Was There

feed, fight, flee, and fuck

2012-01-29T11:53:00.000-08:00

So this is the 4-f rule of living organism, or animals with incisors, or claws, or beak, sting, whatever.

The rule was mentioned by a biologist on NPR as "the four F ... feed, fight, flee, and .... reproduce!"

Anyway, I just find myself obsessed with movies of dogfight scenes. And I have dug out quite a few of them on youtube:

http://www.youtube.com/watch?v=TFnnivSgH0Q

http://www.youtube.com/watch?v=llqoqei-k1Y

http://www.youtube.com/watch?v=Q4n4rRozpys

http://www.youtube.com/watch?v=b79zgKgRDBk

Well, it's not about the violence, you know what I mean. For that I have made up my mind to become a sport pilot. Let's see how long it will take for me to get there.

automated online english editing

2012-01-12T13:46:00.000-08:00

"Thecustom bigWig track can be used in every way a server-providedheatmap track could ever be used."

When I was struggling with this sentence for my book chapters writing, I turned to www in hope of finding some service that can do free and automated language editing. Not surprisingly, there wasn't any.

Then I started wondering. Now that Apple is equipped with technologies like enabling Siri to respond to question "I locked myself outside!!!" with answer "go get a locksmith", why don't they make themselves a little bit more useful to make an online version of that, with ability of english language editing?

And of course whatever Apple makes, it's never going to be free. So I turned my prayer to Google instead.

Let the Will be done

2012-01-06T13:06:00.000-08:00

I'm reading Garth Nix' "Keys to the Kingdom" novels. Starting from a month ago, now I just finished book II, "The Grim Tuesday". But I'm already a captive of author's talented imagination. Only not until I finished book I did I realize these novels were written right after the "Sabriel" trilogy, which are also my favorite (I read the Sabriel for 3 times). I couldn't help but contrast the two fantasy series. They were so different apart that I could not draw any similarity in style of writing with my scant experience in English literature.

I'm also writing a book chapter on my little genome browser for Current Protocol in Bioinformatics, who doesn't even provide me a latex template. It's like reorganizing the user manual, but I have to get myself grilled by dealing with a hundred figures. Though there has already been a manual, it could not decrease my pain a tiny bit. I'm just such at writing. And thinking about another book chapter to write right after this one, I just felt beaten and again marvel at Garth Nix's amazing productiveness in writing. Maybe I should start worshiping him instead of programming nerds.

January 6, 2012, temperature is 70F at 3pm in St. Louis. Step outdoor, and greet the sun bear.

Album "trip to Newport"

2012-01-01T19:40:00.001-08:00

DSC_4640, a photo by Xin Zhou on Flickr.

Click photo to view entire album of my trip to Newport, RI for BGI conference on June 6, 2011

Album "trip to Cold Spring Harbor Laboratory"

2012-01-01T19:38:00.001-08:00

DSC_4438, a photo by Xin Zhou on Flickr.

Click photo to view album of my trip to CSHL for Biology of Genomes meeting on May 10, 2011

Album "trip to Boston" on Flickr

2012-01-01T19:36:00.001-08:00

DSC_3940, a photo by Xin Zhou on Flickr.

Click photo to view entire album on my trip to Boston on March 16, 2011 for VIZBI conference at Broad Institute

St. Louis magpie

2011-12-11T07:45:00.001-08:00

I'm sure I saw a magpie near I-70 in St. Peters on December 10th, 2011. It looked so similar as the kind of magpie found everywhere in China, but it is a different species, the Black-Billed Magpie.

According to following online resource, the magpie has not yet been reported in this region:

http://www.allaboutbirds.org/guide/black-billed_magpie/id

Forget the red bird, the Magpies are coming! Everything will be Black'n White then!

Cloud and sky

2011-11-24T13:02:00.001-08:00

Cloud and sky a video by Xin Zhou on Flickr.

High wind, fast moving cloud. High color saturation

seen on Taylor street

Museum wall

2011-11-24T13:00:00.001-08:00

Museum wall, a photo by Xin Zhou on Flickr.

Outside Missouri history museum

Shot with "sepia" effect

Giant flag up

2011-11-21T11:56:00.001-08:00

Giant flag up a video by Xin Zhou on Flickr.

At the intersection between Lindel and Kingshighway, the flag was raised by two fire engines. Color saturation mode was on when shooting.

Nov 5, 2011

street colors

2011-11-06T07:07:00.001-08:00

Cyan - scooter on Euclid street

Yellow - handsome VW by forest park ave

Yellow (2) - school bus on taylor street

White - abandoned vehicle on forest park ave

walking with dad

2011-11-05T08:43:00.001-07:00

walking with dad, a photo by Xin Zhou on Flickr.

Red bird

2011-11-01T06:25:00.001-07:00

Red bird, a photo by Xin Zhou on Flickr.

Congrats, Cardinal!

Posing

2011-10-29T09:08:00.001-07:00

Posing, a photo by Xin Zhou on Flickr.

Family enjoying the day by the Arch

pink bus

2011-10-29T08:58:00.001-07:00

pink bus, a photo by Xin Zhou on Flickr.

Apartment building against sky

2011-10-27T13:00:00.001-07:00

Apartment building against sky, a photo by Xin Zhou on Flickr.

Shot on Euclid street

Trucks by the Inn

2011-10-26T14:05:00.001-07:00

Trucks by the Inn, a photo by Xin Zhou on Flickr.

Lucky the hotel didn't get burnt down

Downtown building

2011-10-26T14:03:00.001-07:00

Downtown building, a photo by Xin Zhou on Flickr.

Wonderful sunlight rendered amazing contrast, even by the Kodak Zx5

precious metal

2011-10-15T14:41:00.001-07:00

precious metal, a photo by Xin Zhou on Flickr.

metal are precious if they carry valuable memory

Coffee shop near medical school

2011-10-11T15:11:00.001-07:00

Coffee shop near medical school, a photo by Xin Zhou on Flickr.

A feast!

2011-10-09T08:34:00.001-07:00

A feast!, a photo by Xin Zhou on Flickr.

Hotpot dinner at friend's place

This post is made by "sharing on Blogger" function on Flickr, which is cool! But why Blogger doesn't take Flickr-exposed image URL?

snapshots, genetics retreat

2011-09-25T09:07:00.000-07:00

Jim Skeath declared the procedures to notify overtime speakers: an iPad with words "2 min left" on the screen, and an anti-Ting Wang device: a miniature gong. It's just ordinary and uninteresting but it appeared so funny in that occasion. Jim could hardly conceal his complacent in that.

(anyone being in 2010 genetics retreat would understand what "anti-Ting Wang" means: the three talks from our lab [Ting, Brett, me] were all severely overtime, and we collectively ignored the warning of timer)

When I talked, I was so nervous that words just gushed out like a drain pipe out of control. None of my deliberately designed little jokes worked -- or merely not uttered at all.

Learned to play ultimate frisbee, in that calm, cool, beautiful afternoon on the backyard slope of Oak Creek. Everyone was yelling and chasing the flying disc like mad, several with bare foot. The water-laden cloud hovers above us, gazing at us.

