testing...

Must write more. Must write more.

Solstice!

Wow!!!! bill bissett is coming over for dinner tonight! I'm making my spectacular baked asparagus pasta recipie, garlic bread and salad. Yummy!

Some real gems on gnutella, found a 70MB mp3 called "Liquid Acid" that is a sweet sweet mix, right trippy.

Captain Tractor rocks. Sadly, they don't have an MP3 for their best song (IMHO) The Last Saskatchewan Pirate. I didn't know until recently that the Arrogant Worms wrote that song. Interesting.

Sadly, can't listen to the beautiful stream below, it's from Finland and is too choppy on our connection.

Oh my god/goddess!

Imagine being on a planet without rain, there would be no trees, no grass, no flowers. Most planets don't have rain, it's a miracle of the planet earth. Rain is beautiful!

Beautiful day today, a little cloudy, the green really comes out on days like this. I am amazed that I live in such a beautiful place on earth.

Babaji Full Moon meditation this morning at 5am. Very gentle and energetic. Had an incredible dream before the meditation, I was in the back seat of a car, my friend went inside a building, left the car's engine running, but parked. The car started driving itself in front of the building, first just moving a little bit backwards and forwards, then in circles. The car was so tiny that I couldn't get over the front seat to push the break, I was stretching but couldn't make it. A female cop was outside, pointing her gun at the car and being very excited generally. It was very hilarious! We got the car stopped finally, I think it just stopped by itself. Then, they took me back to my friends place, I shook the hand of the male cop, but the female cop went upstairs before I could shake her hand, so I waited downstairs. She didn't come down, so I just sat at a table, and talked to a very intense young woman with very intense eyes, looked like she had been up for a long time, she had a voice I sort of rememberd, but couldn't place it. She was talking about "The Idiots" and said that the furthest extent was having the family involved in middle part. I wanted to agree, but then noticed my parents at the table, so I didn't say anything. It was funny, they weren't there, then they were, I was bringing them in myself, holding myself back, internalized sociatel pressures. This is the current theme in my life now, breaking through these limitations.

Oh wow! This weekend I had tea and oranges with bill bissett one of Canada's most amazing poets! He's been a hero of mine for years, he's inspired me so much over the years, and I love love love his poetry (some of it is on my site). Wow!

Many strange dreams lately, very real dreams, bubbling to the surface. This happened months ago,
and the same things are bringing up the same dreams. Like a pot tightly covered, when the dreams are supressed, they come up later with much force. Now, getting to the gentle dreams, some very gentle and beautiful dreams lately. This morning, I woke up so happy from my dream, such a pleasant country dream, staying at a house in the country, visiting a quiet shop/restaurant and talking to gentlepersons.

Oh dear. A month without any updates! That just won't do!

Hanging out with Spencer, talking some wild theories about the nature of time and how to represent in film. Lots of cool things.

mmmmm... aromatheraphy bath... reading 2001 and having a blue stress relief bath. Life is sweet.

Busy day, even though it's the weekend, getting stuff *done*.

Reinstalled Windows 2000 on Vayu, made yummy omlettes with bacon, went and bought the new Sheila Chandra, This Sentence is True, loaded up on Escents soaps (Tea Tree mostly, but also Mint Eucalyptus and Siam Spice), had coffee with Melissa, made a huge pot of chili and installed a whole bunch of software on Vayu. Listening to Sheila Chandra now, it is very awesome.

Truth, Love, Simplicity. Love. Service.

Yeeee haw! emrctg lives!

emrctg = Enumerated Mountain Rule to build Contigs

Solar Eclipse vs.
Lunar Eclipse

Origami beetles yay! Paper beetles!

Working working working.

sness is back and there's gonna be some trouble!!!

(sang to the tune of "my boyfriend's back")

Yay! It compiles and doesn't segfault! Now, tomorrow, check the output and make the data
structure more funky so that it resembles real contig/clone data. Wow, that was a one to fit the
brain around, let me tell YOU! :)

Wow, had an intense holiday. I'm almost always more tired at the end of the holiday than the beginning, I always do a lot of internal work, and it's tiring. If you want to hear what I did, you'll have
to wait for the short book entitled My Holydays or Deep in the belly, in the belly of the earth.

