BioPHP: PHP for Biocomputing
iFAQ stands for "I frequently ask (myself these) questions". The following content, when taken too seriously, can be hazardous to your health.
Q: Why the choice of colors for GenePHP?
A: Those are the colors of the earth, the cradle of life, home to myriads of diverse organisms. Blue for the sky, yellow for the (rays of) the sun, green for the plants (without which we cannot live), and brown for the earth that we walk upon.
Q: Why write GenePHP using PHP?
A: Well, if I wrote it in Perl it wouldn't be GenePHP, right?
Q: Let me rephrase that. Why write GenePHP when there's BioPerl, BioJava, BioPython, etc?
A: When asked why they climb Everest, mountain climbers would say, "because it's there". Well, I write Genephp because "it's not there" (or there isn't one). Who knows? I might write a GeneCOBOL one of these days. Any volunteers?
Q: What's the difference between CHENEY and SADDAM?
CHENEY is heavier than SADDAM.
Q: What made you say that (CHENEY is heavier)?
CHENEY has a molecular weight of 794 versus SADDAM's 609.
Q: Did you use GenePHP to get that?
A: You bet your life I did. I also wrote a Bioperl script to double-check the answers.
Q: How do you get the molecular weight using GenePHP?
A: Read my lips. R-T-F-M! Oh, it sure feels great to say that (having been on the receiving end so many times)!!!
Q: Okay, now what's the difference between BUSH and BLAIR?
A: Ummm... BUSH is lighter than BLAIR?
Q: No, you idiot! There's no "U" in the protein alphabet! Try again.
A: Ummm... I've got it! It's 4! Three replacements and one insertion makes a levenshtein distance of 4! (prances around)
Q: Hehehe, nice try. The correct answer? BUSH is an Adolf, Blair is a Benito.
Q: Why are you wasting your time on GenePHP?
A: I don't know yet. But I'll tell you when I figure it out. *grin*
Q: Why are you writing this iFAQ?
A: Gene therapy is good but laughter is still the best medicine.