That night at bar, Kevin, in the middle of traditional, unconventional, beer-drenched ping-pong game with Gautam, yelled at me how he admired my talk and work, all those restless weekends, ... stuff. I was so pleased at the comment that I got six Schlafly in, 300% over capacity, stumbling to my room before falling into slumber.

I was little disappointed that Jim didn't make more jokes during his closing remark. But I'm really thinking about filming such and his opening remark at all the future events.

Be solemn for a day

2011-09-11T13:55:00.000-07:00

It has been a solemn day. I watched the memorial event at Ground Zero live over internet. Though I missed President's readings, I got to watch most of the victim families' remembrance over their loses. I recorded a few of their words, some are especially moving to me:

"for my mother, a firefighter, you are part of New York"
"for my amazing father, we love you, please keep watching over us"
"may there in, comfort you"
"alphabet of names, in a green field, in a warehouse of memory"
"to my uncle, we miss you more than words could describe"
"to my great husband, your little daughter turned 20 today, you'll be so proud"
"your dad, your three children, we'll never forget you, we miss you"
"I'll pass on your legacy, I will teach the children everthing you've taught us"
"we miss you so aweful, but we knew you're watching us, we'll meet again"
"we live every day in your honor"
"my dear dad, I hope I can play a round of golf with you"
"the world is a lesser place without you"
"it's been ten years, but it's still not easy without you"
"Danniel, we want you to know you'll always be our baby boy"
"Daddy, I wish you could see me now, because everyday, I try to make you proud"
"Steve, I still see you face every single day when I look at Hanna and Hannous"
"And for my father, who I never met, because I was in my mother's belly. I love the idea of having me, I wish you can be here enjoying with me"
"we keep you in our heart every day"
"we never found you, we never recovered you, but we know where you are"
"dad I'm still learning to cook, I'm working on it, we miss you"
"thank you for the pennies, Ketrina and I love finding them"
"dad I love you, your spirit lives on with your five grandchildren"
"to the world you've just been one person, but to me you are the world"
"I believe Teddy, and all those beautiful souls, have been walking around us here today"
"and my brother, a family man, a navy man, a holy man"
"my father, everyone knew you were lucky, and everyone you loved were blessed"
"for my dad, I wish I could have known you better"
"my dad, I know, everytime I'm in the woods, or catch big fish, you are there smiling at me"

In the afternoon I attended a memorial event organized by Wash U students:

Genome browser paper accepted

2011-09-09T10:04:00.000-07:00

Boss walked out of his office door, with excitement he declared, "Xin's paper is accepted by Nature Methods!"

I jumped up and rushed into his office, glanced at his correspondence with editor, and hugged with him. After been overwhelmed for 1 second, I was back to normal, and concluded succinctly, "this is a good start."

**** flash back ***
paper submitted around first days of June, before I went to Newport for meeting. Got Decision and Reviews back on the night my friend lidaof arrived at St. Louis (7/28). Revised in one week and re-submitted, and kept waiting till just now.

Je ne comprends rien

2011-09-08T10:59:00.001-07:00

New blog for Human Epigenome Browser

2011-09-01T09:38:00.000-07:00

I created a new blog for Human Epigenome Browser

http://washugb.blogspot.com/

Here's a snapshot, of its current appearance, in case it changes in future...

Support for KEGG

2011-06-23T07:54:00.000-07:00

I'm showing my THANK and SUPPORT for KEGG (Kyoto Encyclopedia of Genes and Genomes) here as I have made use of their service at various occasions, and am currently benefiting from that in my on-going genome browser project. I've sent comments through their comment form and I've made tweets about the support (#WashUGBrowser).

European press

2011-05-04T06:51:00.000-07:00

There is a hot water heater in the break room which used to serve us well, where tea other hot drinks can be instantly made by pulling a handle to get the hot running water, as long as you don't put your hand down there. But recently it's not working anymore, and it's left there unfixed for about two month, well, until now. Fellow workers who are used to a hot drink once in a while expressed their frustration by putting tags on the tap saying "my name is BROKEN!". Just now I saw two plumbers bending over the thing working on it.

But I got to use a French press I had in possession during this period. Soon after the incident, coffee makers starts to appear on breakroom table one after another, and I'm the only one who uses a french press (I use microwave to heat it). In the beginning I had no idea it is actually called a "French press". One morning while I was using it, a lady walked by. I think she is European, but I never confirmed that. She said to me, "emm, a nice French Press there you have". And I replied with correction: "yes... ehh, acutally it is made in Germany,".

The lady showed some surprise, then quickly turned to normal and said, "well, then that's a European press!"

temperature

2011-05-03T15:14:00.000-07:00

We are getting frosted morning tomorrow. According to weather report, temperature will be low to 38F.

Man, that's FROST, in May 4th. Are we in Siberia?

And we had a 70F warm & humid day around December 20th, 2010. I don't remember exactly which day that was. There was tornado warning that day.

Excess of snow this winter, latest snow fall in April when the temperature was around 80F.

What's happening there?

Horrible weekend

2011-05-02T07:30:00.001-07:00

I just learned that one of my coworker was almost ran over by a car last Saturday afternoon, when he was walking pass a busy road in front of the park I jog daily. AND he was pushing a stroller with his few-month-old son in it. The car barely missed him, but the tire ran over his foot and injured spring. All the luck, his son was not hit. Later we figured out that I was actually running nearby at that time. But I didn't notice them, because my attention was attracted by a car accident right at that time, when a green Camry was hit by a white sedan on the right side, rear door. I remember that slightly damaged Camry pulled over in front of me and a man ran out of the car to meet his accident mate. One young child was sitting in the backseat of that Camry looking out of the window, seemingly calm.

While on the other side of the globe, a man was killed in a Surgical Raid by the US force who has killed +3000 people in US ten years ago.

Join the chat

2011-05-01T09:06:00.000-07:00

I made a feature request to Google Talk, basically to set up a chat group, so whenever two guys in the group start chatting, other people in the group will notice that they are talking through their contact panel -- e.g. the two talkers are placed next to each other, their status icons are changed from a green disc to animated face, or even a vibrating curve connecting the two faces... And guys in that group can request joining the chats they see.

And that's it.

So yes... I will continue writing on this blog, perhaps all in English.

