Difference between revisions of "Lecture 24"

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__NOTOC__
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<small>[[Lecture_23|(Previous lecture)]] ... [[Lecture_25|(Next lecture)]]</small>  
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'''Update Warning!'''
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This page has not been revised yet for the 2008 Fall term.
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Some of the slides will probably be reused, but please consider the page as a whole out of date
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as long as this warning appears here. Also, the lectures may be taught in a different sequence.
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</div -->
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&nbsp;
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<small>[[Lecture_23|(Previous lecture)]] ... [[Lecture_25|(Next lecture)]]</small>
  
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==Protein-Protein Interactions==
 
  
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...
 
  
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<!--
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<div class="toclimit-3">__TOC__</div>
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Add:
 
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* Summary points
 
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* Exercises
 
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* Further reading
 
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-->
 
  
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==Lecture Slides==
 
  
  
 +
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<br>
 +
&nbsp;<br>
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<div style="padding: 2px; background: #879BFA; border:solid 1px #AAAAAA;">
 +
==Interaction Databases used in Computational Biology==
 +
</div><br>
 +
&nbsp;
 +
 +
 +
BCH441 Guest lecture:
 +
 +
;Francis Ouellette
 +
:Associate Director, Informatics and Biocomputing and Senior Scientist, [http://www.oicr.on.ca/ '''OICR''']<br>
 +
 +
 +
 +
&nbsp;<br>
 +
<div style="padding: 10 px; background: #B0B8D7;  border:solid 1px #AAAAAA;">
 +
====Links summary====
 +
</div><br>
 +
*[http://www.ebi.ac.uk/intact '''IntAct''' - The EBI open access, archival interaction database]<br>
 +
*[http://www.thebiogrid.org/ '''BioGRID''']<br>
 +
*[http://dip.doe-mbi.ucla.edu DIP (archival, not open access)]<br>
 +
*[http://mint.bio.uniroma2.it/mint MINT Topical, curatedl interaction sets ]<br>
 +
*[http://mips.gsf.de/genre/proj/mpact Mpact]<br>
 +
*[http://bind.ca BIND (non-commercial component not curated since 2003)]<br>
 +
*[http://www.hprd.org/ HPRD]<br>
 +
 +
 +
*[http://www.pathguide.org Gary Bader's '''pathguide''' database]<br>
 +
*[http://www.cisreg.ca/ulysses Ulysses: Projection of Protein Networks across Species]<br>
 +
*[http://tinyurl.com/yqx9jb Lu ''et al.'' (2005) Assessing the limits of genomic data integration for predicting protein networks.]<br>
 +
*[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ypl240c YPL240c]<br>
 +
 +
 +
*[http://creativecommons.org/licenses/by-sa/2.5/ca/ Creative Commons License: '''atribution, share alike.''']<br>
 +
*[http://www.earlham.edu/%7Epeters/fos/overview.htm Open Access overview]<br>
 +
*[http://www.biomedcentral.com/openaccess/ Open Access Now]<br>
 +
*[http://www.doaj.org/ DOAJ]<br>
 +
*[http://www.cihr-irsc.gc.ca/e/34846.html CIHR Open Access policy]<br>
 +
 +
 +
&nbsp;<br>
 +
<div style="padding: 10 px; background: #879BFA; border:solid 1px #AAAAAA;">
 +
==Lecture slides==
 +
</div><br>
 +
&nbsp;<br>
 +
 +
&nbsp;<br>
 +
<div style="padding: 10 px; background: #B0B8D7;  border:solid 1px #AAAAAA;">
 +
===Introduction===
 +
</div><br>
 +
&nbsp;<br>
  
 
======Slide 001======
 
======Slide 001======
−
[[Image:L24_s001.jpg|frame|none|Lecture 24, Slide 001<br>
+
[[Image:24_slide001.jpg|frame|none|Lecture 24, Slide 001<br>
−
 
+
These lecture notes are provided under a [http://creativecommons.org/licenses/by-sa/2.5/ca/ Creative Commons License: '''atribution, share alike.'''] (You can also use the "tinyurl" service that compresses long links and automatically redirects your browesr to the right page to access this link through the shorthand http://tinyurl.com/3cw4ql .
 
