Alex on February 9th, 2010

Alex on November 5th, 2009

This is one of the saddest emails I’ve ever received:

Dear CCP4 Community:

I write today with very sad news about Dr. Warren Lyford DeLano.

I was informed by his family today that Warren suddenly passed

away at home on Tuesday morning, November 3rd.

While at Yale, Warren made countless contributions to the computational tools
and methods developed in my laboratory (the X-PLOR and CNS programs),
including the direct rotation function, the first prediction of helical coiled coil

structures, the scripting and parsing tools that made CNS a universal computational
crystallography program.

He then joined Dr. Jim Wells laboratory at USCF and Genentech where he pursued
a Ph.D. in biophysics, discovering some of the principles that govern protein-protein interactions.

Warren then made a fundamental contribution to biological sciences by creating the
Open Source molecular graphics program PyMOL that is widely used throughout
the world. Nearly all publications that display macromolecular structures use PyMOL.

Warren was a strong advocate of freely available software and the Open Source

movement.

Warren’s family is planning to announce a memorial service, but arrangements have

not yet been made. I will send more information as I receive it.

Please join me in extending our condolences to Warren’s family.

Sincerely yours,
Axel Brunger

Alex on October 14th, 2009

“Imagine life as a game in which you are juggling some five balls in the air. You name them work, family, health, friends, and spirit and you’re keeping all of these in the air. You will soon understand that work is a rubber ball. If you drop it, it will bounce back. But the other four balls—family, health, friends, and spirit—are made of glass. If you drop one of these, they will be irrevocably scuffed, marked, nicked, damaged or even shattered. They will never be the same. You must understand that and strive for balance in your life.”

~ Brian G. Dyson, former CEO of Coca-Cola

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Alex on August 3rd, 2009

Arel and I have both signed up for the Las Vegas marathon. I’m stepping up my training to 30 miles a week. I’ve signed up and just had a beautiful 6.5 mile run today.

Alex on July 19th, 2009

One simple thing that the US Patent agency could do that would save
corporations millions of dollars is use first to file, instead of first
to invent. The entire concept of the patent office is to give people an
incentive (a temporary monopoly) in exchange of sharing information
(their patented ides.) To me, it seems unjust to reward someone who
invests something and doesn’t share that knowledge with society.

By using first to file, bona fide research and development companies
wouldn’t need to squander man hours signing and countersigning
notebooks for fear of losing a patent. These R&D companies would
have more pressure to file quickly and disclose to society new and
improved information. There would be a lower chance of companies
sitting on documented ideas, hoping that they will become part of
industry standards and focusing on increased licensing revenue.

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Alex on July 19th, 2009

Amor é um fogo que arde sem se ver,

é ferida que dói, e não se sente;
é um contentamento descontente,
é dor que desatina sem doer.

É um não querer mais que bem querer;
é um andar solitário entre a gente;
é nunca contentar se de contente;
é um cuidar que ganha em se perder.

É querer estar preso por vontade;
é servir a quem vence, o vencedor;
é ter com quem nos mata, lealdade.

Mas como causar pode seu favor
nos corações humanos amizade,
se tão contrário a si é o mesmo Amor?

Luis de Camões

Alex on July 17th, 2009

This is a spoof of Lipinski’s rule of five, however this is focused on weightloss. These are just observations that I’ve made while losing over 50 lbs. They are:

1. Run at least 5K a day or at least 5 days a week (Running is the only exercise that helps me to lose weight);
2. Eat at least 5 times a day (try to eat ~300 calories per meal/protein bar);
3. Eat at least 5 cooked, egg whites a day (focus on protein and building muscle); and
4. Eat yogurt 5 times a week (focus on culturing good bacteria).

Oh yeah, the usual disclaimer please talk to your doctor before reading this post and/or trying any of my advice.

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Alex on March 8th, 2009

I recently decided to use skype instead of my vonage system. It’s a little more portable when I’m on the road in my cell phone-less existence. My major gripes about skype are these:

1) Making calls from to a phone number, which is one of the few ways skype makes money; therefore, this interface should be intuitive. Yet, there’s no apparent way to save a real phone number as a contact. The best way I’ve found to deal with this is to enter the event history and click on the number.

2) I couldn’t tell an easy way to define a default country. I’m currently in the USA so I’m usually calling numbers here, as opposed to when I was in Brazil. The worst case for using a default country is to have to change the country, which is the best case of not having a default country.