Blog moved 博客搬家了

2010-04-29T08:57:00.000-07:00

新博客地址 New blog is here:

http://blog.sina.com.cn/walkingmagpie

即日起本博客暂停止更新
I will cease to update this blog from now.

day 29 30 农民

2010-02-27T12:15:00.000-08:00

29
work & read 9:30-11:00 2:30-4:00 20:20-21:00

30
read 14:30-15:30

＝＝
本科时班长自封绰号“无敌农民”，有一回打星际的时候造了200个工蜂（俗称农民）往敌人家里涌，口里大喊：看我无敌农民用口水灭了你！

day 28 牢骚

2010-02-25T10:56:00.000-08:00

seminar 8:30-9:30
work 10:00-12:00 13:30-15:30 20:30-21:30
talk with lanlan 15:30-17:00

＝＝
牢骚：有感于大学讲师也加入到社会下等阶层中的不幸现实

遵从几千年的封建传统，现代中国人仍是分等级的。这三六九等中，物质精神各为两个正交的指标。本人向来不啻以最阴暗的心理猜测，国人中物质精神均下等者众也，此乃灰暗的背景色调；物质上等但精神下等者虽乏，但却如猪圈里泥巴中的肉猪一般耀眼夺目，又如凤爪，每只鸡身上肯定有俩；而精神上等者就如散落猪圈里的珍珠，或鸡身上的凤凰毛－－您哪儿找去？

days 26, 27 CNRC

2010-02-24T06:48:00.000-08:00

day 26
work 8:20-11:00 13:30-14:30 20:30-23:00
talk 12:00-13:00
meeting 15:30-17:30
day 27
work 8:40-12:00 13:00-16:30
==
昨天的CNRC报告还算顺利，但听者寥寥，有两个家伙还睡死过去了，最重要的是PPMM一个都没来啊。。。问题比较严重，需要认真对待～

看了《恶童》，竟发现是以前瞅过却没赏脸看完的片子。讲得什么完全没看懂，但说不定以后还会再看二遍。因此只能对画面评价了：相当的精彩和专业啊，破败陈旧的建筑却色彩斑斓，一片混沌中透着一股子莫名其妙的魅力。这也应该算是非主流动画了～

day 25 Beaudet

2010-02-23T06:19:00.000-08:00

seminar 9:00-10:00
work 10:30-12:00 12:30-16:00 20:00-21:00

＝＝
昨天头昏脑胀竟然忘了记日志

昨天荣幸参与Beaudet lab meeting 并做报告，嗯，不算差吧。今天中午还要在系里讲一遍，不怎么紧张了。

报告早上八点半开始，有我和一个莱斯大学的本科生John。大家陆续进入狭小的会议室，并都摸到后排去拿吃的（有早点供应）。我和John忙着鼓捣电脑投影仪，刚弄好，一个面无表情的老头走进来，不高，微胖，直接冲到后排嗖一下拿了个面包圈，又扭头坐到最前排离我和John就一米半的距离。把面包圈掰一半放桌子上（也不嫌脏），另一半拿手里啃，一边看了我们一眼。这时大家在周围一圈鸦雀无声，这架势真... 老头不戴眼镜，但眼神非常锋利。问的问题也不少。

听说这老头是我老板的mentor（辅导员啥的），看来是有来路有背景有故事的。但我这次匆忙之间的聊聊几句对他没什么了解，只是感觉他应该是个性格非常强的人。

I got the chance to present at Beaudet lab meeting. Thanks Rob! Well that's not so bad, thanks again, Rob!

day 24 累

2010-02-21T20:18:00.000-08:00

reading 10:00-12:00
meeting 13:00-15:00
＝＝
累

day 23 吃

2010-02-20T19:42:00.000-08:00

reading 10:00-12:00 14:30-16:00
discussion 13:00-14:30
working 20:00-22:00

＝＝
今天印证了一下人对长期单一食谱的适应性...

今天心情不错，就去那个破墨西哥超市（消防车堵门口那个）买了鲜猪肉回来炖。足足整了一个小时，猪肉一部分切成块在滚烫的汤里和土豆胡萝卜香菇滚啊撞啊，另一部分整理好摆在冰箱里冻着。我饿得头晕眼花，翻翻锅，于是就开始－－

吃啊吃啊吃啊吃

... 然后就心满意足的来办公室了

我以往晚上只吃素菜，待到10点准时会饿；可今天不，头和肚子一起嗡嗡直响－－吃多了。

今天还近距离拍了反舌鸟 Northern mockingbird 的照片，一个个头比较大的家伙不怎么怕我似的，我就在离它三四米的地方给它上了相。（真想捉到手里捏捏～）明天贴吧，今天懒得动了。

day 22 doing reading

2010-02-19T11:57:00.000-08:00

reading 8:50-11:30 12:00-15:30 19:20-20:40

==
For years my comfort zone is been assigned a task, with a clear goal, that is. And I do some programming to solve it. That includes stirring different flavours of data, computing the data, and generating new data out of old data!

Now things is likely to change a bit. My dear boss is pushing me out of my comfort zone, and he is pushing hard! >_<

So I have been doing reading for over two weeks and fighting my inertia while trying to find a "task with clear goal" on myself. Not only I get exhausted and want to throw the chair, but also I feel I'm getting closer bit by bit...

昨晚用热毛巾敷了敷脖子，发现真有效，不怎么难受了，难道被压迫的那根神经受热缩回去了？就如同那只企鹅绊倒同伴后缩回去的脚...

貌似国内又能访问blogger了，不赖...

day 21

2010-02-18T19:20:00.000-08:00

work 9:30-12:30 13:30-16:00 20:00-21:00
seminar 8:30-9:30

day 20 被赶着跑

2010-02-17T20:01:00.001-08:00

reading & work 8:30-12:00 13:00-15:00 20:00-22:00
meeting 15:30-17:00

＝＝
前段时间的懒惰，导致现在如赶鸭子上架

day 19 转变中

2010-02-16T13:29:00.000-08:00

work 8:30-12:00 13:30-17:00 20:00-21:00
preparing for seminar

＝＝
我觉得我自己处在一个转变的过程中。这过程大概开始于一次改变，一系列乱七八糟的事，和自己每天那些微不足道的选择。很自然的，自己目前也说不清是在往哪里转。周遭的一切似乎在往各个方向牵扯着我，试图把我推向各种可能；我自身的惰性也在跟它们懒散的较力。就这样，在时间的雪地上缓缓划出人生的轨迹。

十年以后肯定就能明白些了。我想这就是我进行那种无聊的记录的意义。

days 16, 17, 18 在美国过农历年

2010-02-16T06:18:00.000-08:00

day 16
work 12:50-16:00
day 17
none
day18
reading 9:00-11:00
work 13:00-17:00 19:30-22:00

＝＝
大年除夕夜去作客，光脚踩在冰冷的木地板上让我头重脚轻，吃了一堆YAO餐馆的剩菜剩饭让我怀疑餐馆的大厨是不是都甩袖子回家过年去了。众人在窄小的空间中进行局促的社交，但空气依旧陌生冷淡。壁炉中的几块木头冒着奄奄一息的火焰，徒劳地想融化人们脸上僵硬的表情。我穿行于水泥台子，沙发和人群间，用思想把室内的一切都泼上灰色油漆，给他们披上黯淡的光泽，让他们渐渐凝固。然后我就找个角落，木然蹲了下来。

People like to behave in front of strangers as if they are real gentlepeople.

