Sleep, Braveheart

Haven't been getting too many sleep these days, slowly killing myself by overdoing it, first selected a novel gene (was too boring), then the next gene (doesn't satisfy the project criteria of homology) then hopefully this last one is going to be the last. It better because the deadline is in 2 weeks! If I stucked with my first gene then I would have been looong done by now but heck, I'm learning more stuff going down this ragged terrain, so thinking back it's all worth it in the end, no matter what the outcome is, the journey I think matters more than the destination.

As an aside, read an article about standing out in a crowd and this writer mentions the old Braveheart quote,

"Everybone dies, but not everyone lives"

and this one is good too

"Challenge, by definition is the death of the old and the birth of the new."

Desrochers.

Knife

Knife ... cuts like a knife ... how will I ever heal ... I'm so deeply wonded .... Knife

Rockwell "Cuts Like A Knife"

Shouldn't have checked, shouldn't have visited the blog site ... at least someone's happy I guess.

Logo Design

Hmm... As far as I can remember, I've entered 3 logo contests to date. First one was about a restaurant, drew a plate (with a fork and spoon too), it was pretty cool and but didn't win :( Second logo was for a school union group, drew a building that resembles the place, drew tiny little windows too, again, didn't win :( Both were drew using Photoshop on Windows. But this last one, submitted yesterday was for the school's new mail webapp, submitted two of them, this time, using Vector, that's right, adios Photoshop, and welcome Inkscape. We'll see what happens this time ... But hey, even if I don't win, I gotta admit, these recent logos actually look like logos for a change and it's in vector so no loss of quality when resized, and it has only two colors, 2 logos in 4 hrs, not bad for a newbie!

Web programming

Spent the last two days working on a site 20% writing code and another 80% uploading/refreshing/testing/googling, learned some more javascript/php/css along the way. Fun stuff. Had this crazy idea of doing a web-based sequence viewer too.

PyMol script
# show all surfaces with 50% transparency.
set transparency, 0.5
set ray_opaque_background, off
png ~/Videos/dna1.png, dpi=300

PHP DB
http://www.designdetector.com/archives/04/10/FlatFileDatabaseDemo.php
http://www.designdetector.com/archives/04/12/FlatFileDatabaseDemo2.php

IFrame Height Fix
http://guymal.com/mycode/100_percent_iframe/

XSLT
http://xslt.sitesfree.com/

CSS
http://www.webreference.com/programming/css_frames/



Now on to homework ...

Graduate Studies

So, been thinking about graduate school or not,

I say to myself, once I find a good topic that I want to do, correction, really really want to do, then I'll go for it.... Maybe I'll take 1 yr break or something, spend time volunteering, free landscape, work part-time or something ...

Links about what graduate school is:
http://www.cs.sfu.ca/~mori/gradStudies.pdf
http://bioinfo.icapture.ubc.ca/mywiki/GradStudentAdvice

Presentation Tips

Some presentation tips from http://web.cba.neu.edu/~ewertheim/skills/oral.htm#strategy

US Presidential

I guess I should at least document this somewhat monumental event (I'm not really into politics), but Barack Obama (Democratic party) won the election.

Isn't it nice?

Isn't it nice to get a simple 'hi' from someone you don't see/talk/communicate/interact with everyday?


.... then on the other hand, waiting for a reply take its toll on you as well, Yin-yang of life? Perhaps.

A Lesson on Exponential

Went to a speaker today, something todo with the past, present and future of technology. Anyways, the speaker pointed out something about exponentials, so 2^x. Then he gives this example (from Mathworld)

Assuming it were possible to fold paper without restriction, the height of a piece of folded paper would double in thickness each time it was folded. Since one sheet of typical 20-pound paper has a thickness of about 0.1 millimeter, folding 50 times (if this were physically possible, which of course it is not) would produce a wad of height 1.13*10^11 meters, and folding one more time would make the stack higher than the distance between the Earth and Sun.

I didn't believe it at first, I did some rough calculation, so 2^50, then to simplify, 2^10 = 1024 then 1024^5 is approx 10^(15). Big number, then I go, ok, assuming the paper is 1 cm thick, so in meter terms, move 2 zeroes over, so 10^12 m. OK, still sizable I think, Earth's bigger than that I thought. So I go home, look at my friend Wikipedia, and found out that Earth's diameter is only 12,742 km. I go what, only that much? And Mount Everest is 8,848 m above local sea level and the Mariana Trench is 10,911 m below local sea level.

