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Difference between revisions of "BOSC 2009 Schedule"

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Return to [[BOSC_2009 | BOSC 2009]] main page.
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* Return to '''[[BOSC_2009 | BOSC 2009]]''' main page.
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* Click on the talk title to view the individual abstract as a PDF file.
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* Click '''[[Media:BOSC2009_program_20090601.pdf | here]]''' to download full program in PDF format (2 MB).
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* Important '''[[BOSC_2009#Information_for_Speakers | Information for Speakers]]'''
  
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== Keynote Speakers ==
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== Schedule ==
  
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The BOSC 2009 Organizing committee is pleased to announce our two Keynote Speakers:
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{| border="1" cellspacing="0" cellpadding="10" align="left"
 +
! Day 1
 +
! Saturday
 +
! June 27
 +
|-
 +
| 9:00-9:15am
 +
| Kam Dahlquist
 +
| [Welcome] [http://www.slideshare.net/bosc/bosc-intro-20090627 ***SLIDES***]
 +
|-
 +
| 9:15-10:15
 +
| [[BOSC_2009#Alan_Ruttenberg | Alan Ruttenberg]]
 +
| [Keynote] Can we reduce the burden of data integration?  Challenge and opportunity in building the web of data
 +
|-
 +
| '''10:15-10:45'''
 +
| '''Coffee Break'''
 +
|-
 +
| 10:45-11:05
 +
| Jean-Stéphane Varré
 +
| [Multicore & GPGPU Computing] [[Media:Bosc2009_submission_22.pdf | Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics]] [http://www.slideshare.net/bosc/varrebiomanycoresbosc2009 ***SLIDES***]
 +
|-
 +
| 11:05-11:25
 +
| Josh Buckner
 +
| [Multicore & GPGPU Computing] [[Media:Bosc2009_submission_32.pdf | Enabling GPU Computing in the R Statistical Environment]] [http://www.slideshare.net/bosc/bucknergpurbosc2009 ***SLIDES***]
 +
|-
 +
| 11:25-11:40
 +
| Mikhail Fursov
  
−
=== Alan Ruttenberg ===
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(cancelled)
 +
| [Multicore & GPGPU Computing] [[Media:Bosc2009_submission_18.pdf | UGENE – A practical approach for complex computational analysis  in molecular biology]]
 +
|-
 +
| 11:40-11:48
 +
| Oswaldo Trelles
  
−
[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg] is a Principal Scientist at [http://sciencecommons.org Science Commons].  He works with Semantic Web technologies in computational biology, with an emphasis on the creation and application of structured biological knowledge to interpret experimental results. He is currently involved in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that will form the upper level ontology for the OBO foundry, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), the Information Artifact Ontology (IAO), and BioPAX-OBO for representing molecular and cellular pathways. These interests and efforts come together in my project at Science Commons - the Neurocommons, a large scale Semantic Web knowledge base of biological information aimed at supporting, initially, the neurosciences. He is also an active participant in W3C Semantic Web activities. In 2006 and 2007 he was a member of the Health Care Life Sciences Interest Group, and early work on the Neurocommons became the core of the prototype life sciences knowledge base that the group has documented. He is a chair of the OWL Working Group specifying OWL 2, and a coordinating editor of the OBO Foundry.  
+
(talk given by Pjotr Prins)
−
His graduate work was at the MIT Media Lab in the Music and Cognition Group, and he has an undergraduate degree in Physics and Mathematics from Brandeis University.
+
| [Multicore & GPGPU Computing Lightning Talk] [[Media:Bosc2009_submission_11.pdf | Qnorm: A library of parallel methods for gene-expression Q-normalization]] [http://www.slideshare.net/bosc/trellesqnormbosc2009 ***SLIDES***]
 +
|-
 +
| 11:48-12:08pm
 +
| Hajo N. Krabbenhöft
 +
| [Computational Grids] [[Media:Bosc2009_submission_31.pdf | Taverna workflows across Grids, web services and the command line]] [http://www.slideshare.net/bosc/krabbenhofttavernaarcbosc2009 ***SLIDES***]
 +
|-
 +
| 12:08-12:23
 +
| Ann-Kristin Grimm
  
