Software

I've developed a number of tools in the course of my teaching and research others may find useful.

Testy: Testing Software for Command Line Programs

Testy is a program designed to test command line programs that are often written by students in introductory programming courses. I use it often in my CS courses (CMSC216 and CSCI2021) to allow students to run prescribed test cases associated with credit. The program is under active development: if you want to help or find it useful, shoot me an email.

ShellSlayer Command Line Tutorial

ShellSlayer is a tutorial on the command line and traditional UNIX tools for text processing. It was developed during Fall 2024 and presented at a meeting of the UMD ACM Student Chapter who have expressed interest in expanding the tutorial and making it a regular offering. Anyone who has Docker installed can run the tutorial which has a series of "stages" that teach tools like grep, sed, and bash.

gradescope-submit Submission Script

gradescope-submit is a small script that allows projects to be submitted from a UNIX / Linux command line to the excellent Gradescope assignment service. It is particularly relevant for programming assignments which I use in my courses which are usually run in command line environments often on remote servers. So long as a reasonable Python installation is present on the system, the script should work out of the gate. Write me if you end up using it.

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.