Software

PDF: I have simple bash scripts to convert PDFs, e.g. from JSTOR, of journal articles in the primary Economics literature (e.g. AER, etc) into compact forms for printing. For instance, for AER, it strips the JSTOR header page, expands each page (reduces margins), compresses the document into two-per-side format, and shifts even and odd doubled pages to optimise for double-sided printing. The result is four article pages per sheet (two per side) but large enough font to be very readable. Ask me if you want them; they work on Unix, Linux, and probably OS-X.

2006: I have now made a more useful tool to assess where the content is in an arbitrary PDF document and, taking into account also where the bounding box is, arrange it for optimal two-per-side two-sided printing. This is scripted in Matlab, but the algorithm is clear in the code. I am also compiling a list of magic pstops incantations produced by this code for different journals.

I have worked on software in Matlab for projecting star fields / star positions (keywords: Matlab, astronomy, pointing) for determining precise pointing of digitized video frames. This toolbox includes a celestial database and projects the astral component of the night sky for a given location and time. It then uses least squares fitting to determine where a video image was looking.

Do you wish your colleagues were using Matlab instead of IDL? (Or vice versa!?) I believe that IDL has astonishingly primitive plotting, inflexible variable types, and a nearly inconceivable lack of built in utilities. Matlab 5 comes with code to write MAT file format files from C. I have written a tool to write Matlab-format files from within IDL (keywords: converting from IDL to Matlab MAT file convert from IDL to Matlab writing MAT file format from IDL). This may be more convenient than using the "idl2matlab" software, which requires starting up a Matlab kernel each time it's used. My software is juvenile [2002] -- please let me know if you use it, and tell me if you extend its functionality -- but it works perfectly and I would like to help others not waste their time starting from scratch! There are just two files: cpblwritemat.c and writemat.pro. The latter is ugly (presumably there is a proper way?!), and a lovely example of why I sometimes loathe IDL. If you use these files, also email me for the most up to date versions.

[2000] I have worked on developing a sensible set of tools for writing my PhD dissertation, with the goal of having others in our field use a common LaTeX bibliography database (BibTeX) of all the sprites papers and presentations, and in improving some default behaviours of LaTeX in the thesis.sty style. Please see my LaTeX page for advice on theses and BibTeX (and PDF.)

[2008] I have spent much time dealing with tables and making scripts to format regression table output into LaTeX using various features. A bunch of what I've learned about tables is in cpblTables.sty

Some other customisations for thesis, beamer, etc are in cpblRef.sty Questions:

How can I centre an over-wide table? When it breaks margin rules, I still want it centred, rather than aligned with the left margin.

www.gnu.org gnu
I use a lot of open source (freedom, not freebie!) software.

I now keep some notes on GNU/Linux experience on my Wordpress blog.
I keep/kept notes on useful software and on installations Ubuntu GNU/Linux on a Zareason laptop bought in 2008.
I also have notes from installation of of Mandrake (9.2 to 10.1), Mandriva (2005LE), and Ubuntu (5.10+) GNU/Linux on a Toshiba Satellite 2410 laptop.
I also have notes within the same page (see Chapter 6?) on how amazingly easy and fast it is now to set up a full-fledged unix server.

iClicker (i>clicker) with Linux

See my struggles with this.

I write horrible Perl; you can ask me for:

[2004] I have started a database/processor for digital images, in my case mostly 35 mm slides. The idea is to store images in their high resolution, original scanned form but efficiently produce chosen sets of ordered images appropriately modified and of reasonable resolution whenever needed for shows (projection) or web display (e.g. in a few years when higher a resolution is appropriate, one command would recreate a given set etc). It makes use of a simple spreadsheet (the database) and the ImageMagick routines.
[2002+] I have written a somewhat elaborate routine to make interactive (HTML) "concept maps", with automatic (wiki-like) referencing and other features.
[2004+] I have also administrated a couple of GNU/Linux servers and unix accounts. I have a set of Perl and PHP tools for administering unix accounts (solicit account requests; grant them; create accounts / initial passwords / default web pages / default unix email forwarding; automatically require users to set a new (secure) unix password within two days for a new account; monitor disk usage; etc.) with really minimal support / administration. It is aimed at providing web, email, and file service accounts for those uninitiated with UNIX (ie Windows / Mac users) securely from a standard GNU/Linux box. It does the tasks above just by running a cron job every night to process requests etc. Please ask me for the scripts!

[2004+] I wrote a simple community photo / contact info / interests etc directory for Green College at UBC. It allows the individuals to update the information and photos themselves, so requires no maintenance. It seems well used. It is also fully controls a majordomo email list, so it acts as a self-serve email list for which you can look up info/photos of any subscriber. It has a number of other features, such as showing a randomly-ordered facebook with people's names visible by mouse rollover: nice for learning faces in your community. The interface is passworded, but just ask if you want to see it or have the code. It requires PHP and MySQL.

