Difference between revisions of "User:Sven"

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{|border=0 width=100%
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====User: Sven====
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|- valign=top
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;My Wiki Userpages
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|{{Portlet|[[Documentation]]|3=300|{{:Technical documentation}}}}
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*[[Wikipedia:User:Zven|Wikipedia/Zven]]
 
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*[[Wikipedia:User:5ven|Wikipedia/5ven]]
 
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*[http://www.mediawiki.org/wiki/User:Zven Mediawiki/Zven]
 
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*[http://meta.wikimedia.org/wiki/User:Zven WikiMedia/Zven]
 
  
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;Bookmarks
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|- valign=top
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*[[Wikipedia:Wikipedia:Template messages|Wikipedia templates]]
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|{{Portlet|OS X|3=300|
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*[[metawikipedia:Help:Variable| Mediawiki variables]]
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*[http://developer.apple.com/documentation/MacOSX/index.html Apple documentation]
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*[[metawikipedia:Interwiki_map|WikiMedia Interwiki map]]
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*[http://www.macosxhints.com/ Mac OS X hints]
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*http://meta.wikimedia.org/wiki/Help:Editing
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**[http://forums.macosxhints.com/ MacOS X forums]
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*[http://en.wikipedia.org/wiki/Interwiki Wikipedia Interwiki map]
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*[http://www.osxhelp.com/ OS X help]
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*[http://meta.wikimedia.org/wiki/LocalSettings.php LocalSettings.php]
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*[http://www.entropy.ch/software/macosx/php/ OS X PHP]
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;Books
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*[http://guides.macrumors.com/ Macrumors wiki]
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}}
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;Finance
 
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*[http://finance.yahoo.com/currency Exchange rates]
 
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*[http://www.asbbank.co.nz/story206.asp ASB rates]
 
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;Notes
 
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Alanah-340
 
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----
 
  
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== Installing MediaWiki on OS X==
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|{{Portlet|Computer Security|3=300|
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Media wiki requires:
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*[http://www.technicalinfo.net/index.html Antivirus/Phishing]
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#Apache webserver
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*[http://centralops.net/co/DomainDossier.aspx Domain dossier]
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#PHP
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*[http://www.cs.auckland.ac.nz/~pgut001/pubs/vista_cost.html Vista whitepaper]
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#Mysql
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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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See [http://www.mediawiki.org/wiki/Download mediawiki.org] and [http://sourceforge.net/projects/wikipedia/ sourceforge] for installation details.
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|{{Portlet|R programming language|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://cran.stat.auckland.ac.nz CRAN mirror]
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If you want to run Apache as a secure webserver then you probably have to build Apache from source.
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*[http://www.biocondcutor.org Bioconductor]
 +
*[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]
 +
*[http://www.itp.phys.ethz.ch/econophysics/R/ R metrics]
 +
*[http://www.burns-stat.com/ Burns statistics]
 +
*http://www.stat.auckland.ac.nz/~paul/
 +
*[http://ebimage.wordpress.com/ Image analysis for R blog site]
 +
*[http://www.maths.lth.se/help/R/ R help (Henrik Bengtsson)]
 +
*[http://www.stat.auckland.ac.nz/~ihaka/Workshop/ Ihakas R courses]
 +
*[http://www.stat.uiowa.edu/~luke/R/codetools/ codetools_0.0-7.tar.gz]
 +
*[http://www.cs.uiowa.edu/~luke/talks/DSC07.pdf DSC talk]
 +
*[http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#R_clustering Statistics resource]
 +
*[http://tolstoy.newcastle.edu.au/R/help/03b/0140.html X11 and R]
 +
}}
  
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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|3=300|Reading|
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*'''[[XmlWiki]]'''
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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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=== Apache in OS X (tiger) ===
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|{{Portlet|3=300|Books|2=
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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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*[http://www.amazon.com/gp/product/0393317552/002-1121960-7876808?v=glance&n=283155 Guns Germs and Steel ]
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pre-compiled.  
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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]
 +
*[http://www.doctorsaredangerous.com/ Take control of your Health] ''by elaine Hollingsworth'' available at ''Takapuna Health Store''
 +
*[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]
 +
*[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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:Start your personal webserver under;
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|{{Portlet|3=300|Interesting Software|
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preferences → Sharing → Personal Web Sharing
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*[https://www.gotomeeting.com/ GoToMeeting]
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*http://www.supermodel.co.nz/ (commercial CMS)
 +
}}
  