−
=== Robert S. Hanmer ===
+
(talk given by Steffen Moeller)
 +
| [Computational Grids] [[Media:Bosc2009_submission_12.pdf | Grid-based expression QTL analysis]] [http://www.slideshare.net/bosc/moellergridqtlbosc2009 ***SLIDES***]
 +
|-
 +
| 12:23-12:31
 +
| Joel Hedlund
 +
| [Computational Grids Lightning Talk] [[Media:Bosc2009_submission_28.pdf | The Nordic BioGrid project -- Bioinformatics for the grid]] [http://www.slideshare.net/bosc/hedlundbiogridbosc2009 ***SLIDES***]
 +
|-
 +
| '''12:31-2:00'''
 +
| '''Lunch'''
 +
|-
 +
| 2:00-2:20
 +
| Allan Kuchinsky
 +
| [Visualization] [[Media:Bosc2009_submission_23.pdf | Cytoscape Springs Forward: Re-architecture for Version 3.0]] [http://www.slideshare.net/bosc/kuchinskycytoscapebosc2009 ***SLIDES***]
 +
|-
 +
| 2:20-2:33
 +
| Frederik Decouttere
 +
| [Visualization] [[Media:Bosc2009_submission_8.pdf | Bioinformatics simplified with seqpad]] [http://www.slideshare.net/bosc/decouttereseqpad-bosc2009 ***SLIDES***]
 +
|-
 +
| 2:33-2:46
 +
| Bernat Gel
 +
| [Visualization] [[Media:Bosc2009_submission_26.pdf | DASGenExp: an interactive web-based DAS client with client-side rendering]] [http://www.slideshare.net/bosc/geldasgenexpbosc2009 ***SLIDES***]
 +
|-
 +
| 2:46-2:59
 +
| Kazuharu Arakawa
 +
| [OS Software] [[Media:Bosc2009_submission_39.pdf | Web Service Interface for G-language Genome Analysis Environment]] [http://www.slideshare.net/bosc/arakawaglanguagebosc2009 ***SLIDES***]
 +
|-
 +
| 2:59-3:12
 +
| Sylvain Brohée
 +
| [OS Software] [[Media:Bosc2009_submission_3.pdf | Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases]] [http://www.slideshare.net/bosc/broheewikibosc2009 ***SLIDES***]
 +
|-
 +
| 3:12-3:30
 +
| Bartek Wilczynski
 +
| [Regulatory Genomics] [[Media:Bosc2009_submission_29.pdf | BNfinder: free software for effective Bayesian Network inference]] [http://www.slideshare.net/bosc/wilczynskibnfinderbosc2009 ***SLIDES***]
 +
|-
 +
| '''3:30-4:00'''
 +
| '''Coffee Break'''
 +
|-
 +
| 4:00-4:20
 +
| Morris Swertz
 +
| [Data & Analysis Management] [[Media:Bosc2009_submission_27.pdf | MOLGENIS by example: generating an extensible platform for genotype and phenotype experiments]] [http://www.slideshare.net/bosc/swertz-molgenis-bosc2009 ***SLIDES***]
 +
|-
 +
| 4:20-4:40
 +
| Robert Murphy
 +
| [Data & Analysis Management] [[Media:Bosc2009_submission_34.pdf | PSLID, the Protein Subcellular Location Image Database: Subcellular location assignments, annotated image collections, image analysis tools, and generative models of protein distributions]] [http://www.slideshare.net/bosc/murphypslidbosc2009 ***SLIDES***]
 +
|-
 +
|4:40-5:00
 +
| Mark Welsh
 +
| [Data & Analysis Management] [[Media:Bosc2009_submission_10.pdf | BioHDF: Open binary file formats for large-scale data management – Project Update]] [http://www.slideshare.net/bosc/welshbiohdfbosc2009 ***SLIDES***]
 +
|-
 +
| 5:00-5:15
 +
| Brad Chapman
 +
| [Data & Analysis Management] [[Media:Bosc2009_submission_14.pdf | Lowering barriers to publishing biological data on the web]] [http://www.slideshare.net/bosc/chapmanpublishingwebbosc2009 ***SLIDES***]
 +
|-
 +
| 5:15-5:30
 +
| Kam Dahlquist
 +
| [Data & Analysis Management] [[Media:Bosc2009_submission_35.pdf | XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources]] [http://www.slideshare.net/bosc/dahlquistxmlpipedbbosc2009 ***SLIDES***]
 +
|-
 +
| 5:30-6:00
 +
|  
 +
| [Lightning Talks]
 +
5:30 Matias Piipari - [http://imotifs.pearcomp.com/ iMotifs]: a motif viewer/editor for the Mac [http://www.slideshare.net/bosc/piipariimotifbosc2009 ***SLIDES***]
  
