Programming Pages

May 31, 1998 -- I haven't updated this page is quite some time (not that I think anyone is reading it), but I have come quite a long way with my programming, as my major is now almost entirely "bioinformatics".

I've written a number of small, albeit useful programs in C++ and Java using Metrowerks' Codewarrior and a number of Perl scripts. I'll try to put them on this page soon:

Databaser - this program (C++) helps me do some of the more repretitive tasks for my sequence similarity project
Gregolus - I wrote this program (two versions: C++ and Java) to analyze ESTs
Blastparser - A collection of Perl and Java routines to parse BLAST output

I've been interested in computers and programming since I was in grade school and I got a Commodore VIC-20. Although a wonderful machine, it had 3K of memory, no way to back up whatever programs I had written, and it used my cheezy B&W TV for a monitor! Eventually I bought a cartridge which expanded the memory and a tape drive so I could save the simple programs I wrote.

From: the timeline of microcomputers page: "January 1981 - Commodore announces the VIC-20, with full-size 61-key plus four function key keyboard, 5KB RAM expandable to 32KB, 6502A CPU, 22 character by 23 line text display, and color graphics, for US$300. During its life, production peaks at 9,000 units per day"

Although a wonderful machine, it had 3K of memory, no way to back up whatever programs I had written, and it used my cheezy B&W TV for a monitor! Eventually I bought a cartridge which expanded the memory and a tape drive so I could save the simple programs I wrote.

When I began high school, I got an Apple ][e with a disk drive and a monitor of its very own! I even took some programming classes!

During one of my summer jobs, I managed to obtain an IBM PC AT. From the timeline of microcomputers page: "August 1984 - IBM announces the PC AT, a 6MHz 80286 computer using PC-DOS 3.0, a 5.25-inch 1.2MB floppy drive, with 256KB RAM, for US$4000, which doesn't include hard drive or monitor/card. With a 20MB hard drive, color card and monitor: US$6700." It was used, had no documentation and was used as a file server before I got it. So, I learned how to: low-level format a PC HD, use DOS, troubleshoot errors, etc. Great experience!

Now, I'm at Cornell, using a Power Macintosh 8500/150. I've come a long way from copying programs from Nibble magazine, typing them into a VIC-20 which was sitting on a card table in my room, only to lose the program once it was time to go to bed!

My primary use of this machine is for digital imaging. We use both a microscope attached to the AV port via an old video camera for computer aided microscopy as well as a scanner for examining fruit shape and size. Some of this information is detailed in my research pages.

I'd like to create this web page to chart my progress in programming.

I'm using Metrowerks Codewarrior to learn how to program and to develop software for analyzing sequence information.

I find PERL to be the single most valuable tool in programming for scientific applications. I use MacPerl quite a bit and then transfer things over to UNIX

BUT, I'll also hopefully work on some other cool projects which I'd like to include here.

For now, however, here are some programming links I've found useful:

More are sure to come!

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If you would like to send me electronic mail, please send it to alm13@cornell.edu

I'd appreciate your comments!