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Difference between revisions of "BOSC 2013 Schedule"
From Open Bioinformatics Foundation
(→Day 1: Friday, July 19: Nils Gehlenborg's slides) |
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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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| Line 60: | Line 60: | ||
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| 11:55 | | 11:55 | ||
| − | | [Open Science] Ten Simple Rules for the Open Development of Scientific Software (followed by discussion) ([http://www.open-bio.org/bosc2013/day1/BOSC2013_TenSimpleRules_-_Prlic_Procter_Lapp.pdf PDF]) | + | | [Open Science] Ten Simple Rules for the Open Development of Scientific Software (followed by discussion) ([http://www.open-bio.org/bosc2013/day1/BOSC2013_TenSimpleRules_-_Prlic_Procter_Lapp.pdf PDF] [http://www.youtube.com/watch?v=IULl7gk8sng YouTube]) |
| Andreas Prlic, Jim Procter, Hilmar Lapp | | Andreas Prlic, Jim Procter, Hilmar Lapp | ||
|- | |- | ||
| Line 165: | Line 165: | ||
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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.slideshare.net/hlapp/obf-address-bosc2013 SlideShare]) | + | | [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.youtube.com/watch?v=nUwQqwl_VlI YouTube]) |
| Sean Eddy (Janelia Farm) | | Sean Eddy (Janelia Farm) | ||
|- | |- | ||
| Line 185: | Line 185: | ||
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| 10:45 | | 10:45 | ||
| − | | [Interoperability] BioBlend - Enabling Pipeline Dreams ([http://www.open-bio.org/bosc2013/day2/BOSC2013_BioBlend_-_Enis_Afgan.pdf PDF]) | + | | [Interoperability] BioBlend - Enabling Pipeline Dreams ([http://www.open-bio.org/bosc2013/day2/BOSC2013_BioBlend_-_Enis_Afgan.pdf PDF] [http://www.youtube.com/watch?v=QnC8ND9q1sk YouTube]) |
| Enis Afgan | | Enis Afgan | ||
|- | |- | ||
| 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], [http://www.slideshare.net/hlapp/phylo-commons-bosc2013 SlideShare]) | + | | [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 | ||
|- | |- | ||
| 12:20 | | 12:20 | ||
| − | | [Interoperability] GEMBASSY: an EMBOSS associated package for genome analysis using G-language SOAP/REST web services ([http://www.open-bio.org/bosc2013/day2/BOSC2013_GEMBASSY_-_Hidetoshi_Itaya.pdf PDF]) | + | | [Interoperability] GEMBASSY: an EMBOSS associated package for genome analysis using G-language SOAP/REST web services ([http://www.open-bio.org/bosc2013/day2/BOSC2013_GEMBASSY_-_Hidetoshi_Itaya.pdf PDF] [http://www.youtube.com/watch?v=zzfezywfGKQ YouTube]) |
| Hidetoshi Itaya | | Hidetoshi Itaya | ||
|- | |- | ||
| 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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| Line 237: | Line 237: | ||
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| 2:00 | | 2:00 | ||
| − | | [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]) | + | | [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 ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Infrastructure_-_John_Chilton.pdf PDF]) | + | | [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] GEPETTO: An Open Source Framework for Gene Prioritization ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Gepetto_-_Vincent_Walter.pdf PDF]) | + | | [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]) |
| Vincent Walter | | Vincent Walter | ||
|- | |- | ||
| 2:55 | | 2:55 | ||
| − | | [Cloud/Genome-Scale] RAMPART: an automated de novo assembly pipeline ([http://www.open-bio.org/bosc2013/day2/BOSC2013_RAMPART_-_Daniel_Mapleson.pdf PDF]) | + | | [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 ([http://www.open-bio.org/bosc2013/day2/BOSC2013_OmicConnect_-_Joeri_van_der_Velde.pdf PDF]) | + | | [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] [http://www.youtube.com/watch?v=0gLhALQn0cw YouTube]) |
| 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 ([http://www.open-bio.org/bosc2013/day2/BOSC2013_Galaxy_-_Jeremey_Goecks.pdf PDF]) | + | | [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 | ||
Revision as of 10:16, 29 July 2013
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 YouTube) | 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 (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.) |
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 (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 YouTube) | 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 YouTube) | 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 YouTube) | 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