]]
 
]]
 
======Slide 002======
 
======Slide 002======
−
[[Image:L24_s002.jpg|frame|none|Lecture 24, Slide 002<br>
+
[[Image:24_slide002.jpg|frame|none|Lecture 24, Slide 002<br>
−
 
+
The way this works is shown in the example from the lecture notes: Boris Steipe has lifted some material from Francis Ouellettte's lecture slides. He is allowed to do so, since he has attributed the source of the material and is sharing the results under the same conditions.
−
]]
 
−
======Slide 003======
 
−
[[Image:L24_s003.jpg|frame|none|Lecture 24, Slide 003<br>
 
−
 
 
 
]]
 
]]
 
======Slide 004======
 
======Slide 004======
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[[Image:L24_s004.jpg|frame|none|Lecture 24, Slide 004<br>
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[[Image:24_slide004.jpg|frame|none|Lecture 24, Slide 004<br>
  
 
]]
 
]]
 
======Slide 005======
 
======Slide 005======
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[[Image:L24_s005.jpg|frame|none|Lecture 24, Slide 005<br>
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[[Image:24_slide005.jpg|frame|none|Lecture 24, Slide 005<br>
  
 
]]
 
]]
−
======Slide 006======
 
−
[[Image:L24_s006.jpg|frame|none|Lecture 24, Slide 006<br>
 
  
−
]]
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<br>
 +
&nbsp;<br>
 +
&nbsp;<br>
 +
<div style="padding: 10 px; background: #B0B8D7;  border:solid 1px #AAAAAA;">
 +
===Bioinformatics and Databases===
 +
</div><br>
 +
&nbsp;<br>
 +
 
 +
 
 
======Slide 007======
 
======Slide 007======
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[[Image:L24_s007.jpg|frame|none|Lecture 24, Slide 007<br>
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[[Image:24_slide007.jpg|frame|none|Lecture 24, Slide 007<br>
  
 
]]
 
]]
 
======Slide 008======
 
======Slide 008======
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[[Image:L24_s008.jpg|frame|none|Lecture 24, Slide 008<br>
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[[Image:24_slide008.jpg|frame|none|Lecture 24, Slide 008<br>
  
 
]]
 
]]
 
======Slide 009======
 
======Slide 009======
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[[Image:L24_s009.jpg|frame|none|Lecture 24, Slide 009<br>
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[[Image:24_slide009.jpg|frame|none|Lecture 24, Slide 009<br>
  
 
]]
 
]]
 
======Slide 010======
 
======Slide 010======
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[[Image:L24_s010.jpg|frame|none|Lecture 24, Slide 010<br>
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[[Image:24_slide010.jpg|frame|none|Lecture 24, Slide 010<br>
  
 
]]
 
]]
 
======Slide 011======
 
======Slide 011======
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[[Image:L24_s011.jpg|frame|none|Lecture 24, Slide 011<br>
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[[Image:24_slide011.jpg|frame|none|Lecture 24, Slide 011<br>
  
 
]]
 
]]
 
======Slide 012======
 
======Slide 012======
−
[[Image:L24_s012.jpg|frame|none|Lecture 24, Slide 012<br>
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[[Image:24_slide012.jpg|frame|none|Lecture 24, Slide 012<br>
  
 
]]
 
]]
 
======Slide 013======
 
======Slide 013======
−
[[Image:L24_s013.jpg|frame|none|Lecture 24, Slide 013<br>
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[[Image:24_slide013.jpg|frame|none|Lecture 24, Slide 013<br>
 +
 