Referencing the last post, I don't know why I got a deja-vu from that code window, I don't think I've seen anything like that before, it's just a sness occurrence. Like all things sness, hard to quantify, and even harder to wrap your head around. Ah sness. :)

Reasons it's good to be sness #102033

You get a deja-vu's from looking at this

Back at work.

Hail Eris, Hack Linux! ;)

Today is Sweetmorn, the 23rd day of Discord in the YOLD 3167!

Urchin - Candlelight

Wow! It's been a few months since I've used ddd, and it's really improved! Check out the following
for the emr display

Chemical Brothers - The Private Psychedelic Reel.

Finished the Yoga Outreach web site last night! Check it out, let me know what you think.

Today, in pictures.

$8 = (struct PathItem *) 0x804a9a8
(gdb) print list_node->next
$9 = (struct PathItem *) 0x804a9f0
(gdb) print list_node->next->next
$10 = (struct PathItem *) 0x804a9c0
(gdb) print list_node->next->next->next
$11 = (struct PathItem *) 0x804a9c0
(gdb) print list_node->prev->prev->prev
$12 = (struct PathItem *) 0x804a9a8
(gdb) print list_node->prev->prev->prev->next
$13 = (struct PathItem *) 0x804a9d8
(gdb) print list_node->prev->prev->prev->next->next
$14 = (struct PathItem *) 0x804a9f0
(gdb) print list_node->prev->prev->prev->next->next->next
$15 = (struct PathItem *) 0x804a9c0
(gdb) print list_node->prev->prev->prev->next->next->next->next
$16 = (struct PathItem *) 0x804a9c0
(gdb) print list_node->prev->prev->prev->prev
$17 = (struct PathItem *) 0x804a9a8
(gdb) print list_node->prev->prev->prev->prev->prev
$18 = (struct PathItem *) 0x804a9a8
(gdb) print list_node->prev->prev->prev->prev->prev->next
$19 = (struct PathItem *) 0x804a9d8
(gdb) print list_node->prev->prev->prev->prev->prev->next->next
$20 = (struct PathItem *) 0x804a9f0
(gdb) print list_node->prev->prev->prev->prev->prev->next->next->next
$21 = (struct PathItem *) 0x804a9c0
(gdb) print list_node->prev->prev->prev->prev->indx
$22 = -1
(gdb) print list_node->prev->prev->prev->prev->next->indx
$23 = 2
(gdb) print list_node->prev->prev->prev->prev->next->next->indx
$24 = 7
(gdb) print list_node->prev->prev->prev->prev->next->next->next->indx
$25 = -1

Taught my first Yoga class tonight!
I taught a group of 16-18 year olds, it was about an hour long
class, I showed them the Sun Salutation, twists and a lot of
breathing. Wow, it was very cool.

bindi.

Here's a Dia drawing of my data structures for the Enumerated Mountain Rule

Ahh, I love coding. Check this out:


// Iterate through this list until all clones are in paths
in_paths = contigs[ctgnum]->num_show;
while ((i < tot) && (in_paths > 0)) {
// Look at both clones
inlist1 = check_inlist(bl[i]->indx1,&c);
inlist2 = check_inlist(bl[i]->indx2,&c);
if (inlist1)
endlist1 = check_endlist(bl[i]->indx1,&c);
if (inlist2)
endlist2 = check_endlist(bl[i]->indx2,&c);

// If both clones are already in the middle of lists
// - yay! do next one
if ((inlist1 && inlist2) && ((!endlist1) && (!endlist2)))
continue;

// If neither clone is in a list
// - make a new list out of these two
if ((!inlist1) && (!inlist2)) {
}

// If one of the clones is the end of a list
// - Add other clone to the end of this list
// Do for indx1
if ((!inlist1) && (endlist2)) {
}

// Do for indx2
if ((!inlist2) && (endlist1)) {
}

// If one of the clones isn't in a list, and other is internal in a list
// - add these clones to appropriate PathItem->link
// Do for indx1
if ((!inlist1) && ((inlist2) && (!endlist2))) {
}

// Do for indx2
if ((!inlist2) && ((inlist1) && (!endlist1))) {
}

}

.

Latest screenshot of contiger. Notice the cool marker display below the contigs, with both maximum
extents of marks, as well as the consensus region. Little colored boxes identify the different
markers and are matched with the clones above.

Blessed equinox to all!

Latest screenshot of contiger. It's getting cleaner and more featureful all the time. Going to add graphical display of markers next.