大年初一回到college station，老高要去Dallas了，到他家吃了顿散伙饭。估计再见面就难了。我和老高一起来到美利坚，我也跟他们一家三口度过这一年的大半时间。高兴的时候聚聚，困难的时候互相提携一把；期间遇到过多少不顺心，遭受过多少折腾，彼此都明白。

这次去他家没带礼物，就把蹦跳的小高拉到僻静角落塞了40块钱当压岁钱。小高激动的上窜下跳，拿不准这钱是该要还是不该要。想当年我自己每个春节都厚着脸皮理直气壮的拿长辈的压岁钱，那我们的孩子也理应如此，不管是在中国还是鸟不拉屎的这里。于是我就要求他要了，并叫他不要告诉他爹娘。

老高后来还是知道了，说，你来一次还让这小子发一笔横财～

老高夫妇比我大9岁，小高比我小12岁，都是我的好朋友。

day 15

2010-02-12T19:14:00.000-08:00

work 9:20-12:00 13:00-16:30

＝＝
今儿国内已经大年三十了诶诶～有那么点想家

day 14

2010-02-12T07:10:00.000-08:00

reading 9:20-11:30
talking with Lanlan 13:00-15:00
work 15:30-16:30 19:30-22:30

＝＝
冷啊，阴雨绵绵，零度左右的天气已经好几天了，美国北部都被大雪埋没了...

饭前便后崇拜你～
饭后便前继续崇拜你～

day 13

2010-02-10T13:56:00.000-08:00

reading 8:50-11:30 13:00-16:00

＝＝
读了一个帖子，有感而发写了如下评论。帖子主人是一个叫任志强的家伙。

（评论略有修改）

貌似有理，但俺觉得是在和稀泥

说买不起房的80后是站着说话不腰疼？你任志强才是真正的站着说话不腰疼。我们80后已然在重重压力下的苟延残喘，健康退化，想必你任志强这个成功人士能够理解，你说把这个和你们那一辈比比呢？你们18－28岁的时候在干嘛呢？

什么都不多说了，俺82年生的，现在是背井离乡，规避京城里房价的大棒，顺便在美国卖命挣钱。回国？等在北京北五环买得起房再说吧！

P.S. 咱说得都是真心话啊～

day 12

2010-02-10T06:46:00.000-08:00

reading 8:20-11:00 12:20-15:00 20:00-21:00
meeting 15:30-17:00

＝＝
野心家读史为明志，哲人读史为明辨是非，庸人读史仅为增加谈资

所以再怎么妆点自己，庸人也还是庸人

day 11

2010-02-08T14:39:00.000-08:00

reading 8:20-12:00 12:50-15:00

＝＝
看了一整天的大文章，思路越发支离破碎，想把电脑砸了

昨天去超市买下一周口粮的时候，在超市门口见到一辆消防车，不知道发生了什么事。这消防车长得挺拉风的。

day 10

2010-02-08T06:25:00.000-08:00

work 9:20-11:00
work & reading 14:00-16:00

＝＝
看了晓昕写的总结09年的长帖子，一字不漏的看了。

没留言，眼有些直。突然发现又一年就这么过去了，前一段时间还想过用一个字总结我的2009该是什么呢，“混”？“晃”？取舍不定。

“时间就是无可阻止的前进”，如果不保持奔跑，就会离理想越来越远。

day 9 别太把自己当回事！

2010-02-06T19:22:00.000-08:00

work 9:00-10:50 15:00-17:00 20:00-21:30

＝＝
别太把自己当回事

“都说别把自己太当回事
可是偏偏我不小心给忘了”，

“想要工作单位给个好待遇
是太把自己的能力当回事了
想要生活能有个好住所
是太把自己的享受当回事了”，

“我可以把自己当回事
可是我不能要求别人也一样
这就是矛盾”，

“因为把自己当回事了
心就容易不满足”，

“唯一的办法就是踏踏实实
证实自己”。

days 7, 8

2010-02-05T06:26:00.000-08:00

day 7
work 8:40-9:50
paper & work 10:00-11:30 12:00-15:30
meeting 15:30-17:30

day 8
paper 9:00-10:30
talk with Lanlan 10:30-11:30
work on Lanlan's project 12:30-17:00

＝＝
昨天脖子还是有些疼。今天基本好了，哦耶～

晚上总是睡不好觉啊！后果很严重，导致白天精神不济思想涣散。认识的N多人都能脑袋一挨枕头就着，啥时候我也能呢？？？昨晚做梦了还，梦到高中同学，而且又一起去坝上那个胡人墓里头转悠去了。而且还扒在那细长的、形状独特的木头棺材边上看了看，里头似乎有些东西，但黑糊糊的又辩不清楚。吓人吧，呵呵。其实我亲眼见到的棺材是空的。

里头的小故事，以后有闲心了再讲。

day 6

2010-02-04T06:45:00.000-08:00

paper 9:30 - 12:00

＝＝
脖子疼啊，疼得心情很糟糕，啥都没干成。三十岁前你找病，三十岁后病找你。不好好照顾自己身体就活该受罪吧。

老D买了Nikon D3000，我找他要了几个样张来瞅瞅，还把Ricoh GR3 和 Sanyo vpc-hd2000a的样张都找来比了比，就能瞅出来三洋的那个最疵，别的也看不出什么名堂来了，暂时作罢。

days 4, 5

2010-02-02T14:18:00.000-08:00

day 4

paper 8:40-9:40
Lanlan's project 10:30-11:40 15:00-16:10
paper (enhancer) at night

going to think more on enhancers and epigenetic marks...

day 5

paper 9:30-12:00
work 15:30-16:30

==
颈椎旁边似乎被扭到了，昨天一下子开始疼啊，千万别犯病～～

今日老板的文章二次被拒，先是nature，后是science，增添些许郁闷

day 3

2010-01-31T14:44:00.000-08:00

paper... 9:20 - 11:20, 15:00-16:30

agreed with the approach?

＝＝
今天得知童话大王郑渊洁还创作了一部并非童话的小说《仇象》，读者对象为成年人。于是囫囵吞枣的在网上将之看完－－到第7章就嘎然而止，令正沉浸在郑大创造的世界中的我跌回现实。因为尚未知晓的原因，这部书停止连载。其实猜也能猜到，没能通过审查。

希望有朝一日能看到这部作品的全文。

郑渊洁是中国少有的杰出作家，极富想象力，关注对儿童的正确教育，当真是偶像级人物。同样在他的众多作品中反映出其对不公正不正常现象的关注和批判。他的被禁言，实在糟糕。

day 2

2010-01-30T15:12:00.000-08:00

paper: additional gene ontology structure for improved biological reasoning 2h20m

(will continue thinking on this tomorrow)

==
今天又去帮人搬了个家。自从来美国，已经参加过7次搬家活动了，其中1次给自己搬，6次帮别人搬，成了干搬家公司的了。

完后晚上可能又要去中国城下馆子了，不太想去啊，脏兮兮的。

从老姐的博客上看到，让大脑活跃的办法之一居然是：把钱花掉！细细想挺有道理，花钱买开心，大脑自然兴奋起来，前提是得有钱可花。

day 1

2010-01-29T09:01:00.000-08:00

Paper: ontology of gene ontology 30m
paper: object-oriented model for GO 2h
work: 50m

