Permalink
Browse files

Fix broken links

  • Loading branch information...
michaelbarton committed Jul 11, 2012
1 parent 56e1941 commit b0c41d4732092682a702f950d31b11ed423eaf4a
@@ -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
@@ -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/
@@ -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
@@ -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
@@ -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
@@ -8,7 +8,7 @@ Short and to the point - the tips &amp; 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>
@@ -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/
@@ -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/
@@ -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/
@@ -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

0 comments on commit b0c41d4

Please sign in to comment.