Had so much fun out tonight with Di, Brian and Heather. Went to a nice Indo-American fusion place, Sami's and then to
Delilah's for some wonderful martinis (virgin for me, of course) and conversation! Yay!

Shiva level in Nethack

A portal is generated at around level 10-15 that takes you to the Shiva level. There are 4 levels,
3 are big rooms, but completely filled with really nasty monsters that don't leave any items. First level is elementals, second is golems, third is demons. Here's the trick, if you have been a pacifist, all these monsters will instead be figurines of these monsters. The fourth level is empty, except for a throne in the middle of the room. Around the throne are an amulet of life saving, a bag of holding,and two blessed figurines of a Archons, Ida and Pingala.

If you have been a pacifist, Shiva is seated in the middle of the room in meditation, and will give you the "Mantle of Shiva", which you can wear for huge AC, protection from fire, cold, level
drain and shocking. You can apply it in a direction and all monsters in that direction will be
turned into figurines. You can invoke it, when invoked it summons another high level pet.

Shiva!

More Yoga!

sweeter.

sweet.

Back home! Listening to SomaFm, mmm, chilled ambient beats. So nice.

Hee hee, check this out:

//
// Enumerated Mountain Rule
//

struct PathList;

// One item in a path
struct PathItem {
int indx; // Index into clones[]
struct PathItem *next; // Next PathItem in the list

struct PathList *links;
};

// One path
struct PathList {
struct PathItem *head;
struct PathItem *z;
};

// All the paths
struct PathCollection {
struct PathList *head;
struct PathList *z;
};



Hee hee! Lots of recursive data structures here! Isn't the PathList in PathItem a cute multi-dimensional treat?

Man, I love coding little cute algorithms, I love thinking about the most efficient way to implement
algorithms, weird little data structures.. Cool.

I find in C that I stick with simpler data structures like arrays, not like how I used to work in C++,
but then there is more to keep track of in C, which makes it fun and challenging.

Interesting day today, got a great start on the Enumerated Mountain Rule, wrote this cute little bit of code:


int compare_sulstons(const void* a, const void* b)
{

if((*(struct MatrixListItem**)a)->score < (*(struct MatrixListItem**)b)->score) return -1;
if((*(struct MatrixListItem**)a)->score > (*(struct MatrixListItem**)b)->score) return 1;
return 0;
}
int build_bestlist(struct Clone **clones, struct Contig **contigs, int ctgnum, int tolerance)
{
int i, j, k;
int num, tot;

// 1) Allocate memory for list and clear list
num = contigs[ctgnum]->num_show;
tot = num * (num - 1) / 2;
bestlist = (struct MatrixListItem **) malloc (sizeof (struct MatrixListItem*) * tot);

for (i = 0; i < tot; i++) {
bestlist[i] = (struct MatrixListItem *) malloc (sizeof (struct MatrixListItem));
bestlist[i]->indx1 = -1;
bestlist[i]->indx2 = -1;
bestlist[i]->score = 0.0;
}

// 2) Build the list (half the matrix)
k = 0;
for (i = 0; i < num; i++)
for (j = i+1; j < num; j++) {
bestlist[k]->indx1 = contigs[ctgnum]->show_indx[i];
bestlist[k]->indx2 = contigs[ctgnum]->show_indx[j];
bestlist[k]->score = sulston(clones[contigs[ctgnum]->show_indx[i]],clones[contigs[ctgnum]->show_indx[j]]);
if (DEBUG >= 2)
printf("Adding %3i %3i %3i\t\t1=%3i\t2=%3i\t%.1e\n",i,j,k,bestlist[k]->indx1,bestlist[k]->indx2,bestlist[k]->score);
k++;
}

// 3) Sort this list by sulston score
qsort(bestlist, tot, sizeof(struct MatrixListItem*), compare_sulstons);

// 4) Print the list out
if (DEBUG)
for (i = 0; i < tot; i++) {
printf("Score = %.1e\ti = %i\tClone A %3i (%s)\tClone B %3i (%s)\n",bestlist[i]->score,i,
bestlist[i]->indx1, clones[bestlist[i]->indx1]->clonename,
bestlist[i]->indx2, clones[bestlist[i]->indx2]->clonename);
}


return tot;


}


Isn't that cute? :)

Wow! More fun work today! Pulled out all the code from ,gactg and put it into ga.c and ga.h, then made gactg just call these routines to do it's work. Then, used ga.[ch] to add gactg functionality to contiger! So, now you can look at your contigs, and interactively run
genetic algorithms on them to fix them up. Hopefully will put this right into FPC which would rock, but might be difficult. I'll get it going in contiger first, then go crazy after that.