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An interface to the statistical software, Stata, and between it and LaTeX. I do almost all my Stata analysis and programming in Python. This is motivated partly by some custom repetitive statistical tasks I needed, partly to save the hassle of compiling multiple regression outputs into one table, partly 'cause I could not stand to start programming in Stata's own language. Much of what I can now do is captured in my pystata [zip] package. As an example, running the demo regressions-demo.py a few in a row will

Generate a .do file
Execute Stata
Generate LaTeX code with the resultsCompile the LaTeX

You can see the sample output, also in the git repository, though it doesn't demo many available options.
The form of the actual latex table is also quite customisable without actually changing the underlying .tex table file that corresponds to each table of results. The preview tex file (corresponding to the pdf, above) that incorporates all the tables gives examples and a wide range of choices for formats in case you want to tweak how things look in your your final document. (See the cpbl-tables>/a> repository)
This code is set up to run under GNU/linux or UNIX with Stata installed, though mostly it has facility to sense Windows or cygwin as well.
This package has evolved towards reading Stata log files directly and extracting regression results, covariance matrices, etc into numpy and pandas forms in Python, and various tools to generate LaTeX from those. It also generates the Stata code that produces those log files.

[2006+] I now write most things in Python. Great for manipulating data.. etc
Some python scripts are online:

dictTrees.py: a favourite. A class which manages nested "dict"s (dicts a Python data type) in an elegant way.

Definitions:

tree: a nested set of dicts with a list of some kind of list at the bottom level of each dict. Typically, the terminal lists are lists of dicts which have discrete-valued properties used to separate them in the tree heirarchy. For instance, a set of dicts describing properties of fruit could be turned into a tree based on the sequence of properties: 'colour','shape','sweetness'. The resulting tree might have top-level keys 'red','green','yellow'.

subtree: a tree

address: a list of keys that specifies the heirarchy of dict entries leading to a particular subtree or a leaf.

branch: an address to a subtree or to a leaf

keynames: the sequence of properties (of a set of dicts distributed within lists at leaves) used to define the tree structure.

leaf: a list or other object at a bottom-level of a tree.

regular tree: a tree with the property that at a particular level (depth), dicts are similar, ie have the same set of keys...... By convention, we ensure that non-regular trees have the property of no empty leaves.

cpblUtilities.py: various utilities. Includes a good text file (tsv,csv) reader that deals with column names, numeric columns, etc.
circuit.py: timer for circuit training!?
emailMyIP.py: useful for DHCP servers?

Some other stuff, not yet documented or put online:

I do almost all my Stata programming in Python. The python code generates stata .do files. Loops, string manipulation, coordination with LaTeX output etc etc looks much better in Python than Stata (actually, maybe I just don't know Stata). I use EST2TEX and CORRTEX in Stata... but I've now replaced all the formatting functions with Python.
Comments
- est2tex needs lots of modifications and extensions. I've used a modified version (by Ben Sand). It does not use math type minuses for negative coefficients
Python wrapper for Stata regressions and for est2tex interface: coordinates creation of an entire table (several regressions) with one command; insertion of indicator lines giving comments or checkmarks by column for given included properties / dummys / controls. etc, some other cleanup.
Now, fairly general routines to turn Stata output into fancy LaTeX tables, transposed or not, multi-page or not, made for Beamer or articles, ...
A number of web spidering (I guess it's called database scraping) codes, some rather elaborate. This is not very useful, generally, since the data cannot be saved due to its proprietary nature. Parkers.co.uk; whatcar.co.uk; maps.google.ca; etc. I have the locations of all wal-mart's in canada, all public libraries in canada, skytrain stations.
Python interface to geocoder.ca.

For my dissertation I worked on some code for simulation of electromagnetic fields' interaction with the lower ionosphere and resultant optical emissions. Some literate-programming source code (using noweb) is online, and you can ask me (or the VLF group at Stanford) for more details if you like.
There are three parts to the codes:

the FWEM calculation (my latest incarnation is version 4.0 of "em3"),
the optical calculation (optCrossSection), and
the geometric/optical integration (which I have called optVideo)

WANTED!

If I were a C.S. prof, all my courses would be design courses of real, open source projects. One could make a major contribution to the world every term! Here are some of the many things I have wished for as a unix user: (Possibly out of date, thankfully!)

Here's a quickie: a somewhat clever (or not) converter from article class into beamer class in LaTeX.
An editor (word processor) which has a gmail-like ability to attach "tags" or labels to different paragraphs or bullet points, etc. This is key for a process I usually go through in organising notes for a paper: notes/thoughts may come with a certain organisation (by source, or etc), but then get reorganised according to some new logic of the paper to be written. If portions of text were objects with possibly multiple simultaneous properties, they could be listed /sorted different ways within the same document, much facilitating the organisation of thoughts.
A really smart GUI to edit latex tables. Possibly an interface for LyX to import spreadsheet tables, etc.
A plotting package for Python / Pylab that is more like Matlab's (more dynamically updatable).
Similarly, a plotting system for Octave that is more like Matlab's: object oriented, dynamically updating, interactive.
A quickie: a tool to strip out the uninteresting mail headers from text files (ie text-based email files consisting simply of concatenated messages, e.g. in order to archive email from my Pine folders). Maybe it could re-sort the messages in the file too.
I still cannot find a vector graphics editor (e.g. scribus, inkscape, etc?) which can open an .eps or .pdf file and edit it, just like ancient Adobe Illustrator could. Typically, I want to be able to open an .eps made by Matlab, get rid of the background to make the thing transparent, and edit some text a bit. Advice?

G.I.S. in Matlab

I've not bothered to learn a real GIS software, and am used to having the control of a scripting language. Sometimes it's really slow to plot, or awkward, to use Matlab's Mapping Toolbox, but I have been doing a lot of that. Finding the outlines (not convex hull) of a group of contiguous polygons...

I used to have mild RSI from typing too much. As everyone says, treating this in time is invaluable to your livelihood and happiness. Here is information, graphics, etc on RSI.