A4 format).

- Download the complete program

Day 1: Friday, July 19

Time Topic Speaker or Moderator
7:30-9:00 Registration (Early arrival is recommended as there are usually long lines) Registration
9:00-9:15 Introduction and welcome (PDF, YouTube) Nomi Harris (Chair, BOSC 2013)
9:15-10:15 [Keynote] Network ready research: The role of open source and open thinking (SlideShare YouTube) Cameron Neylon (Public Library of Science)
10:15-10:45 Coffee Break
10:45-12:30 Session: Open Science Chair: Hilmar Lapp
10:45 [Open Science] Open Science Data Framework: A Cloud enabled system to store, access, and analyze scientific data (PDF) Anup Mahurkar
11:00 [Open Science] myExperiment Research Objects: Beyond Workflows and Packs (PDF, SlideShare) Stian Soiland-Reyes
11:15 [Open Science] Empowering Cancer Research Through Open Development: The National Cancer Informatics Program Open Development Initiative (PDF) Juli Klemm
11:30 [Open Science] DNAdigest - a not-for-profit organisation to promote and enable open-access sharing of genomics data (PDF) Fiona Nielsen
11:45 [Open Science] Jug: Reproducible Research in Python (PDF) Luis Pedro Coelho
11:50 [Open Science] OpenLabFramework: A Next-Generation Open-Source Laboratory Information Management System for Efficient Sample Tracking (PDF) Markus List
11:55 [Open Science] Ten Simple Rules for the Open Development of Scientific Software (followed by discussion) (PDF) Andreas Prlic, Jim Procter, Hilmar Lapp
12:30-1:30 Lunch
1:00-2:00 Poster Session I
2:00-3:30 Session: Visualization Chair: Jan Aerts
2:00 [Visualization] Refinery Platform - Integrating Visualization and Analysis of Large-Scale Biological Data (PDF) Nils Gehlenborg
2:25 [Visualization] MetaSee: An interactive visualization toolbox for metagenomic sample analysis and comparison (PDF) Xiaoquan Su (delayed to Day 2)
2:25 [Substitute Talk] Genomics applications in the cloud with the DNAnexus Platform (PDF) Andrey Kislyuk
2:40 [Visualization] DGE-Vis: Visualisation of RNA-seq data for Differential Gene Expression analysis (PDF) David Powell
2:55 [Visualization] Genomic Visualization Everywhere with Dalliance (Slides) Thomas Down
3:10 [Visualization] Robust quality control of Next Generation Sequencing alignment data (PDF) Konstantin Okonechnikov
3:25 [Visualization] Visualizing bacterial sequencing data with GenomeView (PDF) Thomas Abeel
3:30-4:00 Coffee Break
4:00-5:15 Session: Bioinformatics Open Source Project Updates Chair: Hans-Rudolf Hotz
4:00 [Project Updates] BioRuby project updates - power of modularity in the community-based open source development model (PDF) Toshiaki Katayama
4:15 [Project Updates] Biopython project update 2013 (PDF, SlideShare) Peter Cock
4:30 [Project Updates] InterMine - Collaborative Data Mining (PDF) Alex Kalderimis
4:45 [Project Updates] The GenoCAD 2.2 Grammar Editor (PDF) Jean Peccoud
5:00 [Project Updates] Improvements and new features in the 7th major release of the Bio-Linux distro (PDF) Timothy Booth
5:15 Announcements Nomi Harris (Chair, BOSC 2013)
5:20-6:30 Poster Session II
5:20-6:30 BOFs -- suggest a BOF topic here!
7:00 Pay-your-own-way BOSC dinner, Hendrik’s, Straße des 17. Juni 13, 10623 Berlin. (Space limited--you must RSVP to attend.)