Alex on November 26th, 2008
Lesson 1:
A man is getting into the shower just as his wife is finishing up her shower, when the doorbell rings.  The wife quickly wraps herself in a towel and runs downstairs…  When she opens the door, there stands Bob, the next-door neighbor.  Before she says a word, Bob says, ‘I’ll give you $800 to drop that towel.’  After thinking for a moment, the woman drops her towel and stands naked in front of Bob, after a few seconds, Bob hands her $800 and leaves.  The woman wraps back up in the towel and goes back upstairs.  When she gets to the bathroom, her husband asks, ‘Who was that?  ”It was Bob the next door neighbor,’ she replies.  ‘Great,’ the husband says, ‘did he say anything about the $800 he owes me?’
Moral of the story: If you share critical information pertaining to credit and risk with your shareholders in time, you may be in a position to prevent avoidable exposure.
Lesson 2:
A priest offered a Nun a lift.  She got in and crossed her legs, forcing her gown to reveal a leg.  The priest nearly had an accident. After controlling the car, he stealthily slid his hand up her leg. The nun said, ‘Father, remember Psalm 129?’  The priest removed his hand.  But, changing gears, he let his hand slide up her leg again.  The nun once again said, ’Father, remember Psalm 129?’  The priest apologized ‘Sorry sister but the flesh is weak.’  Arriving at the convent, the nun sighed heavily and went on her way.  On his arrival at the church, the priest rushed to look up Psalm 129.  It said, ‘Go forth and seek, further up, you will find glory.’
Moral of the story: If you are not well informed in your job, you might miss a great opportunity.
Lesson 3:
A sales rep, an administration clerk, and the manager are walking to lunch when they find an antique oil lamp.  They rub it and a Genie comes out.  The Genie says, ‘I’ll give each of you just one wish. ”Me first! Me first!’ says the admin clerk. ‘I want to be in the  Bahamas , driving a speedboat, without a care in the world. ’Puff! She’s gone. ’Me next! Me next!’ says the sales rep. ‘I want to be in Hawaii , relaxing on the beach with my personal masseuse, an endless supply of Pina Coladas and the love of my life. ’Puff! He’s gone. ’OK, you’re up,’ the Genie says to the manager.  The manager says, ‘I want those two back in the office after lunch.’
Moral of the story: Always let your boss have the first say.
Lesson 4:
An eagle was sitting on a tree resting, doing nothing.  A small rabbit saw the eagle and asked him, ‘Can I also sit like you and do nothing?’  The eagle answered: ‘Sure, why not.’ So, the rabbit sat on the ground below the eagle and rested.  All of a sudden, a fox appeared, jumped on the rabbit and ate it.
Moral of the story: To be sitting and doing nothing, you must be sitting very, very high up.
Lesson 5:
A turkey was chatting with a bull.  ’I would love to be able to get to the top of that tree’ sighed the turkey, ‘but I haven’t got the energy.  ”Well, why don’t you nibble on some of my droppings?’ replied the bull.  They’re packed with nutrients.  ’The turkey pecked at a lump of dung, and found it actually gave him enough strength to reach the lowest branch of the tree.  The next day, after eating some more dung, he reached the second branch.  Finally after a fourth night, the turkey was proudly perched at the top of the tree.  He was promptly spotted by a farmer, who shot him out of the tree.
Moral of the story:  Bull Shit might get you to the top, but it won’t keep you there.
Lesson 6:
A little bird was flying south for the winter.  It was so cold the bird froze and fell to the ground into a large field.  While he was lying there, a cow came by and dropped some dung on him.  As the frozen bird lay there in the pile of cow dung, he began to realize how warm he was.  The dung was actually thawing him out!  He lay there all warm and happy, and soon began to sing for joy.  A passing cat heard the bird singing and came to investigate.  Following the sound, the cat discovered the bird under the pile of cow dung, and promptly dug him out and ate him.
Moral of the story:
(1) Not everyone who shits on you is your enemy.
(2) Not everyone who gets you out of shit is your friend.
(3) And when you’re in deep shit, it’s best to keep your mouth shut.
Alex on November 17th, 2008

I’m not sure how the Milwaukee Brewers plan on winning:

“It sounds like they’re overbidding,” [Brewer General Manager] Melvin told the Milwaukee Journal Sentinel. “If the speculation is true that we’ve offered CC $100 million, why would you offer $140 million? Why wouldn’t you offer $110 million?”

I have many sins, however, being a Yankees fan (who is not from NY) is not one of them. I definitely respect them and their desire to win. That said, the 00’s have been great to baseball fans.