==
DDOI 的作者终于谈了他那些人像主题的随机街景摄影是怎么搞出来的了，见这里，并表达一下崇拜 :-)。其实这是一篇长帖子，罗列了作者自己比较在意、有所感触、或者有故事的作品。

我几乎没有过这种经历（...），暂且胡说几句自己的“感触”：随机人像摄影好难，你不光得有技术和器材，还得有鉴别能力，超短时间内能判断他／她对你可能的态度，然后告诉对方是自己的创作对象，并避免引起人家反感。语言选择必然重要：与流浪汉、站街女、普通逛街者和示威游行者讲得话肯定不一样！

乱贴一气

2010-01-28T14:47:00.000-08:00

现在每到傍晚（我也只有傍晚才到户外走动），会发现有大群的不明鸟群飞到附近栖息，包括这颗树，树下也落了一地的鸟屎。那个小白点是月亮。

这云彩挺酷的，那天跑步时看到了好漂亮的火烧云，可惜没拍下来，日后吧。

讽刺，谩骂和诅咒

2010-01-24T07:59:00.000-08:00

忽然想起这么一套词，觉得做帖子题目不赖，所以先写这儿，回头再添内容

＝＝
本人住的院子里常停着一辆黑色丰田跑车，车尾巴上贴着“極端速”三个汉字，估计车主是日本人。

最近见到了那车那字时忽然冒出邪恶念头，想给他改成“娘稀屁”。

＝＝
贝勒医学院的内部邮件网站采用牛B的微软webmail服务器，我也被勒令使用它，于是乎我等没钱购买windose的下等劳工也开始享受outlook带来的火星级便利了！资本主义好！！

webmail网址以ex开头，每每以F6跳到地址栏轻敲ex，webmail就变出来了；略有不爽的是，若中文输入法恰好开着，变出来的就成了“恶心”二字～

无奈凑巧，实属不幸；连哭带呕，以表歉意~

... only a joke ...

2010-01-22T11:41:00.000-08:00

以上笑话见于新浪中国，俺最爱的新闻网站

《三体》漏洞

2010-01-21T12:27:00.000-08:00

《三体》《黑暗森林》（刘慈欣）是我非常喜欢的一部国产科幻小说。作者那超人般想象力构筑的世界和事件经常像电影般生动浮现在我眼前。但反复琢磨，还是会发现其中一些漏洞。看来大刘还是没能把情节设定得滴水不漏啊呵呵：

＊＊当史强一伙人敲定“古筝”计划，并大张旗鼓的在巴拿马运河布置“飞刃”来切伊斯文和他的“审判日号”时，三体人竟保持沉默，没有通知伊斯文。难道他被三体人抛弃了？

20100217
＊＊同样，常伟思制作了陨石子弹，并隐秘地谋杀了航天部守旧派高官。他以这种极端方式把地球抵抗运动推向正确的方向。三体人肯定通过智子看到了，但却没捅出去。

革命之路

2010-01-19T08:17:00.000-08:00

革命之路

TBA

Revolution road

影评

2010-01-19T08:12:00.000-08:00

前一阵子花了那么多时间看了一堆电影。日后有些镜头时常在眼前闪动，回味起来颇有些感触。于是乎也想写些三脚猫影评吧，算是对搭上的时间一个交待！就从“革命之路”开始好了。

谷歌，请不要退出中国

2010-01-16T12:12:00.000-08:00

我对谷歌说谷歌请不要退出中国中国人民是爱你的

谷歌说再不退就狗咬狗一嘴毛了

Photos: boring Texas

2010-01-14T13:35:00.001-08:00

以下一组照片名为“无聊之得克萨斯”
Following bunch of photos are named "boring Texas"

Above photo was taken at Galveston on Jan 1, 2010, a sunny yet chill beach day.

The sky is exceptionally clear late in the afternoon of Jan 11. Photo taken near my work place.

日晕和恐怖的云彩 Did you see a ring around the sun? Photo taken behind the window so it looked spooky. 20091228

煤块，学校

2009-12-28T07:59:00.000-08:00

在中国北方，到了冬天，人们生活取暖全靠燃烧煤炭。每年冬季北方城市消耗煤炭数量是多少？不知道具体数字，但一定大的惊人。

河北省张家口市尉县的教育局长葛祥在家中割腕自杀，据推测其动机竟是“没办法弄足够的钱为县里的小学买冬季供暖用煤”。

官方新闻报道

百度贴吧尉县吧里的评论

（待续）

圣诞节，洋人的

2009-12-25T14:08:00.000-08:00

圣诞节，洋人的，别人的，反正不是我的。

今天在实验室电脑前度过了，决定后三天都如此～努力工作，把浪费掉的时间弥补过来。

我之前许下的诺言算是黄掉了...

Heavy fog

2009-12-13T10:09:00.000-08:00

This region's climate interests me. At this moment of the year it is changing drastically. We have been having heavy fog for days. Above photo was taken a few days before. Perhaps that was not fog, that was cloud -- nearly touching the ground.

Seen in my apartment two days later.
“毛脚贼”，呵呵。

冷啊～

2009-12-05T14:36:00.000-08:00

昨天傍晚雪很快就停了，然后低垂的云层很快向南边退去，天空就干干净净地露出来了－－冷啊！

今天一大早出来，给小区里的公寓楼拍一张，发现在色彩明媚的时候这老柯达V550的成像效果非常好啊！理光的那个贼贵的GRDIII还是先不买了。。。

冻雨转大雪

2009-12-04T06:47:00.000-08:00

如同昨天的天气预报，今天一早无比精确的下了冻雨。气温骤降至摄氏1度。

UPDATE：大雪持续了一整天，有时如鹅毛般大！听同事说，休斯敦上一次见到雪是2005年了～对于“本地人”来说，这相当于到西伯利亚了

这种大雪大雾天气在北京一般每年一次吧。。。

问了老兵，他说college station几乎没下多少雪，看来这里是冷锋面啊。跟他说这儿下大雪了，他问那你们是放假了么？又不是刮飓风... 不过最好不要让我碰上啊

We had a heavy snow day in Houston, which lasts till now and will hardly stop. And the temperature drops to 1C (feels like -4C) See how the street looked like under the cover of heavy fog and snow:

作为对比，这是半月之前的某一天。看那明朗的秋日～
As a comparison, this is from the same view angle a few weeks before.

My new powerful Dell T7400 doesn't cooperate well with Ubuntu very well -- when using the terminal, the keyboard sometimes is not responding. Here's the solution from WEB:

http://ubuntuforums.org/showthread.php?t=870490

1. sudo apt-get install scim-bridge-client-qt

2. Edit the file /etc/X11/xinit/xinput.d/scim by typing in a terminal (Applications>Accessories>Terminal):

sudo gedit /etc/X11/xinit/xinput.d/scim

Change the line:

GTK_IM_MODULE=xim

into :

GTK_IM_MODULE="scim-bridge"

Change the line:

QT_IM_MODULE=xim

into :

QT_IM_MODULE="scim-bridge"

I also installed driver for graphic card, then I can activate Ubuntu's *coolest ever* visual effects:

New starting...