−
Robert S. Hanmer is a Consulting Member of Technical Staff in the Technical Component Management area in Alcatel-Lucent’s Operations area. He is based in Naperville, Illinois, USA. Current responsibilities include developing software-sourcing strategies for middleware and open source software. Previous positions within Lucent and Bell Laboratories have included development, architecture and evaluation of highly reliable systems focusing especially on the areas of reliability and performance.  He is active in the software patterns community, including serving as program chair at several pattern conferences.  He has authored or co-authored 14 journal articles, several book chapters and the book Patterns for Fault Tolerant Software. He is a member of the IEEE Computer Society,  a Senior Member of the ACM and current President of [http://hillside.net/ The Hillside Group], the organization that sponsors the PLoP conference.  He received his B.S. and M.S. degrees in Computer Science from Northwestern University in Evanston, Illinois.
+
5:38 Kristian Rother - [http://genesilico.pl/moderna/ ModeRNA] - an Open Source platform for RNA 3D modeling [http://www.slideshare.net/bosc/rothermodernabosc2009 ***SLIDES***]
  
−
== Multicore & GPGPU Computing ==
+
5:46 Tiago Antao - [http://code.google.com/p/openmalaria openmalaria] - A simulator of malaria epidemology and control [http://www.slideshare.net/bosc/antaoopenmalariabosc2009 ***SLIDES***]
  
−
== Computational Grids ==
+
[[BOSC_2009/Birds-of-a-Feather | Birds of a Feather]]
−
 
+
|-
−
== Visualization ==
+
| 6:15
−
 
+
|  
−
== Open Source Software ==
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| <nowiki>OBF</nowiki> Board Meeting and No-host Dinner - Rica Talk Hotel Restaurant
−
 
+
|-
−
Confirmed speakers include:
+
| '''Day 2'''
−
 
+
| '''Sunday'''
−
* Kazuharu Arakawa - Web Service Interface for G-language Genome Analysis Environment (10 min)
+
| '''June 28'''
−
 
+
|-
−
== Data & Analysis Management (shared session with D&AM SIG) ==
+
| 9:00-9:15am
−
 
+
| Kam Dahlquist
−
Confirmed speakers include:
+
| [Announcements]
−
 
+
|-
−
* Kam Dahlquist - XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources (10 min.)
+
| 9:15-10:15
−
 
+
| [[BOSC_2009#Robert_S._Hanmer | Robert Hanmer]]
−
== Bio* Update ==
+
| [Keynote] Software Patterns for Reusable Design [http://www.slideshare.net/bosc/hanmer-software-patterns-bosc2009 ***SLIDES***]
−
 
