Difference between revisions of "User:Sven"

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Making articles [[foo]] and [[fodda]] (again) to see search engine side effects. New Article [[Sven/Thesis]]
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{|border=0 width=100%
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|- valign=top
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|{{Portlet|[[Documentation]]|3=300|{{:Technical documentation}}}}
  
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== Installing MediaWiki on OS X==
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|- valign=top
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Media wiki requires:
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|{{Portlet|OS X|3=300|
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#Apache webserver
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*[http://developer.apple.com/documentation/MacOSX/index.html Apple documentation]
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#PHP
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*[http://www.macosxhints.com/ Mac OS X hints]
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#Mysql
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**[http://forums.macosxhints.com/ MacOS X forums]
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*[http://www.osxhelp.com/ OS X help]
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*[http://www.entropy.ch/software/macosx/php/ OS X PHP]
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*[http://guides.macrumors.com/ Macrumors wiki]
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}}
  
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See [http://www.mediawiki.org/wiki/Download mediawiki.org] and [http://sourceforge.net/projects/wikipedia/ sourceforge] for installation details.
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|{{Portlet|Computer Security|3=300|
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As OS X ships with a built in Apache webserver, installation of PHP, and Mysql is all that is required.
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*[http://www.technicalinfo.net/index.html Antivirus/Phishing]
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If you want to run Apache aas a secure webserver then you probably have to build Apache from source.
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*[http://centralops.net/co/DomainDossier.aspx Domain dossier]
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*[http://www.cs.auckland.ac.nz/~pgut001/pubs/vista_cost.html Vista whitepaper]
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*[http://www.honeynet.org/papers/enemy/ Honeynet enemy]
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*[http://www.honeynet.org/papers/enemy2/ Honeynet enemy2]
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*[http://www.honeynet.org/papers/enemy3/ Honeynet enemy3]
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}}
  
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PHP 5.0.4/4.3.11 is available as a [http://www.entropy.ch/software/macosx/php/ dmg], and Mysql 4.1.13a is  [http://www.apple.com/downloads/macosx/networking_security/mysql.html available] A [http://www.apple.com/downloads/macosx/networking_security/mysqlbackup.html Mysql backup] tool is also available from the apple website
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|{{Portlet|R programming language|3=300|
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*[http://cran.stat.auckland.ac.nz CRAN mirror]
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*[http://www.biocondcutor.org Bioconductor]
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*[http://cran.r-project.org/src/contrib/Views/Finance.html Empirical finance]
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*[http://people.su.se/~ma/R_intro/ Econometrics with R]
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*[http://www.mayin.org/ajayshah/KB/R/R_for_economists.html R for economists]
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*[http://www.itp.phys.ethz.ch/econophysics/R/ R metrics]
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*[http://www.burns-stat.com/ Burns statistics]
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*http://www.stat.auckland.ac.nz/~paul/
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*[http://ebimage.wordpress.com/ Image analysis for R blog site]
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*[http://www.maths.lth.se/help/R/ R help (Henrik Bengtsson)]
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*[http://www.stat.auckland.ac.nz/~ihaka/Workshop/ Ihakas R courses]
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*[http://www.stat.uiowa.edu/~luke/R/codetools/ codetools_0.0-7.tar.gz]
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*[http://www.cs.uiowa.edu/~luke/talks/DSC07.pdf DSC talk]
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*[http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#R_clustering Statistics resource]
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*[http://tolstoy.newcastle.edu.au/R/help/03b/0140.html X11 and R]
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}}
  
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=== Apache in OS X (tiger) ===
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|{{Portlet|3=300|Reading|
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Apache/1.3.33 is shipped with a standard install of OS X on Jaguar, Panther, and Tiger. It does not come with php
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*'''[[XmlWiki]]'''
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pre-compiled.  
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*'''[[XmlWiki Installation]]'''
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*'''[[Peer Installation]]'''
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*'''[[Talk:Nodal-wikid.pl]]'''
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}}
  