2009-12-03T09:46:00.000-08:00

终于决定要继续更新日志了，至少每周一帖！（有够懒－－）

照片是%#@&%地方，猜吧... 休斯敦的天气不错，云彩变换无常，而且距地面高度很低。这张照的模糊了，隔着有色玻璃照的，而且模式选错了，对焦失败，但觉得这云彩不是什么时候都能碰得上的（或者碰巧有机会掏出相机来照）凑合看吧。

（下次再看到那羊群一样的云朵一定要照好...）

Hi all, I will continue to update my blog and document my thought (hopefully)...

Westerners and Beijing migrant schools

2009-10-24T16:15:00.000-07:00

发现了一个网站，记录着一些西方慈善人士对北京市的一所民工子弟学校的关心和帮助。

http://beijingholidayparty.com/kids/

民工子弟学校可能是北京的特有现象了。与北京高楼大厦、灯红酒绿的印象相左，它们灰头土脸，忙于生计和享受的城市人很难注意到它们的存在。看了这个网站里的照片，才从这些西方世界来的慈善者角度对那里有了些了解。

北京市普通小学的学生可能都有自己的手机和笔记本电脑了，这里的娃娃们还那样一无所有；在圣诞节拿到了白皮肤大叔送来的玩具，笑得那样开心！

从这些照片让我回想起我当时上小学的情景，但那是20年之前了！

最后想到，那些建立民工子弟学校、教育那些被忽略的祖国花朵的人是真正伟大的人。

Like any other big and modern cities, Beijing has a lot of gray figures behind its prosperity: they are construction workers, janitors, service persons, ... Majority of them come from rural areas all over the country and they do labor-intensive jobs to make a modest living, and make the city runs happily. Perhaps unlike other cities on the same level, Beijing has migrant schools, where a classroom is provided for children of those workers at day time. The schools are operating on a condition that's similar as I used to be studying 20 years ago -- impoverished, and so are the children staying there. Perhaps one block away children from the ordinary family could already have their own laptops and mobile phones -- a contrast that's astonishing. I'm not sure but perhaps the fees prevent those children from attending an elementary school -- it could be astronomical for migrant workers.

Citizens are usually too busy to pay any attention to these schools. Now some westerners are bringing toys to those children and concerning on their existence. I want to say THANK YOU to these nice people. I also think that the persons who build and operate these schools are real great, too.

10个多月

2009-10-22T09:01:00.000-07:00

跟adug聊天，他第一句就是：lidaof的文章终于接收了

我说：我已经知道了真不容易有10个月了跟生孩子似的

想想我1月初将要离开北京的时候他正在打稿，聊天的时候我答应帮他看。几经波折，终成正果。这通常意味着可以博士毕业了... 我跟他第一句话是：我这个职位要空出来了你赶紧拿了学位过来吧... lidaof痛苦道：老板不放我走啊

lidaof十个月整出篇文章（adug也是），我这10个月整出个屁来了么？

Got the news that one of my friend has just got a paper accepted. This took him 10 months and finally he is eligible for Ph.D. degree with the publication... Thinking about what I have done in the same period, I felt really bad for a moment because I did nothing...

But I will keep up working. All my friends are watching and I won't disappoint them.

Tuzki for “兔斯基” for "TUZKI"

2009-10-19T10:25:00.000-07:00

看了兔斯基和王卯卯的博客～都是同龄人，而且实在太羡慕人家能这么自如的用图画来表达自己（为啥咱好像就对画画一窍不通呢？）

TUZKI is the name of little rabbit created by Momo Wang, which enjoys astonishing popularity in Chinese Internet community. The author is an artist and works as a professional illustrator in Hong Kong. I'm so impressed by her ability to express herself freely via painting...

我们的好总理 Our Premier

2009-10-12T08:27:00.000-07:00

这是温家宝总理致新华社的一封手写信件，更正自己在发言中犯得一个地质学上的错误。如果我没记错的话，温总理正是地质学出身。总理对待事实一丝不苟，并且敢于公开承认自己的错误，让我十分敬佩！总理此书不仅言表个人，更对中国官员有一种示范作用。

Here I try to make a description in English....

This is from news.sina.com.cn, publishing a hand-written letter from our Premier Wen Jiabao to Xinhua News Agency. In his letter he pointed out a minor mistake in one of his article discussing his personal view of teachers' role in education. The mistake is so minor (and technical) that only geologists will recognize it. I admire his action of openly admitting his personal mistake as Premier, as this should set good example for all the Chinese officials!

http://news.sina.com.cn/c/2009-10-12/212418814077.shtml

New photo album: August 31, 2008

2009-08-31T08:17:00.000-07:00

This is our fantastic hiking in Hawk Peak, Beijing. See the original post here.

Now one year later, the photos were published in my Picasa Web Album. Enjoy!

lollipop of mediocrity (end)

2009-08-22T20:46:00.000-07:00

I'm quitting my current job for a postdoc position in Baylor College of Medicine. Above picture was taken from the Hilton hotel where I stayed for interview, overlooking Houston downtown. The city was so busy in rush hour when I arrived there, but now it looks just peaceful.

Lollipop of mediocrity 2

2009-07-29T14:12:00.000-07:00

In horticulture building for International Student Lunch. Lining up to fetch food which was prepared by students from various countries.

Dining at an American restaurant.

Lollipop of mediocrity 1

2009-07-24T14:01:00.000-07:00

Welcome to the Horticulture Building.

Fragmented, hand-made whole scale view. This is what you see when you look outside from the broad & luxury window of graduate student's office in Horticulture building, 5th floor.

Also luxury is the hall. So many useless items that give people illusion of how restful the life seems to be.

In one corner of the hall there's one thing that firmly caught my eyes: a section of a trunk, which used to be a great tree. Probably a pine? I can't tell. I can stare at its growth rings for long time and trying to read what it used to witness, as if reading the great tree's memory.
(Update: the name of the tree is redwood)

Shocked

2009-07-09T07:35:00.000-07:00

Beware the lollipop of mediocrity, lick it once and you'll suck forever.

I was shocked by this sentence. I've decided to see how far can I go.

好了伤疤忘了疼。都4个月过去了罢，偶尔再次看到这句话，那当头棒喝的感觉又回来了。

Never a dragon

2009-06-15T20:01:00.000-07:00

You westerners please see this picture:

which comes from http://www.loong.cn

which is: the symbol of Chinese culture is never a nasty dragon, but the Loong! We are working to correct the mistake!!

librdf Python API summary

2009-06-15T09:08:00.000-07:00

I reviewed my code written using the Redland librdf Python API, and made a brief summary as a memoir. For more advanced and powerful parsing, I'm turning to some Java libraries, such as Jena, owlapi, Pellet, ...

Update: but I have been working with python-librdf for all the time and got my Java stuff put away...