+
|-
−
Confirmed speakers include:
+
| '''10:15-10:45'''
−
 
+
| '''Coffee Break'''
−
* Martin Senger - Soaplab: Open Source Web Services Framework for Bioinformatics Programs (10 min.)
+
|-
−
* Pjotr Prins - BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA (15 min.)
+
| 10:45-11:00
−
 
+
| Peter Rice
−
== Regulatory Genomics ==
+
| [Bio* Update] [[Media:Bosc2009_submission_5.pdf | EMBOSS: European Molecular Biology Open Software Suite]] [http://www.slideshare.net/bosc/rice-emboss-bosc2009 ***SLIDES***]
−
 
+
|-
−
== Design Patterns Panel Discussion ==
+
| 11:00-11:15
 +
| Peter Cock
 +
| [Bio* Update] [[Media:Bosc2009_submission_19.pdf | Biopython Project Update 2009]] [http://www.slideshare.net/bosc/cock-biopython-bosc2009 ***SLIDES***] [http://biopython.org/DIST/docs/presentations/Biopython_BOSC_2009.pdf ***PDF***]
 +
|-
 +
| 11:15-11:30
 +
| [http://biojava.org/wiki/Andreas_Prlic Andreas Prlic]
 +
| [Bio* Update] [[Media:Bosc2009_submission_15.pdf | BioJava 2009: an Open-Source Framework for Bioinformatics]] [http://www.slideshare.net/bosc/prlic-bio-java-bosc2009 ***SLIDES***]
 +
|-
 +
| 11:30-11:45
 +
| Jim Procter
 +
| [Bio* Update] [[Media:Bosc2009_submission_16.pdf | Application of VAMSAS enabled tools for the investigation of protein evolution]] [http://www.slideshare.net/bosc/procter-vamsas-bosc2009 ***SLIDES***]
 +
|-
 +
| 11:45-12:00pm
 +
| Martin Senger
 +
| [Bio* Update] [[Media:Bosc2009_submission_13.pdf | Soaplab: Open Source Web Services Framework for Bioinformatics Programs]] [http://www.slideshare.net/bosc/senger-soaplab-bosc2009 ***SLIDES***]
 +
|-
 +
| 12:00-12:20
 +
| Pjotr Prins
 +
| [Bio* Update] [[Media:Bosc2009_submission_4.pdf | BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA]] [http://www.slideshare.net/bosc/prins-bio-lib-bosc-2009 ***SLIDES***]
 +
|-
 +
| 12:20-12:28
 +
| Steffen Möller
 +
| [OS Software Lightning Talk] [[Media:Bosc2009_submission_30.pdf | Debian adopts and disseminates Bioinformatics Open Source Software]] [http://www.slideshare.net/bosc/moeller-debian-bosc2009 ***SLIDES***]
 +
|-
 +
| '''12:30-2:00'''
 +
| '''Lunch'''
 +
|-
 +
| 2:00-2:20
 +
| Quinn Snell
 +
| [OS Software] [[Media:Bosc2009_submission_33.pdf | PSODA: Open Source Phylogenetic Search and DNA Analysis]] [http://www.slideshare.net/bosc/snell-psoda-bosc2009 ***SLIDES***]
 +
|-
 +
| 2:20-2:40
 +
| Finn Drablos
 +
| [Regulatory Genomics] [[Media:Bosc2009_submission_6.pdf | Computational discovery of composite motifs in DNA]] [http://www.slideshare.net/bosc/drablos-composite-motifs-bosc2009 ***SLIDES***]
 +
|-
 +
| 2:40-2:55
 +
| François Fauteux
 +
| [Regulatory Genomics] [[Media:Bosc2009_submission_40.pdf | SEEDER: PERL MODULES FOR CIS-REGULATORY MOTIF DISCOVERY]] [http://www.slideshare.net/bosc/fauteux-seeder-bosc2009 ***SLIDES***]
 +
|-
 +
| 2:55-3:10
 +
| Matias Piipari
 +
| [Regulatory Genomics] [[Media:Bosc2009_submission_24.pdf | Large-scale gene regulatory motif discovery and categorisation with NestedMICA]]
 +
|-
 +
| 3:10-3:30
 +
| Sophie Schbath
 +
| [Regulatory Genomics] [[Media:Bosc2009_submission_38.pdf | R'MES]] [http://www.slideshare.net/bosc/schbath-rmes-bosc2009 ***SLIDES***]
 +
|-
 +
| '''3:30-4:00'''
 +
| '''Coffee Break'''
 +
|-
 +
| 4:00-4:15
 +
| Lonnie Welch
 +
| [Regulatory Genomics] [[Media:Bosc2009_submission_7_21.pdf | Open Source Implementation of Batch-Extraction for Coding and Non-coding Sequences/An Open Source Framework for Bioinformatics  Word Enumeration and Scoring]] [http://www.slideshare.net/bosc/welch-wordifier-bosc2009 ***SLIDES***]
 +
|-
 +
| 4:15-4:50
 +
| Robert Hanmer (moderator), [[Media:Bosc2009_submission_9.pdf | Lonnie Welch]], [[Media:Bosc2009_submission_17.pdf | Aleksi Kallio]] and Jim Procter.
 +
| [Panel Discussion] On the Applicability of Design Patterns for the Bioinformatics Open Source Community [http://www.slideshare.net/bosc/software-patterns-panel-bos2009 Panel ***SLIDES***][http://www.slideshare.net/bosc/kallio-chipster-bosc2009 ***Kallio SLIDES***]
 +
|-
 +
|4:50-5:30
 +
| [[BOSC_2009/Birds-of-a-Feather | Birds of a Feather]]
 +
|}

