Fix broken links

content/markup/data/longform/data-analysis-using-r-functions-as-objects.markdown

@@ -144,8 +144,8 @@ Again this is an example of how one function can accept another function as an a
 [dry]: http://en.wikipedia.org/wiki/Don't_repeat_yourself
 [cap]: http://en.wikipedia.org/wiki/Copy_and_paste_programming
 [hadly]: http://had.co.nz/
-[plyr]: http://had.co.nz/plyr/
-[foreach]: cran.r-project.org/web/packages/foreach/index.html
+[plyr]: http://plyr.had.co.nz/
+[foreach]: http://cran.r-project.org/web/packages/foreach/index.html
 [iter]: http://cran.r-project.org/web/packages/iterators/index.html
 
 ### A four-minute video introduction

content/markup/data/longform/dealing-with-big-data-in-bioinformatics.markdown

@@ -65,15 +65,15 @@ Object relational management (ORM) libraries like ActiveRecord allow the databas
 Quite a long post I know. I know code performance is a weighty topic and probably what I'm outlining here isn't the best way to go about dealing with large data. I'm there are better ways better technologies to manage large amounts of data too, e.g. map/reduce or schemaless databases. I'm not a trained computer scientist or a software engineer, but a biologist and what I've outlined is what allowed to me to produce the results I need. I'd be happy to read any further suggestions in the comments though.
 
 [ar]: http://ar.rubyonrails.org/
-[database]: http://www.bioinformaticszen.com/software/using_a_database/
+[database]: /post/using-a-database/
 [ar_index]: http://api.rubyonrails.org/classes/ActiveRecord/ConnectionAdapters/SchemaStatements.html#M001911
 [ree]: http://www.rubyenterpriseedition.com/
 [jruby]: http://jruby.org/
 [ruby19]: http://www.ruby-lang.org/en/news/2009/07/20/ruby-1-9-1-p243-released/
 [csv]: http://blog.grayproductions.net/articles/getting_code_ready_for_ruby_19
 [norm]: http://en.wikipedia.org/wiki/Database_normalization
-[merge]: http://wiki.r-project.org/rwiki/doku.php?id=tips:data-frames:merge
+[merge]: http://rwiki.sciviews.org/doku.php?id=tips:data-frames:merge
 [premature]: http://fetter.org/optimization.html
-[batches]: http://ryandaigle.com/articles/2009/2/23/what-s-new-in-edge-rails-batched-find
+[batches]: http://archives.ryandaigle.com/articles/2009/2/23/what-s-new-in-edge-rails-batched-find
 [assoc]: http://guides.rubyonrails.org/active_record_querying.html#eager-loading-associations
 [ilya]: http://www.igvita.com/2007/10/29/boosting-activerecord-performance/

content/markup/data/longform/organised-bioinformatics-experiments.markdown

@@ -125,7 +125,7 @@ also run. In my example, before my gene sequences are loaded, any pre-existing
 rows in the database are first cleared. I've also created a task called rebuild
 that clears all the data project and repeats the analysis from scratch.
 
-[2]: http://www.bleedingedgebiotech.com/blog/ruby/a-pipeline-is-a-rakefile/
+[2]: http://www.bleedingedgebiotech.com/blog/2008/05/02/a-pipeline-is-a-rakefile/
 
 Calling `rake -T` at the command line list all the tasks outlined in the file.
 This is a handy way of keeping track of what all the tasks in your project are
@@ -187,7 +187,7 @@ start codon, finishes with a stop codon, and contains only valid DNA sequence.
 I use this in the following method so that any sequences that don't match this
 criteria will print an error at the command line, when the data is loaded.
 
-[3]: http://www.michaelbarton.me.uk/2007/12/dirty-laundry-in-public/
+[3]: http://www.michaelbarton.me.uk/research/2007/12/dirty-laundry-in-public/
 
 <%= highlight %>
     # Checks that the sequence has a start codon,
@@ -222,5 +222,5 @@ languages have libraries to implement all these techniques, so the [language
 you choose][5] is less important than using good programming practices for the
 task you're working on.
 