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:Start your personal webserver under;
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|{{Portlet|3=300|Books|2=
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preferences → Sharing → Personal Web Sharing
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*[http://www.amazon.com/gp/product/0393317552/002-1121960-7876808?v=glance&n=283155 Guns Germs and Steel ]
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*[http://www.amazon.com/Collapse-Societies-Choose-Fail-Succeed/dp/0670033375 Collapse]
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*[http://www.amazon.com/gp/product/1841126918/002-1121960-7876808?v=glance&n=283155 Wake Up]
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*[http://www.springer.com/west/home/generic/search/results?SGWID=4-40109-22-46634499-0&referer=www.springeronline.com&SHORTCUT=www.springer.com/sgw/cda/frontpage/0,11855,4-40109-22-46634499-0,00.html BioConductor book] [http://books.google.com/books?hl=en&lr=&id=e8-CfJ5RIgAC&oi=fnd&pg=PA3&dq=%22Gentleman%22+%22Bioinformatics+and+Computational+Biology+Solutions+Using+...%22+&ots=J1YwJLhmga&sig=4uRuKsF9iH1W8ue3MNj9UNg2sCA#PPA62,M1 Google scholar]
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*[http://www.doctorsaredangerous.com/ Take control of your Health] ''by elaine Hollingsworth'' available at ''Takapuna Health Store''
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*[http://www.elgar.govt.nz/search/X+++stupidity&searchscope=6&SORT=R/X+++stupidity&searchscope=6&SORT=R&SUBKEY=%20%20%20stupidity/1%2C22%2C22%2CB/frameset&FF=X+++stupidity&searchscope=6&SORT=R&4%2C4%2C In search of Stupidity]
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*[http://www.elgar.govt.nz/search/tmemes/tmemes/-3%2C0%2C0%2CB/frameset&FF=tmeme+machine&1%2C1%2C/indexsort=- The meme machine]
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*[http://www.trademe.co.nz/Browse/SearchResults.aspx?searchType=0193-0465-0226-2240-&searchString=The+fifth+discipline&x=0&y=0&searchRegion=100&type=Search  The fifth Discipline ''Peter Senge'']
 +
}}
  
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There are  differences as to the locations of installed directories from standard binary/source linux installations. Its worth
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|{{Portlet|3=300|Interesting Software|
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checking the build with the terminal command '''httpd -V'''
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*[https://www.gotomeeting.com/ GoToMeeting]
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<table class=document-code><tr><td>[[+httpd -V]]</td></tr></table>
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*http://www.supermodel.co.nz/ (commercial CMS)
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}}
  
