If you want to install Oracle’s SQL Developer on Ubuntu (or another DEB based system such as Debian) you can do one of the following: Download the RPM package and install using rpm (not advisable). Download the RPM package and convert to a DEB package using alien Download the ZIP file titled “Oracle SQL Developer [...]

These are rough notes on how to compile Eigensoft on Ubuntu Jaunty. Create a location to build the code: Warning: /tmp is for temporary files, and any files & directories you create there will be remove upon some subsequent reboot. cd /tmp; mkdir EIGEN; cd  EIGEN; Get the Eigensoft source code: wget  http://www.hsph.harvard.edu/faculty/alkes-price/files/EIG3.0.tar.gz; tar xzvf [...]

This is a brief HOWTO on compiling OSRA, (Optical Structure Recognition) on Ubuntu Jaunty. To quote the OSRA home page, OSRA is … is a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES (Simplified Molecular Input Line Entry Specification – [...]

Some links to stuff I’ve either read or plan to read which I think is interesting: Python is not Java, tips for Java programmers starting w/ Python: http://dirtsimple.org/2004/12/python-is-not-java.html Python for Bioinformatics: http://www.pasteur.fr/recherche/unites/sis/formation/python/index.html BioPython: http://biopython.org/DIST/docs/tutorial/Tutorial.html I need to know Selenium better, it’s possible that I might consider using it for a project I might be working [...]

By default Emacs saves a copy of the previous version of a file you are editing in the same directory as where the original file is located. It saves a copy with ~ appended to the end of the name. ~ is pronounced tilde. However, some tools and programming environments don’t know how to handle [...]

If your installing RAD 7.5 (IBM Rational Application Developer) on Debian or Ubuntu, install the libstdc++5 package: apt-get install libstdc++5

Aha! There is RoR support for Eclipse, via Aptana. I’ve just installed it and the instructions are a bit cryptic. Basically you have to install Aptana first (you can do this as an Eclipse plug-in). Then restart Eclipse and then install the Rails plugin called RadRails. Aptana also has Python and PHP support. Install Aptana: [...]

While writing some RoR code at home (or at least trying to grok the RoR way) I’ve alternating between using Emacs & Netbeans 6.5. Emacs is one true editor to rule them all, but what it’s lacking is code completion such as in Netbeans. I was working on test RoR project last night with Emacs, [...]

To enable mod_perl with Apache2 on Debian & Ubuntu for all directories served up by Apache2, including user directories such as ~/public_html, add the following lines to /etc/apache2/sites-available/default # enable mod_perl     <Files ~ “\.(pl|cgi)$”>            SetHandler perl-script            PerlResponseHandler ModPerl::Registry            Options +ExecCGI            PerlSendHeader On     </Files> In a real production environment you [...]

Doesn’t perform badly, I’ve been using it recently with Ruby code, and I like how it colourises the code to make editing code easier, and performs it auto-completion and method lookup (basically all the features you’d expect with a modern IDE). It’s does’t startup as fast as using Emacs, or vi, but I find the [...]