 +
]]
 +
======Slide 014======
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[[Image:24_slide014.jpg|frame|none|Lecture 24, Slide 014<br>
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 +
]]
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======Slide 015======
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[[Image:24_slide015.jpg|frame|none|Lecture 24, Slide 015<br>
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 +
]]
 +
======Slide 016======
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[[Image:24_slide016.jpg|frame|none|Lecture 24, Slide 016<br>
 +
 
 +
]]
 +
======Slide 017======
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[[Image:24_slide017.jpg|frame|none|Lecture 24, Slide 017<br>
 +
 
 +
]]
 +
======Slide 018======
 +
[[Image:24_slide018.jpg|frame|none|Lecture 24, Slide 018<br>
 +
 
 +
]]
 +
======Slide 019======
 +
[[Image:24_slide019.jpg|frame|none|Lecture 24, Slide 019<br>
 +
 
 +
]]
 +
 
 +
&nbsp;<br>
 +
<div style="padding: 10 px; background: #B0B8D7;  border:solid 1px #AAAAAA;">
 +
===Interaction Databases===
 +
</div><br>
 +
&nbsp;<br>
 +
 
 +
======Slide 020======
 +
[[Image:24_slide020.jpg|frame|none|Lecture 24, Slide 020<br>
 +
 
 +
]]
 +
======Slide 021======
 +
[[Image:24_slide021.jpg|frame|none|Lecture 24, Slide 021<br>
 +
[http://www.pathguide.org Gary Bader's '''pathguide''' database]
 +
]]
 +
======Slide 022======
 +
[[Image:24_slide022.jpg|frame|none|Lecture 24, Slide 022<br>
 +
 
 +
]]
 +
======Slide 023======
 +
[[Image:24_slide023.jpg|frame|none|Lecture 24, Slide 023<br>
 +
 
 +
]]
 +
======Slide 024======
 +
[[Image:24_slide024.jpg|frame|none|Lecture 24, Slide 024<br>
 +
*[http://www.ebi.ac.uk/intact The IntAct database]<br>
 +
[[http://www.thebiogrid.org The BioGrid database]
 +
]]
 +
======Slide 025======
 +
[[Image:24_slide025.jpg|frame|none|Lecture 24, Slide 025<br>
 +
 
 +
]]
 +
======Slide 026======
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[[Image:24_slide026.jpg|frame|none|Lecture 24, Slide 026<br>
 +
 
 +
]]
 +
======Slide 027======
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[[Image:24_slide027.jpg|frame|none|Lecture 24, Slide 027<br>
 +
 
 +
]]
 +
======Slide 028======
 +
[[Image:24_slide028.jpg|frame|none|Lecture 24, Slide 028<br>
 +
[http://www.cisreg.ca/ulysses Ulysses: Projection of Protein Networks across Species]
 +
]]
 +
======Slide 029======
 +
[[Image:24_slide029.jpg|frame|none|Lecture 24, Slide 029<br>
 +
 
 +
]]
 +
======Slide 030======
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[[Image:24_slide030.jpg|frame|none|Lecture 24, Slide 030<br>
 +
 
 +
]]
 +
======Slide 031======
 +
[[Image:24_slide031.jpg|frame|none|Lecture 24, Slide 031<br>
 +
[http://tinyurl.com/yqx9jb Lu ''et al.'' (2005) Assessing the limits of genomic data integration for predicting protein networks.]
 +
]]
 +
======Slide 032======
 +
[[Image:24_slide032.jpg|frame|none|Lecture 24, Slide 032<br>
 +
 
 +
]]
 +
 
 +
&nbsp;<br>
 +
<div style="padding: 10 px; background: #B0B8D7;  border:solid 1px #AAAAAA;">
 +
===Genetic Interaction Networks===
 +
</div><br>
 +
&nbsp;<br>
 +
 
 +
 
 +
======Slide 033======
 +
[[Image:24_slide033.jpg|frame|none|Lecture 24, Slide 033<br>
 +
 