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The webpage is accessable as localhost or 127.0.0.1, with access to your personal home page at:
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|- valign=top
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:<nowiki>http://127.0.0.1/~USER_NAME</nowiki>
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|
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The webserver pages are located in the directories
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{{Portlet|URLs|3=300|2=
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*/Library/WebServer (System pages)
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*[http://mail.google.com/mail/ Gmail]
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*/Users/USER_NAME/Sites (User page)
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*[http://www.interest.co.nz/6hjk8as0s.asp Interest.co.nz]
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*[http://finance.yahoo.com/currency Yahoo exchange rates]
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*[http://www.asbbank.co.nz/story206.asp ASB exchange rates]
 +
*[http://www.perl.com Perl website]
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*[http://www.edwardtufte.com/tufte/ Edward tuftes visualization books]
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*[http://www.stat.auckland.ac.nz/~ihaka/color-talk.pdf Ross Ihaka's colour talk]
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*[http://www.1stweb.co.nz/ 1stWeb]
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*[http://www.illwillpress.com Illwillpress]
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*[http://www.joecartoon.com Joe Cartoon] &nbsp; [http://www.fat-pie.com/ Fat Pie]
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*[http://www.garethmorgan.com/articles.asp Gareth Morgan]
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*[http://www.companies.govt.nz/pls/web/dbssiten.main Companies office]
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*[http://www.directbroking.co.nz/ Direct broking] Tickers:TZN ANH
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*http://scientific.thomson.com/products/wos/
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*[http://www.stat.wisc.edu/~newton/ Micheal Newton]
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*[http://www.biostat.wisc.edu/~kendzior/ Christina Kendiorski]
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*[http://www.bmbolstad.com/misc/MAS5diff/Mas5difference.html MAS5 vs GCOS]
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*[http://faculty.chicagogsb.edu/john.cochrane/research/Papers/index.htm John Cochrane]
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* DSC:89730
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*[http://www.timeanddate.com/worldclock/city.html?n=1100 Lethbridge time]
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*[http://www.pedrottiphotography.com/ Photogapher]
 +
*[http://www.cut-the-knot.org/index.shtml Cut the knot education website]
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*[http://www.autogeek.net/dual-action-polisher.html Car polisher guide]
 +
*[http://www.energyrating.gov.au Energy ratings]
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*[http://www.consumer.org.nz Consumer.org]
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*[[w:Internet archive|Internet archive]]
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*[http://jfly.iam.u-tokyo.ac.jp/color/index.html#triple Presentation tips for colourblind people]
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*R 5426593 8322277 11171585
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*C 1815655 2060625 2249987
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*[http://wikimapia.org/#y=-36875634&x=174807002&z=18&l=0&m=a wikimapia]
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*[http://www.cs.waikato.ac.nz/~olena/publications/milne_wikipedia_final.pdf Waikato uni wikipedia paper]
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*[http://philip.greenspun.com/materialism/money investment skepticism]
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*[http://www.zeald.com/ Zeald ''so called'' website experts]
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*[http://www.geobytes.com/IpLocator.htm?GetLocation iplocator]
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*[http://www.readwriteweb.com/archives/semantic_web_difficulties_with_classic_approach.php Semantic article]
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*[http://ca.expasy.org/swiss-2dpage/viewer 2D gel viewer]
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*[http://www.w3.org/MarkUp/Guide/Style CSS]
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*[http://www.looklearninvest.org.nz/ Look learn invest]
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*[http://www.bachcare.co.nz/bach_search/property_details.asp?propertyID=545 Coopers Beach]
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*[http://www.federalreserveeducation.org/fed101/policy/money.htm FED education]
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*[http://finance.yahoo.com/currency/convert?from=NZD&to=USD&amt=1&t=5y $NZ versus $US]
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*http://www.omf.co.nz
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*http://www.cmcmarkets.co.nz/
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*http://swoogle.umbc.edu/
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*[http://stats.wikimedia.org/EN/TablesWikipediaEN.htm Wikipedia stats]
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*http://www.shl.com/shl/en-int
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*http://wiki.ts.wikimedia.org/
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*http://tools.wikimedia.de/~magnus/
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*http://korrekt.org/talks/Wikimania2007/SMW.html
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*[http://leuksman.com/log/ Brions blog]
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*https://wikitech.leuksman.com/
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*http://www.technicalinfo.net/papers/CSS.html
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*http://www.download.com/VirtualLab-Data-Recovery/3000-2274_4-10298807.html?part=dl-10298807&subj=dl&tag=button
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*[http://osdir.com/ml/org.wikimedia.mediawiki/2004-03/msg00022.html MediaWiki Latex support post (Brion Vibber)]
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*http://tools.wikimedia.de/
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*[https://wiki.toolserver.org/view/Main_Page ToolServer wiki]
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*[http://invention.swmed.edu/etblast/etblast.shtml eTBlast]
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*[http://bp0.blogger.com/_SfxDExxUukY/RvpYc_LhARI/AAAAAAAAAJM/Pe3JgMUfGXU/s1600-h/housingmarket_nytimes.jpg US housing chart]
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*[http://www.broad.mit.edu/cancer/software/genepattern/ Genepattern -broad]
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*[http://g2.trac.bx.psu.edu/ Galaxy -interactive and reproducible genomics]
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*[http://www.pharmazie.uni-kiel.de/chem/ BioTeX]
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*[http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/ Affymetrix guide]
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*[http://www.blueleafsoftware.com/Resources/Templates/ Word style]
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*[https://secure.bioconductor.org/SeattleNov08/ BioC sequencing]
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*[http://www.poweratlas.org/ Affymetrix power calculations]
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*[http://www.blaisdonbrotherhood.info/Alastair%20Bourne.pdf Alistair Bourne
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*[http://www.ncdc.noaa.gov/oa/climate/ghcn-monthly/index.php Climate change] ([http://cran.r-project.org/web/packages/sspline/ source: sspline package])
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*http://bioanalysis.otago.ac.nz [https://caarray.otago.ac.nz/wiki/article/User:MDavy (wiki)]
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*[http://www.elliottwave.com/freeupdates/default.aspx Financial reading]
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**[http://www.elliottwave.com/freeupdates/archives/2009/01/26/U.S.-Stocks-How--Undervalued--Are-They-Really.aspx Stocks How undervalued are they really?]
 +
*[http://www.withouthotair.com/ Sustainable energy book]
 +
*[http://www.giant-bicycles.com/en-AU/bikes/mountain/1055/29610/ Mountain bike geometry]
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*[http://www.nzherald.co.nz/business/news/article.cfm?c_id=3&objectid=10575531 Ben Graham's The Intelligent Investor ]
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*[http://htseq.ucr.edu/HT_BioC_Manual HT Sequence Analysis with R and Bioconductor]
 +
*[http://www.clarku.edu/~djoyce/complex/ Complex numbers]
 +
*[http://bsrweb.burnham.org/metadot/index.pl?iid=2577 Microarray resource]
 +
*[http://microgen.ouhsc.edu/tutorials/blastonosx.htm blast for OS X]
 +
*[http://massgenomics.wordpress.com/2008/05/14/short-read-aligners-maq-eland-and-others/ aligners comparison]
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*[http://bioinformatics.oxfordjournals.org/cgi/content/full/24/5/713 SOAP publication]
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*[http://www.sanger.ac.uk/Users/lh3/NGSalign.shtml NGS Alignment Programs]
 +
*[http://www.sanger.ac.uk/Users/lh3/ Heng Li's homepage]
 +
*[http://ocw.mit.edu/OcwWeb/Electrical-Engineering-and-Computer-Science/6-00Fall-2008/LectureVideos/index.htm MIT open learning lectures]
 +
}}
  