-[4]: http://github.com/michaelbarton/organised_experiments/tree/master
+[4]: https://github.com/michaelbarton/organised_experiments/tree/master
 [5]: http://network.nature.com/forums/bioinformatics/1611

content/markup/data/longform/organising-yourself-as-a-dry-lab-scientist.markdown

@@ -91,4 +91,4 @@ My example is just one way to do this however and I think any system is better
 than nothing for keeping track of what you've been doing.
 
 [1]: http://wikiomics.org/
-[2]: http://wikiomics.org/wiki/Bioinfo_tutorial#Before_you_start
+[2]: http://openwetware.org/wiki/Wikiomics:Bioinfo_tutorial

content/markup/decomplected-workflows/longform/functional.markdown

@@ -11,7 +11,7 @@ Makefiles can result in simple and reproducible workflows][make]. Here I'm
 going to outline simplifying workflows further by taking a functional approach
 to building them.
 
-[make]: /post/decomplected-workflows-makefile/
+[make]: /post/decomplected-workflows-makefiles/
 
 Functional programming is an alternative paradigm to imperative programming
 such as C or object orientated programming with Java. There are two concepts in

content/markup/misc/longform/bio-blog-special-edition.markdown

@@ -8,7 +8,7 @@ Short and to the point - the tips & tricks supplement to this month's
 bio::blogs edition has been compiled. The link to the pdf is at the end of this 
 post. But first I want to thank those who contributed.
 
-Thanks to <a href="http://eridanus.net/blog/">Dan Swan</a>, <a 
+Thanks to <a href="http://eridanusdotnet.wordpress.com/">Dan Swan</a>, <a 
 href="http://plindenbaum.blogspot.com/">Pierre Lindenbaum</a> and <a 
 href="http://konradscons.blogspot.com/">Konrad Forstner</a>, who contributed 
 particularly large articles covering every aspect of being a bioinformatian.
@@ -17,9 +17,9 @@ particularly large articles covering every aspect of being a bioinformatian.
 revision control, creating applications and blogging. <a 
 href="http://scienceroll.com/">Bertalan Meskó</a> sent in a list of genetic 
 disorder databases. <a href="http://nftb.net/">Roland Krause</a> offers tips on 
-managing and searching data sets. <a href="http://ryancastillo.org/">Ryan 
+managing and searching data sets. <a href="http://myfakeif.blogspot.com/">Ryan 
 Castillo</a> wrote about his experiences in bioinformatics. <a 
-href="http://www.paraschopra.com/blog/">Paras Chopra</a> offers advice for 
+href="http://paraschopra.com/blog/">Paras Chopra</a> offers advice for 
 undergraduates on how to use their summers. <a 
 href="http://pbeltrao.blogspot.com/">Pedro Beltrao</a>, editor of bio::blogs, 
 discusses the importance of keeping up to date on the literature. Also, <a 
@@ -35,4 +35,4 @@ but you should definitely go and take a look.
 
 Enjoy.
 
-<a href="http://www.bioinformaticszen.com/wp-content/uploads/2007/05/bioblogs_special.pdf" title="Download"><img src="http://bioinformatics-zen.s3.amazonaws.com/icons/pdf.png" alt="Download" class="centre" /></a>
+<a href="http://bioinformatics-zen.s3.amazonaws.com/bioblogs/special_edition.pdf" title="Download"><img src="http://bioinformatics-zen.s3.amazonaws.com/icons/pdf.png" alt="Download" class="centre" /></a>

content/markup/philosophy/longform/bioinformatics-wide-set-of-transferable-skills.markdown

@@ -73,12 +73,12 @@ but also because the skills learnt are useful in other professions if you
 decide your career lies elsewhere.
 