** RDF.Model object

import RDF

model = RDF.Model(RDF.MemoryStorage())
Model using in-memory storage

model = RDF.Model(RDF.HashStorage(bdb_location,options="hash-type='bdb'"))
Model using Berkeley DB storage

p = RDF.Parser('raptor')

file_uri = RDF.Uri('file:/path/to/rdf_file')
Create a URI indicating a local file

p.parse_into_model(model,f_uri)
Parse a rdf file into model. Return boolean to indicate whether this operation is successful or not. (can parse multiple files into one model)

len(model)
Returns number of statements in model, only applies for models with in-memory storage. Won't work for Berkeley DB storage.

** RDF.Node object type

The node.type attribute is an integer indicating type of the node:
1: Resource node, can get RDF.Uri object by node.uri
2: literal node, the value of which can be extracted as node.literal_value['string']
4: blank node, which usually appears in owl as object of rdfs:subClassOf as a restriction on properties.

Better to use node.is_literal(), node.is_resource(), node.is_blank() to make judgment on node types, to avoid confusion.

** Simple query methods (bound to RDF.Model object)

All simple query methods supported by RDF.Model object can accept RDF.Node object. These methods also returns RDF.Node objects.

(model indicates RDF.Model object)

result = model.get_target(a,b)
result = model.get_predicate(a,b)
result = model.get_source(a,b)
Returns a RDF.Node object, or None upon failure

results = model.get_targets(a,b)
results = model.get_predicates(a,b)
results = model.get_sources(a,b)
Always return a RDF.Iterator object, containing the sequence of RDF.Node objects.

Iteration:
for result in results:

Check for end:
results.end() # return 0 or 1 on whether it is exhausted.

Membership test:
my_node in results # return boolean

** Not simple query methods

Create a RDF.Query object:
query = RDF.Query(query_string,query_language='xxx')

Query languages are rdql or sparql, default rdql

Sparql query with new string format syntax:
query = RDF.Query('SELECT ?s WHERE {{ ?s <{0}> <{1}> }}'.format(...),query_language='sparql')

results = query.execute(model)
results is a RDF.QueryResults object, also an iterator

Check for end:
results.finished()
for this_re in results:
print this_re['s']

** Blank node

Blank node is specially noted here because it is frequently used in collection-type domain/range declaration, and property restriction for class. All happen in OWL.

Blank node does not have uri attribute, and cannot be converted to RDF.Uri object. It can be easily used in RDF.Model object-bound queries, as they readily accepts node object as arguments.

To use it in ``not-simple'' query, Sparql query syntax (but not rdql) has to be used:

# node is a blank node
node_str = '_:'+node.blank_identifier
q = RDF.Query('SELECT ?predicate ?object WHERE {{ {0} ?predicate ?object }}'.format(node_str),query_language='sparql')
results = q.execute(model)

Problem: when working with Uniprot OWL, such a query would retrieve all the blank nodes. For example, a sparql query of blank node with predicate owl:unionOf will retrieve 26 blank nodes as objects, but a get_targets() query will retrieve only 1 blank node correctly. Will check if this is a bug or not.

Nodes with collection parseType are frequently used, eg. in domain/range specification.

Generic genome browser on Ubuntu

2009-06-12T09:10:00.000-07:00

I'm preparing some stuff for the workshop, so I'm getting back to gbrowse again.

** Installation steps:

gbrowse version: 1.69
Ubuntu version: 9.04)
perl version: 5.10.0
bioperl version: don't know how to figure that out...

$ sudo apt-get install libapache2-mod-perl2
$ sudo apt-get install libapache2-mod-perl2-dev
$ sudo apt-get install libapache2-mod-perl2-doc
$ sudo apt-get install apache2-doc

Verify that this directory exists: /usr/lib/cgi-bin, if not, create.

$ sudo apt-get install libgd2-noxpm-dev
$ sudo apt-get install mysql-server
$ sudo apt-get install mysql-client

Use cpan to install all prerequisite Perl modules as listed in INSTALL.

Started to install gbrowse from source code:

$ perl Makefile.PL

Complained that Bio::Graphics module is old. So upgrade it using cpan. (not successful until graphviz software is installed)

$ cpan
cpan> upgrade Bio::Graphics

$ perl Makefile.PL
$ make
$ sudo make install

Finished. Really a bit surprised to see so many fancy features in this version of gbrowse. The last time I was working with gbrowse is 2006.

** It stuffed some scripts into my system directory. For example those are found in /usr/local/bin:
bp_search2alnblocks bp_search2tribe bp_seqfeature_load.pl
bp_search2alnblocks.pl bp_search2tribe.pl bp_seq_length
bp_search2BSML bp_search_overview bp_seq_length.pl
bp_search2BSML.pl bp_seqconvert bp_seqret
bp_search2gff bp_seqconvert.pl bp_seqret.pl
bp_search2gff.pl bp_seqfeature_delete.pl bp_seqretsplit.pl
bp_search2table bp_seqfeature_gff3.pl
bp_search2table.pl bp_seqfeature_load
... and much more!!

Gbrowse configuration files are located in ``/etc/apache2/gbrowse.conf/''

** use bp_seqfeature_load.pl to initialize the mysql database.

** GFF3 format file nuisance:

The gff3 file for E.coli I downloaded from NCBI was rejected by gbrowse!
The scaffold declaration entry (first row of gff contents) is different with the example gff3 file that comes along with gbrowse program. The TYPE (3rd column) has to be ``chromosome'', and there has to be ID,NAME contents in 9th column.

无题

2009-06-08T19:13:00.000-07:00

咚了个咚咚呛！！老乡们，注意了，adug同学的博客....挪窝了！

目前地址是：http://blog.sina.com.cn/adugduzhou

基本上么，虽然还没什么内容，但个人*特色*已初露倪端，所谓``小荷才露尖尖脚，一坨鸟屎糊上头！''

不过还是很羡慕人家的那种满足感，咱什么时候也能那么呢？咱好像从来没那么过...以前听李宁老师说过（不是卖衣服的那个，是克隆牛的那个），人生是艰难的，即便是片刻的满足感也是奢侈的！当时哈哈傻笑来着，现在则是多么的同意他的灼见啊！曾经有过片刻的可供膨胀的空间，却被我当空气般视而不见，哎... 忍了～就让寂寞的空气包裹着我，拖着两条腿继续孤独的前行吧...

Bird nest (2)

2009-06-07T19:46:00.001-07:00

I saw this on Friday: someone has put a little blue flag near the nest!

And I saw the mother bird is still covering her eggs -- and ran away when I approached. I felt sure I can see the eggs hatching.

======

Update on 20090630:

The eggs are gone. The story ends here, on this waste land.

X11 display reconfiguration for Ubuntu on Dell T300

2009-06-05T08:21:00.000-07:00

I just upgraded Ubuntu on our Dell T300 machine to 9.04. Fancy... but we got a surprisingly slow response in gnome-terminal.

I googled, and found out that Ubuntu 9.04 is not working very well with the Intel video chipset of the machine, as discussed here.

The solution is quite simple (though the instructions kept me trying for a while). Sudo to root, edit the file /etc/X11/xorg.conf, add following line to Device section:

Option "MigrationHeuristic" "greedy"

Then logout, and re-login, solved!

