Software
I've developed a number of tools in the course of research others may
find useful.
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
During my doctoral work I wrote a number of tools to deal with
processing protein sequences / structure files. Contact me if any of
the below sound interesting though many of them are written in OCaml
and Matlab.
- 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
There are also a number of code niblets that others might find useful.
- 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.