 +
]]
 +
======Slide 034======
 +
[[Image:24_slide034.jpg|frame|none|Lecture 24, Slide 034<br>
 +
 
 +
]]
 +
======Slide 035======
 +
[[Image:24_slide035.jpg|frame|none|Lecture 24, Slide 035<br>
 +
 
 +
]]
 +
======Slide 036======
 +
[[Image:24_slide036.jpg|frame|none|Lecture 24, Slide 036<br>
 +
 
 +
]]
 +
======Slide 037======
 +
[[Image:24_slide037.jpg|frame|none|Lecture 24, Slide 037<br>
 +
 
 +
]]
 +
======Slide 038======
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[[Image:24_slide038.jpg|frame|none|Lecture 24, Slide 038<br>
 +
 
 +
]]
 +
======Slide 039======
 +
[[Image:24_slide039.jpg|frame|none|Lecture 24, Slide 039<br>
 +
 
 +
]]
 +
======Slide 040======
 +
[[Image:24_slide040.jpg|frame|none|Lecture 24, Slide 040<br>
 +
 
 +
]]
 +
======Slide 041======
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[[Image:24_slide041.jpg|frame|none|Lecture 24, Slide 041<br>
  
 
]]
 
]]
 +
======Slide 042======
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[[Image:24_slide042.jpg|frame|none|Lecture 24, Slide 042<br>
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 +
]]
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======Slide 043======
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[[Image:24_slide043.jpg|frame|none|Lecture 24, Slide 043<br>
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]]
 +
======Slide 044======
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[[Image:24_slide044.jpg|frame|none|Lecture 24, Slide 044<br>
 +
 +
]]
 +
======Slide 045======
 +
[[Image:24_slide045.jpg|frame|none|Lecture 24, Slide 045<br>
 +
[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ypl240c YPL240c]
 +
]]
 +
 +
 +
&nbsp;<br>
 +
<div style="padding: 10 px; background: #B0B8D7;  border:solid 1px #AAAAAA;">
 +
===Open Access===
 +
</div><br>
 +
&nbsp;<br>
 +
 +
 +
======Slide 046======
 +
[[Image:24_slide046.jpg|frame|none|Lecture 24, Slide 046<br>
 +
 +
]]
 +
======Slide 047======
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[[Image:24_slide047.jpg|frame|none|Lecture 24, Slide 047<br>
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]]
 +
======Slide 048======
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[[Image:24_slide048.jpg|frame|none|Lecture 24, Slide 048<br>
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]]
 +
======Slide 049======
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[[Image:24_slide049.jpg|frame|none|Lecture 24, Slide 049
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]]
 +
======Slide 050======
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[[Image:24_slide050.jpg|frame|none|Lecture 24, Slide 050<br>
 +
*[http://dip.doe-mbi.ucla.edu DIP (archival, not open access)]<br>
 +
*[http://www.ebi.ac.uk/intact IntAct - The EBI open access, archival interaction database]<br>
 +
*[http://mint.bio.uniroma2.it/mint MINT Topical, curatedl interaction sets ]<br>
 +
*[http://mips.gsf.de/genre/proj/mpact Mpact]<br>
 +
*[http://www.thebiogrid.org/ BioGRID]<br>
 +
*[http://bind.ca BIND (non-commercial component not curated since 2003)]<br>
 +
*[http://www.hprd.org/ HPRD]<br>
 +
*[http://www.earlham.edu/%7Epeters/fos/overview.htm Open Access overview]<br>
 +
*[http://www.biomedcentral.com/openaccess/ Open Access Now]<br>
 +
*[http://www.doaj.org/ DOAJ]<br>
 +
*[http://www.cihr-irsc.gc.ca/e/34846.html CIHR Open Access policy]<br>
 +
]]
 +
 +
&nbsp;<br>
 +
 +
 +
----
 +
<small>[[Lecture_23|(Previous lecture)]] ... [[Lecture_25|(Next lecture)]]</small>