 [quitting]: http://blog.devicerandom.org/2011/02/18/getting-a-life/
-[wetlab]: http://scienceblogs.com/bioephemera/2011/03/are_biology_graduate_students.php
+[wetlab]: http://scienceblogs.com/bioephemera/2011/03/31/are-biology-graduate-students/
 [shortage]: http://robots.thoughtbot.com/post/3310910483/a-shortage
 [popular]: http://openwetware.org/wiki/Image:Most_Popular_Bioinformatics_Programming_Languages.png
 [test]: http://jamesshore.com/Blog/Red-Green-Refactor.html
-[git]: http://www.bioinformaticszen.com/tools/git/
-[vim]: http://www.bioinformaticszen.com/tools/vim/
+[git]: http://www.bioinformaticszen.com/post/git/
+[vim]: http://www.bioinformaticszen.com/post/vim/
 [better]: http://stackoverflow.com/questions/82639/how-to-become-a-better-programmer
 [hiring]: https://gist.github.com/6443
 [clever-algorithms]: http://www.cleveralgorithms.com/

content/markup/software/longform/preseting-software-on-a-poster.markdown

@@ -43,4 +43,4 @@ visually appealing, design was the good way to attract interest in the software
 and then start a conversation.
 
 [scaf]: http://next.gs
-[post]: /research/experiments-in-genome-scaffolding-and-peer-review/
+[post]: /post/experiments-in-genome-scaffolding-and-peer-review/

content/markup/tools/longform/git.markdown

@@ -25,10 +25,10 @@ Git is useful for collaborating on shared source code repositories. The collabor
 - [Extensive git guide][guide]
 
 
-[history]: http://en.wikipedia.org/wiki/Git_(software)#Early_history
-[gh]: http://www.github.com
+[history]: http://en.wikipedia.org/wiki/Git_(software)#History
+[gh]: https://www.github.com
 [git]: http://git-scm.com/
-[video]: http://www.gitcasts.com/posts/railsconf-git-talk
+[video]: http://schacon.github.com/2008/06/02/railsconf-git-talk.html
 [research]: http://mendicantbug.com/2008/11/30/10-reasons-to-use-git-for-research/
-[new]: http://github.com/blog/120-new-to-git
+[new]: https://github.com/blog/120-new-to-git
 [guide]: http://www-cs-students.stanford.edu/~blynn/gitmagic/

content/markup/tools/longform/vim.markdown

@@ -14,13 +14,19 @@ As Vim is entirely text-based, without the pretty interface of modern editors, m
 
 ### Customise
 
-One reason not to use Vim, is that it doesn't have the code orientated features of integrated development environments (IDE) such as [Eclipse][eclipse] and [Netbeans][netbeans]. But it does. Vim is easy to customise which has lead to a community of developers creating a large number of plugins. [Code snippets][snippets], [project drawers][nerd], and [fuzzy file finding][fuzzy] are just some examples of plugins aimed at using Vim as an IDE. Whatever [language][latex], [file type][html], or [framework][rails] you use, someone will have written a Vim plugin. This gives Vim all the functionality to rival any IDE.
+One reason not to use Vim, is that it doesn't have the code orientated features
+of integrated development environments (IDE) such as [Eclipse][eclipse] and
+[Netbeans][netbeans]. But it does. Vim is easy to customise which has lead to a
+community of developers creating a large number of plugins. [Code
+snippets][snippets], [project drawers][nerd], and [fuzzy file finding][fuzzy]
+are just some examples of plugins aimed at using Vim as an IDE. Whatever
+[language][latex] or [framework][rails] you use, someone will have written a
+Vim plugin. This gives Vim all the functionality to rival any IDE.
 
 [eclipse]: http://www.eclipse.org/
 [netbeans]: http://www.netbeans.org/
 [snippets]: http://www.vim.org/scripts/script.php?script_id=1318
 [nerd]: http://www.vim.org/scripts/script.php?script_id=1658
 [fuzzy]: http://www.vim.org/scripts/script.php?script_id=1984
 [latex]: http://vim-latex.sourceforge.net/
-[html]: http://www.infynity.spodzone.com/vim/HTML/
 [rails]: http://www.vim.org/scripts/script.php?script_id=1567