Did a little redesign on the main site. Productive blue.

// gactg.c

// Read in an fpc file and do a genetic algorithm to fix the named contig
//
// Genetic operators
//
// Crossover probability percentages, should add up to 100
#define CROSSOVER 25
#define MUTATION 25
#define FIXWORST 25
#define BLOCKSHIFT 25
#define MOUNTAIN 25

#define POPSIZE 20
#define NUMGENS 10000
#define NUMREPLACE 3

// Types of scoring metrics
#define RUNSCORE 1
#define NEIGHBOURSCORE 2
#define NEIGHBOURCONF 3
#define SULSTONNEIGHBOUR 4
// Which score we are using
int score_method = SULSTONNEIGHBOUR;


gactg, my new program name. cool, eh?!

Wow, had an *incredible* week! Wrote over 1500 lines of code, got a
full GA up and running that looks very promising for doing our contig
ordering!

This takes 15 seconds to run at home (600 MHz Pentium III) for 10000
generations. Order is perfect, except that 8 should be at the leftmost
end.

Scores are all the sulston exponents between each neighbour and the next.
This tries to minimize that quantity. It's very fast.

Cool, eh!

-----------------------------------------------------------------
Best = 0 Score = 581

499 446 426 399 385 374 311 292 251 224 195 190 162 139 124 94 61 31 8 958 920 892 841 633 626 617 596 562

Total Mutations = 7624 Good Mutations = 36
Total Crossovers = 3707 Good Crossovers = 6
Total SpanXovers = 3724 Good SpanXovers = 8
Total Fix Worst = 7537 Good Fix Worst = 212
Total BlockShift = 7408 Good BlockShift = 27
Total Mountain = 0 Good Mountain = 0
-----------------------------------------------------------------
shakti 107 [~/GDEV/contiger] %




The inital contig order was randomly shuffled 1000 times, giving clones
like below:

Gen = 1 best = 211 (4)
399 311 446 499 162 958 374 633 841 139 190 195 251 292 892 31 61 94 596 426 562 617 626 385 8 920 224 124


This was the best order at the start.

Oh blogger is confused. It's putting my new articles in an archive....

Mittelstandskinder - Ohne Strom - Bug

Another earthquake?

Rush - Tom Sawyer Remix

Blogger, please post the posts. Please work.

March 5th already! Wow, this year is going by very quickly!

TranceGlobalNation - Boiler - Humate Remix

Listening to Run Lola Run.

Saw SNFU this weekend. Chi Pig is just as hardcore as ever. Also, you know
it's a good punk concert when somebody is carried out, head bandaged, on a stretcher.

At the request of Simon I'm posting in my blog again. :)
I've been working on programs to order fingerprinted contigs in the Mouse map, and have been
SUPER busy. More updates soon, I promise.

Must post to blog. Must post to blog.

Wow! A gorgeous sunny day today! I'm right by the window, and the light from outside is beaming
in filtered beams across my computer screen. What a wonderful winter we're having! A wonderful day!

sness!

An article at Feedmag about GEML, the Genome Markup Language.

Terraform Venus!

One of the wonderful things about having a shaved head: Not having to worry about falling alseep with gum in your mouth, no hair for it to get tangled up in! (And yes, I did suffer this trauma once, and after an hour of painful brushing to try to remove it, had to snip some hair off to get it out, yuck!).

Hey! I've figured it out! BOTH! :)

Oh, decisions, decisions! Which one, the Apple Powerbook G4 Titanium or the Sony VAIO Transmeta Picturebook. Hmmm, now I just need a few extra thousand dollars to burn. :)

> Wheat quits job one day
> Lesa shaved off hair on full moon
> Sness also shaved head
>
> - Lesa Fehr


Wow! Lesa with shaved head
Flashing eyes, Kali, Shiva
Tremble in fear, Men.


Shave your head, Wheat,
A nice and chilly wind
makes your head feel neat.