Latest revision as of 19:26, 9 December 2007

  (Previous lecture) ... (Next lecture)





 

Interaction Databases used in Computational Biology


 


BCH441 Guest lecture:

Francis Ouellette
Associate Director, Informatics and Biocomputing and Senior Scientist, OICR


 

Links summary





 

Lecture slides


 

 

Introduction


 

Slide 001
Lecture 24, Slide 001
These lecture notes are provided under a Creative Commons License: atribution, share alike. (You can also use the "tinyurl" service that compresses long links and automatically redirects your browesr to the right page to access this link through the shorthand http://tinyurl.com/3cw4ql .
Slide 002
Lecture 24, Slide 002
The way this works is shown in the example from the lecture notes: Boris Steipe has lifted some material from Francis Ouellettte's lecture slides. He is allowed to do so, since he has attributed the source of the material and is sharing the results under the same conditions.
Slide 004
Lecture 24, Slide 004
Slide 005
Lecture 24, Slide 005


 
 

Bioinformatics and Databases


 


Slide 007
Lecture 24, Slide 007
Slide 008
Lecture 24, Slide 008
Slide 009
Lecture 24, Slide 009
Slide 010
Lecture 24, Slide 010
Slide 011
Lecture 24, Slide 011
Slide 012
Lecture 24, Slide 012
Slide 013
Lecture 24, Slide 013
Slide 014
Lecture 24, Slide 014
Slide 015
Lecture 24, Slide 015
Slide 016
Lecture 24, Slide 016
Slide 017
Lecture 24, Slide 017
Slide 018
Lecture 24, Slide 018
Slide 019
Lecture 24, Slide 019

 

Interaction Databases


 

Slide 020
Lecture 24, Slide 020
Slide 021
Lecture 24, Slide 021
Gary Bader's pathguide database
Slide 022
Lecture 24, Slide 022
Slide 023
Lecture 24, Slide 023
Slide 024

[[Image:24_slide024.jpg|frame|none|Lecture 24, Slide 024

[The BioGrid database ]]

Slide 025
Lecture 24, Slide 025
Slide 026
Lecture 24, Slide 026
Slide 027
Lecture 24, Slide 027
Slide 028
Lecture 24, Slide 028
Ulysses: Projection of Protein Networks across Species
Slide 029
Lecture 24, Slide 029
Slide 030
Lecture 24, Slide 030
Slide 031
Lecture 24, Slide 031
Lu et al. (2005) Assessing the limits of genomic data integration for predicting protein networks.
Slide 032
Lecture 24, Slide 032

 

Genetic Interaction Networks


 


Slide 033
Lecture 24, Slide 033
Slide 034
Lecture 24, Slide 034
Slide 035
Lecture 24, Slide 035
Slide 036
Lecture 24, Slide 036
Slide 037
Lecture 24, Slide 037
Slide 038
Lecture 24, Slide 038
Slide 039
Lecture 24, Slide 039
Slide 040
Lecture 24, Slide 040
Slide 041
Lecture 24, Slide 041
Slide 042
Lecture 24, Slide 042
Slide 043
Lecture 24, Slide 043
Slide 044
Lecture 24, Slide 044
Slide 045
Lecture 24, Slide 045
YPL240c


 

Open Access


 


Slide 046
Lecture 24, Slide 046
Slide 047
Lecture 24, Slide 047
Slide 048
Lecture 24, Slide 048
Slide 049
Lecture 24, Slide 049
Slide 050
Lecture 24, Slide 050
*DIP (archival, not open access)
*IntAct - The EBI open access, archival interaction database
*MINT Topical, curatedl interaction sets
*Mpact
*BioGRID
*BIND (non-commercial component not curated since 2003)
*HPRD
*Open Access overview
*Open Access Now
*DOAJ
*CIHR Open Access policy

 


(Previous lecture) ... (Next lecture)

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