Monthly Archive for January, 2008

Installing redland-1.0.7 from source on Ubuntu 7.10

Published
by
Jason Morrison
on January 28, 2008
in Blog
. 0 Comments

The Ubuntu packages for the Redland RDF libraries seem to have an issue, at least for the Ruby bindings (see Ruby objects to cyclic dependency about the “cyclic include detected” issue), so I installed it from source.

In case I need to do this again (or someone else does), here are the steps I took for installing Redland on Ubuntu 7.10:

1. Get the GNU MP Bignum library:
sudo apt-get install libgmp3-dev

2. Make or go to a scratch directory
cd ~
mkdir redland
cd redland

3. Get redland 1.0.7 and unpack
wget http://download.librdf .org/source/redland-1.0.7.tar.gz
tar xvfz redland-1.0.7.tar.gz
cd redland-1.0.7

4. Build raptor first
cd raptor
./configure && make && make check && sudo make install
cd ..

4. Then build rasqal

NOTE: If you get “Can’t locate XML/DOM.pm in @INC ” during make check, then:
sudo apt-get install libxml-dom-perl

cd rasqal
./configure && make && make check && sudo make install
cd ..

5. Build redland
# We are back in the main redland-1.0.7 directory
./configure && make && make check && sudo make install

6. Get and build redland-bindings
cd ..
wget http://download.librdf.org/source/redland-bindings-1.0.7.1.tar.gz
tar xvfz redland-bindings-1.0.7.1.tar.gz
cd redland-bindings-1.0.7.1
./configure && make && make check && sudo make install

7. Build the language-specific bindings you would like
cd ruby
make && make check && sudo make install
cd ..

Bio eye for the CS guy (or gal!)

Published
by
Jason Morrison
on January 16, 2008
in Blog
. 0 Comments

Lately, as a result of my fascination with Synthetic Biology, I have been reading biology and bioinformatics references voraciously. More on Synthetic Biology to come, but I encourage you to read up on it. It suffices to say that it greatly appeals to me, coming from a Computer Science and engineering background. When you throw “refactoring” and “bacteriophage” into the same paper title, or mention languages and grammars for programming DNA, you’ve got my attention.

To my surprise, I have found several resources that introduce biological concepts to readers with just such a background. In the interest of sharing this information over primping and editing this in Mephisto admin, here’s a work-in-progress of said list.

Some Ruby code that is maybe imaginary

I have partially or fully read, and recommend:

For the last entry, especially note chapters 1, “Molecular Biology for Computer Scientists,” and 2, “The Computational Linguistics of Biological Sequences .”

This last one is not related to programming, but is an amazing introduction to cellular biology that I would highly recommend for its fantastic illustrations and readable prose, whether you are familiar with the material or not: