Software

DrJava Maintenance and Improvements

DrJava is an excellent environment for introductory Java programmers providing all the basic elements of an IDE without the distractions so that students can focus on learning to code. Unfortunately this tool has fallen into some disrepair due to lack of attention. I and some some students have taken on the task small improvements to fix minor problems. This version is unofficial and is distributed here until the changes can be merged into the main branch.

Bioinformatics Tools

aligntool

This package provides basic alignment tools to do pairwise alignment and set up and search a database of sequences with alignment. It is written in Ocaml

pdbtool

PDB files contain information about proteins but are notoriously hard to handle. pdbread.ml is a library of routines designed to process these files and pdbtool is a command line utility for such tasks as sequence and coordinate extraction.

domo

Pre-release of Domo which does distance matrix analysis on proteins using semidefinite programming (see draft paper under my Research). The code for Domo is in two pieces. A modified version of the SDP solver CSDP was used in Domo. It must be downloaded and compiled. The main code for Domo comprises a series of Matlab files.

Code Fragments

org-table-move-single-cell

Move a single table cell around in Emacs org-mode. As near as a I can tell, this capabaility is not provided though moving whole tables and columns is available. Paste the linked code into you .emacs file and use C-M-up and the like to move single cells around. A long time ago asked about this but apparently never got an answer and several versions later org still lacks this feature.