Hmmm.... I guess he was right after all, gotta work on my familiarity on how big stuff are, but at least I learned something new :D

Some more numbers (Wikipedia)

• football field length 100 yd (91 m) long. Including the end zones it is 120 yd (110 m),
• empire state building 449 m
• speed of light 3.00×10^{8 m/s (btw, I should've known that the diameter of earth should be less than this!)}
  

Perl chop-sequence.pl

Perl code that takes a sequence and a read length (N) and outputs reads of size N that overlaps by two nucleotides.

Sample run
[ppt@bioinf tut09]$ ./chop-sequence.pl aacgtacgcttt 5 ; cat ./chopped-sequence.txt
aacgt
gtacg
cgctt
ttt

Code
1 #!/usr/bin/perl
2 #
3 # 1. Takes as input two parameters: (i) a DNA sequence and (ii) the size N of the chopped fragments.
4 # 2. Generates fragments of size N that are such that they overlap in two nucleotides with another fragment at its right side. Each fragment is writte n in a separate line in a file called chopped-sequence.txt.
5 # file: chop-sequences.pl
6
7 my $arg_count = $#ARGV + 1;
8 unless ($arg_count == 2) { die "Need two arguments $!\n"; }
9
10 my $out_file = "chopped-sequence.txt";
11 my $seq = shift;
12 my $chop_len = shift;
13 my $seq_len = length $seq;
14 my $overlap = 2;
15
16 open OUT, ">$out_file" or die "Can't create output file $out_file $!\n";
17
18 if ($seq_len <= $chop_len) {
19 #print "$seq\n";
20 print OUT "$seq\n";
21 close OUT;
22 exit;
23 }
24
25 for (my $i = 0; $i < $seq_len; $i += $chop_len - $overlap) {
26 $contig = substr $seq, $i, $chop_len;
27
28 # for this case, don't output tc on second line
29 # acctcacctcc 5
30 if ((length $contig) == $overlap) {
31 last;
32 }
33
34 #print "$contig $seq $i $chop_len $seq_len \n";
35 print OUT "$contig\n";
36
37 # handle boundary conditions, two case
38 # acctcc 5
39 if ( (length $contig) < $chop_len ) {
40 # reached the end
41 last;
42 }
43 }
44 close OUT;
45

Trivia:
Q. How do you copy-n-paste this code?
A. One way is to use a 1-liner awk script to filter out the first two columns.

tiny RNAs

Victor Ambros, David Baulcombe, and Gary Ruvkun
For discoveries that revealed an unanticipated world of tiny RNAs that regulate gene function in plants and animals

In summary, Ambros was working on the lin-4 gene in C. elegans (worms) which advances worm development. Another gene, lin-14 which Ruvkun is working on works the opposite way (antithesis they call it), it stops development advancement. So, the thing is, this lin-4 gene is only 22 nucleotides (nt) long but useful RNAs are typically 75 nt long. Now this tiny RNA (lin-4) binds to the 3' UTR (untranslated region downstream of the protein coding region) of lin-14, thereby inhibiting the development inhibition (double negative :D) and so development continues. So lin-4 works like a tiny RNA inhibitor of lin-14. Fun stuff.


Diagram from the laskerfoundation link below.

http://www.laskerfoundation.org/awards/2008_b_description.htm

JW FLV MEDIA PLAYER 4.2

http://www.jeroenwijering.com/?item=JW_FLV_Player

Glioma

A glioma is a type of cancer that starts in the brain or spine. It is called a glioma because it arises from glial cells. The most common site of gliomas is the brain.^[1]

http://en.wikipedia.org/wiki/Glioma

Glial cells, commonly called neuroglia or simply glia (Greek for "glue"), are non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system. In the human brain, glia are estimated to outnumber neurons by about 10 to 1.^[1]

Glial cells provide support and protection for neurons, the other main type of cell in the nervous system. They are thus known as the "glue" of the nervous syste

m. The four main functions of glial cells are to surround neurons and hold them in place, to supply nutrients and oxygen to neurons, to insulate one neuron from another, and to destroy pathogens and remove dead neurons. They also modulate neurotransmission.^[2]

^{http://en.wikipedia.org/wiki/Glial_cell}