Latest revision as of 18:11, 7 September 2015

Schedule

Day 1 Saturday June 27
9:00-9:15am Kam Dahlquist [Welcome] ***SLIDES***
9:15-10:15 Alan Ruttenberg [Keynote] Can we reduce the burden of data integration? Challenge and opportunity in building the web of data
10:15-10:45 Coffee Break
10:45-11:05 Jean-Stéphane Varré [Multicore & GPGPU Computing] Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics ***SLIDES***
11:05-11:25 Josh Buckner [Multicore & GPGPU Computing] Enabling GPU Computing in the R Statistical Environment ***SLIDES***
11:25-11:40 Mikhail Fursov

(cancelled)

[Multicore & GPGPU Computing] UGENE – A practical approach for complex computational analysis in molecular biology
11:40-11:48 Oswaldo Trelles

(talk given by Pjotr Prins)

[Multicore & GPGPU Computing Lightning Talk] Qnorm: A library of parallel methods for gene-expression Q-normalization ***SLIDES***
11:48-12:08pm Hajo N. Krabbenhöft [Computational Grids] Taverna workflows across Grids, web services and the command line ***SLIDES***
12:08-12:23 Ann-Kristin Grimm

(talk given by Steffen Moeller)

[Computational Grids] Grid-based expression QTL analysis ***SLIDES***
12:23-12:31 Joel Hedlund [Computational Grids Lightning Talk] The Nordic BioGrid project -- Bioinformatics for the grid ***SLIDES***
12:31-2:00 Lunch
2:00-2:20 Allan Kuchinsky [Visualization] Cytoscape Springs Forward: Re-architecture for Version 3.0 ***SLIDES***
2:20-2:33 Frederik Decouttere [Visualization] Bioinformatics simplified with seqpad ***SLIDES***
2:33-2:46 Bernat Gel [Visualization] DASGenExp: an interactive web-based DAS client with client-side rendering ***SLIDES***
2:46-2:59 Kazuharu Arakawa [OS Software] Web Service Interface for G-language Genome Analysis Environment ***SLIDES***
2:59-3:12 Sylvain Brohée [OS Software] Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases ***SLIDES***
3:12-3:30 Bartek Wilczynski [Regulatory Genomics] BNfinder: free software for effective Bayesian Network inference ***SLIDES***
3:30-4:00 Coffee Break
4:00-4:20 Morris Swertz [Data & Analysis Management] MOLGENIS by example: generating an extensible platform for genotype and phenotype experiments ***SLIDES***
4:20-4:40 Robert Murphy [Data & Analysis Management] PSLID, the Protein Subcellular Location Image Database: Subcellular location assignments, annotated image collections, image analysis tools, and generative models of protein distributions ***SLIDES***
4:40-5:00 Mark Welsh [Data & Analysis Management] BioHDF: Open binary file formats for large-scale data management – Project Update ***SLIDES***