BOSC logo

Day 2: Saturday, July 20

Time Topic Speaker or Moderator
8:45 Announcements Nomi Harris
8:50 Codefest 2013 Report (SlideShare YouTube) Brad Chapman
9:00 Open Bioinformatics Foundation: A Community For, By, and Of You (SlideShare YouTube) Hilmar Lapp (President, Open Bioinformatics Foundation)
9:15 [Keynote] Biological sequence analysis in the post-data era (PDF, YouTube) Sean Eddy (Janelia Farm)
10:15-10:45 Coffee Break
10:45-12:30 Session: Software Interoperability Chair: Jeremy Goecks
10:45 [Interoperability] BioBlend - Enabling Pipeline Dreams (PDF) Enis Afgan
11:10 [Interoperability] Taverna Components: Semantically annotated and shareable units of functionality (PDF YouTube) Donal Fellows
11:35 [Interoperability] UGENE Workflow Designer – flexible control and extension of pipelines with scripts (PDF YouTube) Yuriy Vaskin
11:50 [Interoperability] Reproducible Quantitative Transcriptome Analysis with Oqtans (PDF YouTube) Vipin T. Sreedharan
12:05 [Visualization] MetaSee: An interactive visualization toolbox for metagenomic sample analysis and comparison (PDF YouTube) Xiaoquan Su (postponed from day 1)
12:15 [Interoperability] PhyloCommons: community storage, annotation and reuse of phylogenies (PDF, SlideShare YouTube) Hilmar Lapp
12:20 [Interoperability] GEMBASSY: an EMBOSS associated package for genome analysis using G-language SOAP/REST web services (PDF) Hidetoshi Itaya
12:25 [Interoperability] Rubra - flexible distributed pipelines for bioinformatics (PDF, YouTube) Clare Sloggett
12:30-1:30 Lunch
12:30-1:30 Poster Session III
1:30-3:30 Session: Cloud and Genome-Scale Computing Chair: Peter Cock
1:30 [Cloud/Genome-Scale] Towards Enabling Big Data and Federated Computing in the Cloud (PDF) Enis Afgan
1:45 [Cloud/Genome-Scale] MyGene.info: Making Elastic and Extensible Gene­-centric Web Services (PDF) Chunlei Wu
2:00 [Cloud/Genome-Scale] An update on the Seal Hadoop-based sequence processing toolbox (PDF YouTube) Luca Pireddu
2:15 [Cloud/Genome-Scale] Open Source Configuration of Bioinformatics Infrastructure (PDF YouTube) John Chilton
2:30 [Cloud/Genome-Scale] GEPETTO: An Open Source Framework for Gene Prioritization (PDF YouTube) Vincent Walter
2:55 [Cloud/Genome-Scale] RAMPART: an automated de novo assembly pipeline (PDF YouTube) Daniel Mapleson
3:10 [Cloud/Genome-Scale] OmicsConnect: flexible multi-omics data capture and integration tools for high-throughput biology (PDF) Joeri van der Velde
3:30-4:00 Coffee Break
4:00-4:40 Session: Translational Genomics Chair: Nomi Harris
4:00 [Translational] Community development of human variant calling and validation pipelines (slides YouTube) Brad Chapman
4:25 [Translational] Understanding Cancer Genomes Using Galaxy (PDF YouTube) Jeremy Goecks
4:40-5:30 Panel: Strategies for Funding and Maintaining Open Source Software (YouTube) Moderator: Brad Chapman

Panelists: Peter Cock, Sean Eddy, Carole Goble, Scott Markel, Jean Peccoud

5:30-5:40 Presentation of Student Travel Awards (PDF) Nomi Harris
5:40-6:40 BOFs -- suggest a BOF topic here!

Posters

This table currently only lists presented posters for which the authors have shared the PDF.

Title Presenter
BIOINFO-C: C-based Bioinformatics Library and Web Application Framework (PDF) Detlef Wolf
Reproducible Quantitative Transcriptome Analysis with ocqtans (PDF) Vipin T. Sreedharan


You can also:

- Download schedule as PDF (A4 format).

- Download the complete program

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