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===Useful Links===
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|
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*[http://www.macdevcenter.com/pub/a/mac/2001/12/07/apache.html Apache for OS X]
 
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*[http://www.entropy.ch/software/macosx/php/ PHP for Apache shipped with OS X]
 
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----
 
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:[[Example Article]]
 
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==Backing up wikidb using mysql (OS X)==
 
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Information for doing this came from [http://meta.wikimedia.org/wiki/Backup_Database here].
 
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There are many ways to go about this;
 
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*drop entire databases, and reconstruct
 
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*drop tables if they exist for a particular database and reconstruct
 
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* Insert data only into databases (errors can be introduced if not INSERT IGNORE startments)
 
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Here I want to move the wikidb directory in mysql to a temporary
 
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location (say /tmp directory) so the information is not perminantly lost then use mysql to reconstruct wikidb.
 
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*<s>mysqldump -u root -p --single-transaction wikidb > /tmp/backup.sql</s> creates tables which already exist
 
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*mysqldump -u root -p --single-transaction --no-create-info wikidb > /tmp/backup.sql
 
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*wikipath=`locate wikidb | grep wikidb$`
 
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*sudo mv $wikipath ${wikipath}-bak
 
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*cd /tmp
 
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* [Time to recreate MediWiki which will make the wikidb database]
 
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*mysql -u root -p wikidb
 
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*<s>create database wikidb</s>
 
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*<s>use wikidb</s>
 
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*source /tmp/backup.sql
 
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* <nowiki>#</nowiki> Check the directory sizes match between wikidb and wikidb-bak
 
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* sudo du $wikipath
 
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* sudo du $wikipath-bak
 
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*<nowiki>#</nowiki> Refresh the links using maintenance script
 
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* php refreshLinks.php
 
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== R programming language markup ==
 
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  <table class=document-code><tr><td>[[+CreateDirectories.R]]</td></tr></table>
 
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== LaTeX document class letter markup ==
 
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  <table class=document-code><tr><td>[[+letter.tex]]</td></tr></table>
 
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== xml Wiki Markup ==
 
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<table class=document-code>
 
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<tr>
 
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  <td>
 
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    Table Markup
 
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  </td>
 
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  <td>
 
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    <nowiki>
 
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      <table class=document-code><tr><td>Table Markup</td></tr></table>
 
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    </nowiki>
 
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  </td>
 
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</tr>
 
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</table>
 
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<center>''NOTE: You can be real casual with table syntax and miss out all <nowiki></tr>'s and </td>'s</nowiki> if you like.''</center>
 

Latest revision as of 04:36, 23 July 2011





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