5:00-5:15 Brad Chapman [Data & Analysis Management] Lowering barriers to publishing biological data on the web ***SLIDES***
5:15-5:30 Kam Dahlquist [Data & Analysis Management] XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources ***SLIDES***
5:30-6:00   [Lightning Talks]

5:30 Matias Piipari - iMotifs: a motif viewer/editor for the Mac ***SLIDES***

5:38 Kristian Rother - ModeRNA - an Open Source platform for RNA 3D modeling ***SLIDES***

5:46 Tiago Antao - openmalaria - A simulator of malaria epidemology and control ***SLIDES***

Birds of a Feather

6:15   OBF Board Meeting and No-host Dinner - Rica Talk Hotel Restaurant
Day 2 Sunday June 28
9:00-9:15am Kam Dahlquist [Announcements]
9:15-10:15 Robert Hanmer [Keynote] Software Patterns for Reusable Design ***SLIDES***
10:15-10:45 Coffee Break
10:45-11:00 Peter Rice [Bio* Update] EMBOSS: European Molecular Biology Open Software Suite ***SLIDES***
11:00-11:15 Peter Cock [Bio* Update] Biopython Project Update 2009 ***SLIDES*** ***PDF***
11:15-11:30 Andreas Prlic [Bio* Update] BioJava 2009: an Open-Source Framework for Bioinformatics ***SLIDES***
11:30-11:45 Jim Procter [Bio* Update] Application of VAMSAS enabled tools for the investigation of protein evolution ***SLIDES***
11:45-12:00pm Martin Senger [Bio* Update] Soaplab: Open Source Web Services Framework for Bioinformatics Programs ***SLIDES***
12:00-12:20 Pjotr Prins [Bio* Update] BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA ***SLIDES***
12:20-12:28 Steffen Möller [OS Software Lightning Talk] Debian adopts and disseminates Bioinformatics Open Source Software ***SLIDES***
12:30-2:00 Lunch
2:00-2:20 Quinn Snell [OS Software] PSODA: Open Source Phylogenetic Search and DNA Analysis ***SLIDES***
2:20-2:40 Finn Drablos [Regulatory Genomics] Computational discovery of composite motifs in DNA ***SLIDES***
2:40-2:55 François Fauteux [Regulatory Genomics] SEEDER: PERL MODULES FOR CIS-REGULATORY MOTIF DISCOVERY ***SLIDES***
2:55-3:10 Matias Piipari [Regulatory Genomics] Large-scale gene regulatory motif discovery and categorisation with NestedMICA
3:10-3:30 Sophie Schbath [Regulatory Genomics] R'MES ***SLIDES***
3:30-4:00 Coffee Break
4:00-4:15 Lonnie Welch [Regulatory Genomics] Open Source Implementation of Batch-Extraction for Coding and Non-coding Sequences/An Open Source Framework for Bioinformatics Word Enumeration and Scoring ***SLIDES***
4:15-4:50 Robert Hanmer (moderator), Lonnie Welch, Aleksi Kallio and Jim Procter. [Panel Discussion] On the Applicability of Design Patterns for the Bioinformatics Open Source Community Panel ***SLIDES******Kallio SLIDES***
4:50-5:30 Birds of a Feather
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