Tonight, a full moon,
sness dances crazy moonlight
Shiva, Lunar Eclipse

delicate black bands

vagaries in bandcalling

contiger fixes it

Yoga started again last night with Taylore. Ahh, so nice and relaxing, a really cool class. Taylore rocks, now I need to set up a website for her.

Got a new soundcard and microphone this weekend for my newly refreshed linux box, I've been meaning to get some audio applications and hard disk recording going on this box for some time, but since it was my main mail and web server, I was a bit nervous. Now that my netwinder is bravely taking over these tasks, I'm more adventurous. Got a midi cable as well, because I *have* to get my Roland SPD-11 hooked up to my computer. Now, that will rock.

Beautiful sounds in the radio waves near
Jupiter. Found by the Cassini spacecraft. Sounds like ambient techno. Now, that's what we need, streaming audio from all around the solar system. (hmm, as I write this, doesn't 'solar system' sound a bit 70's? Do we need a new term?)

Beautiful sounds in the radio waves near
Jupiter. Found by the Cassini spacecraft. Sounds like ambient techno. Now, that's what we need, streaming audio from all around the solar system. (hmm, as I write this, doesn't solar system sound a bit 70's? Do we need a new term?)

Ohhhh, such a sweet setup here at home now... 4 computers on the hub, my firewall (cr1008674-a), the netwinder (durga), the windows box (vayu), and shakti. Mmmmm. This rocks. It's creating it's own little reality distortion field here...

Holy Roman Penguins! XFree 4.0 sure is fast!

Hi! I'm switched over to the netwinder now, (durga, hindu goddess of protection), and I'm very happy! Just got Mandrake 7.2 installed, a couple hitches, but it's very sweet right now, got XFree4.0.1, and kernel 2.4.0 ready and waiting for the next reboot!

Here's my KIT:

---

Ahh, the new millennium. So nice! I'm still alive! Wish I could have
come to the reunion with all you nice people, but it just didn't quite
work out. It was so nice seeing some of you on the webcam, and it was SO
SO SO NICE seeing in person a few of my favorite pearsonites. Thank you
for visiting! I was in a fragile state, and got much more fragile as the
summer continuued, and I just couldn't come. There are those of you that
will understand, this is for you, dear ones.

It was quite the year, the whole year was going from one extreme to the
other, from a job that was very very stressful (Stormix, www.stormix.com),
even though I was filthy rich and had big-ass stock options, to a job that
is totally amazing and rewarding, with great people, and doing very
exciting work in Genomics and Bioinformatics at the BC Genome Sequence
Centre (www.bcgsc.bc.ca). Was in a 2 year relationship with a yoga
teacher, which was "!wow!", that ended in August, but we're still best of
friends. Did a huge 10 day Yoga workshop in August which was incredible!
2000 was the year to get back into Yoga, and found Mantra, which has
changed Everything EVERYTHing EVERYTHING! Had some major health concerns,
starting in July, but these are mostly on the mend and under control now.
Shaved my head in August! This is very very cool, and it's still shaved.
;) Basically, went from bottom to top, from top to bottom, and cleared
out a lot a lot a lot of old stuff that wasn't me anymore. I needed to
prove to me and you how hardcore I am, and I've done this, and now I can
come back through gentleness, which is a wonderful way of being me.

After y'all had left the college, I went for a weekend visit, it was the
same place, after all. It was me that was different. Om Namaha Shiva. Om.

Big hugs and love to *all* of you, every last one, even the grumpy ones
who never write KITs! Write me, tell me small secrets, throw your cares
to the wind, love everyone now! I'm at sness@sness.net, http://www.sness.net.

---

Yay! sness rules! peace out!

There's a big article on Red Herring about the biotech industry.

A side-by-side comparison of the background color of Windows 2000 (R58 G110 B165) with SteelBlue from X11 (R70 G130 B180).

Cool, Linus has just released 2.4.0! Here's a local copy, just because.

Wow. Sometimes semi-random websearches can pull up the most beautiful, beautiful, things!. Found this originally because someone had searched for "snez" and had got sness.net, so I wanted to see what else was under snez. So cool because I had a really great friend at Pearson named Snezana, we went to a Jesus and Mary Chain concert back in 1990... Ahh, those were the days. Back then, I was scared of the freaks in downtown Vancouver, now I'm one of them.

ok. it can start now.

THE NEW MILLENNIUM DOESN"T BEGIN UNTIL *I* SAY IT DOES!