Summary Osra is a a utility designed to convert graphical representations of chemical structures create by Igor Filippov at the National Cancer Institute. This page documents how to compile and install Osra on Ubuntu Linux 11.10. These instructions may work on other versions of Ubuntu Linux and on Debian Linux.  Please leave a comment if [...]

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 3 on Ubuntu Jaunty. Update, Eigensoft 4 is available and should compile on more recent versions of Ubuntu: http://www.hsph.harvard.edu/faculty/alkes-price/software/ 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 [...]

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 [...]