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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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|- valign=top
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checking the build with the terminal command '''httpd -V'''
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|
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<table class=document-code><tr><td>[[+httpd -V]]</td></tr></table>
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{{Portlet|URLs|3=300|2=
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*[http://mail.google.com/mail/ Gmail]
 +
*[http://www.interest.co.nz/6hjk8as0s.asp Interest.co.nz]
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*[http://finance.yahoo.com/currency Yahoo exchange rates]
 +
*[http://www.asbbank.co.nz/story206.asp ASB exchange rates]
 +
*[http://www.perl.com Perl website]
 +
*[http://www.edwardtufte.com/tufte/ Edward tuftes visualization books]
 +
*[http://www.stat.auckland.ac.nz/~ihaka/color-talk.pdf Ross Ihaka's colour talk]
 +
*[http://www.1stweb.co.nz/ 1stWeb]
 +
*[http://www.illwillpress.com Illwillpress]
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*[http://www.joecartoon.com Joe Cartoon] &nbsp; [http://www.fat-pie.com/ Fat Pie]
 +
*[http://www.garethmorgan.com/articles.asp Gareth Morgan]
 +
*[http://www.companies.govt.nz/pls/web/dbssiten.main Companies office]
 +
*[http://www.directbroking.co.nz/ Direct broking] Tickers:TZN ANH
 +
*http://scientific.thomson.com/products/wos/
 +
*[http://www.stat.wisc.edu/~newton/ Micheal Newton]
 +
*[http://www.biostat.wisc.edu/~kendzior/ Christina Kendiorski]
 +
*[http://www.bmbolstad.com/misc/MAS5diff/Mas5difference.html MAS5 vs GCOS]
 +
*[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]
 +
*[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]
 +
*[http://ca.expasy.org/swiss-2dpage/viewer 2D gel viewer]
 +
*[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]
 +
*[http://finance.yahoo.com/currency/convert?from=NZD&to=USD&amt=1&t=5y $NZ versus $US]
 +
*http://www.omf.co.nz
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*http://www.cmcmarkets.co.nz/
 +
*http://swoogle.umbc.edu/
 +
*[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
 +
*[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
 +
*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]
 +
*[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]
 +
*[http://www.pharmazie.uni-kiel.de/chem/ BioTeX]
 +
*[http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/ Affymetrix guide]
 +
*[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]
 +
*[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])
 +
*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?]
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*[http://www.withouthotair.com/ Sustainable energy book]
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*[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]
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*[http://microgen.ouhsc.edu/tutorials/blastonosx.htm blast for OS X]
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*[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]
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*[http://www.sanger.ac.uk/Users/lh3/ Heng Li's homepage]
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*[http://ocw.mit.edu/OcwWeb/Electrical-Engineering-and-Computer-Science/6-00Fall-2008/LectureVideos/index.htm MIT open learning lectures]
 +
}}
  
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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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|
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:<nowiki>http://127.0.0.1/~USER_NAME</nowiki>
 
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The webserver pages are located in the directories
 
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*/Library/WebServer (System pages)
 
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*/Users/USER_NAME/Sites (User page)
 
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===Useful Links===
 
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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 tables and data
 
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* Insert data only into databases (errors can be introduced if not using INSERT IGNORE statements)
 
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===Caveat===
 
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When using restore on INSERT statements only where tables already exist, there are two ways to restore
 
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* mysql> source backup.sql <nowiki>#</nowiki>(interactively inside mysql itself)
 
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* mysql -u root -D wikidb < backup.sql  <nowiki>#</nowiki>(bash call using a redirect)
 
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If an error occurs in a redirect then nothing is inserted after the statement that causes the error (e.g. primary keys already exist), whereas interactively from the command line invalid INSERT's provide a warning '''only''' and valid statements are still restored. This is because the bash redirect is being used to stream the file line by line, exiting at the point of failure. Introduced into mysqldump  in version 5.0.15 is ''--insert-ignore'' which allows dumps of '''INSERT IGNORE''' statements. In this case a command line redirect whould work if the dump was;
 
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*mysqldump -u root -p --single-transaction --no-create-info --insert-ignore wikidb > /tmp/backup.sql
 
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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 -D wikidb < /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>
 
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----
 
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==== Contact details====
 
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*Name: Marcus Davy
 
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*Address: 27/3 Raumati Road, Remuera
 
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*Email: [mailto:MDavy@hortresearch.co.nz MDavy@hortresearch.co.nz]
 
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*Phone: 5202 751, 021 500 103
 
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[[Category:Project Developers]]
 
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[[Category:Nad/Contacts|Sven]]
 
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[[Category:Nad/Contacts/Biz|Sven]]
 
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[[Category:Nad/Contacts/Personal|Sven]]
 

Latest revision as of 04:36, 23 July 2011





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