Bird nest

2009-06-02T19:15:00.000-07:00

I spotted a bird nest today, right beside a trail on my daily jogging route!

From the second photo, you can see it's on open ground and very close to the trail, where runners and bikers pass by, and sometimes even cars (luckily very few). I'm really worried that this nest would be easily destroyed, either by people, or by squirrels! I placed some larger rocks around the nest, hope it will do some protection, or at least let others notice it!

When I was there, the nest owner was around me all the time, singing angrily. I really don't know which kind of bird it is.

So interesting...

Today's news

2009-05-29T11:11:00.000-07:00

A few days ago Zhou Du let me know that my blog could not be accessed in China - I did not feel very uncomfortable about that. I started using Blogger in 2007 and I was quite used to its occasional unavailability.

What really suprised me today, is that Zhou Du told me he could not read my blog via Google Reader (subscription attempt will get error message).

When I'm wondering if Google is having a technical problem (and feeling a little bit upset), Zhou Du swiftly opened his new blog in Sina (www.sina.com.cn).

I really don't know what to do, and I will just wait and see what happens. I don't want to open a new blog elsewhere, I mean, I love Sina.com, I always read interesting blog stuff there, and even advised my dad to use it... I think I will continue to make posts on Blogger. I'm sure people in China will be able to view it sometime in future, just like everyone else in the world.

==============

By the way, here's one insteresting blog I just found

Beijing Notebook - Random observations noted in Beijing
http://beijingnotebook.blogspot.com/
(By a friendly lady who is enjoying her life in capital city of China)

去休斯敦机场

2009-05-26T12:41:00.000-07:00

最近没啥事儿，但还是来胡写几句吧：

上周日晚上去休斯敦机场接老兵同学，飞机从芝加哥过来，因为这边雷雨所以晚点半小时，11点半到的。我因为没在美国出过远门，出发前花时间准备了一番：查了从college station到机场的详细路线（还画了个草图），拿上老兵的GPS，把车检查了一下。尽管怀疑车的油泵有问题，但凑合着开了。晚上10点出发，出发前很搞笑，先是Joshua打电话过来，跟我讲他现在有空，如果我没把握不敢去了，他就去接老兵；我刚把车开出小区，老高又打电话来，问我出发了没，要不要让他一起跟着去，我跟他们说不用担心，我能行。看来让我去接人搞的大家比我还紧张，呵呵。路程110英里，绝大部分是高速，跟宣化到北京的路程差不多。

我没什么夜间行驶的经验，发现夜间行车又紧张又枯燥，在远离城镇没有灯火的地方，除了前面那100米的路面，四周就是一片乌黑！幸好路程不长，路况也好。进城以后上了beltway，算是环城线吧，有5车道，我在最右道60mph的速度走，在左边其它的车就快速的超过去。这beltway是收费的，而且收费站就会设在路中央，跟国内一样，呵呵。交费时可以走coin only通道，那里无人执勤，需要自己把六个quarter向扔石子一样抛到一个喇叭型圆筒里，咣铛一声之后挡在车前的栏杆就打开了，挺搞笑的。

到机场后走arrival这个路线，没有去停车场。这个时间要算准，我已经到passenger pick up的位置了，赶快给老兵打电话，但他还在取行李；这里车流繁忙，交通引导员在不停的把车往外赶:-) 我就只得绕这那个航站楼又走了一圈，再回来的时候才把人接上了。

回来的时候出了些差错，先是忘开近光灯了，以至于一个开卡车的人跟我并行了一小会儿，还探出车窗指着我的车头向我示意，我跟老兵居然过了一会才反应过来怎么回事，糗阿～然后是被GPS带错路了，多绕了半小时，最后索性不理GPS了，回头开到我认识的路上才算找对方向。

回来的路上几乎看不到车了。我们孤零零的跑在得州6号高速上，车里放着我最喜欢的那些“口水歌”，高兴的时候俩人就扯着嗓子跟着吼几句。然后就是跟老兵兴奋的胡扯。3点半到家。

＝＝＝＝＝＝＝＝＝

最近通过晓昕的博客得知他目睹了一次事故和悲剧，让我们再次感到生命脆弱且宝贵。我想，对在外漂泊闯荡的我们而言，一定要做到小心谨慎、远离是非，当然，还有安全驾驶。

LCD brightness issue on ubuntu & X61

2009-05-16T19:16:00.000-07:00

My Lenovo X61 (running Ubuntu 8.10) got the problem of not to adjust LCD brightness. This really annoyed me! I thought that this could be inconsistency with the sophisticated hardware... Luckily, someone hacked the problem!

http://ubuntuforums.org/showthread.php?t=1071216

Briefly, modify two files under: /etc/acpi/

Append line ``echo 4 > /proc/acpi/ibm/cmos'' before exit for file ``thinkpad-brightness-up.sh'',

and similarly line ``echo 5 > /proc/acpi/ibm/cmos'' for file ``thinkpad-brightness-down.sh''

Ubuntu install from USB stick and what

2009-05-15T13:11:00.000-07:00

Well, I just made a successful install of Ubuntu from USB stick, not a live CD.

This turns out to be very simple: you just download a Ubuntu install CD image onto a Ubuntu machine, insert a working USB stick (make sure there's no important data), and use the ``USB startup Disk Creator'' to do the thing. It is crucial for the version of system you're running and the CD image to be the same (version 9.04 was tested to be working).

After this, plug the stick onto a PC which can boot from USB device and install the system. I got a Dell studio computer and the installation worked fine.

==========

I went to the library this afternoon, where I saw a kind of ceremony for the graduating cadets (the students going to be officers in military). I joined with their families to watch them.

下午去图书馆的时候在路上看到了一个小的仪式，应该是为毕业的军校生(cadets)举行的。人群很安静。肃立在人群中央的学生（男女都有哦）被叫到名字后就会走上前去与一个军官模样的人，敬礼，然后握手交谈几句，退下。围观的人中应该不少都是学员的家人，忙着用相机记录这一幕，或者静静的注视。

Texas A&M有四千军校生，所以校园里经常能看到最后一张照片里打扮的学生。我在research park跑步的时候还遇见过全副武装的学员背着制式步枪在拉练，有点像在媒体上见到的驻扎在海外的美军士兵。这个学校还有个Memorial student center，那里的草坪是禁止踩踏的（在美国很少见），草坪上的一块小石碑告诉了你原因：这里是专门用来纪念从这个学校毕业的、为美利坚合众国捐躯的军校生。

Frog thinks

2009-05-13T11:38:00.000-07:00

Congratulations to adug, who just have his first first-author paper accepted by a scientific journal. Congratulations to Xiaoxin, who has just made important discovery in his studies. My friends are all doing well. Congratulations to you all! Though I'm right now like ``frog in the well'', I'm really inspired by that. Stop complaining! Hit the gas, change the gear, and journey into the new world ->

很棒的消息！师弟adug刚刚有他的第一篇文章被接收了，“手中有paper，心中不慌了”，:D 恭喜！另外我的好朋友Xiaoxin也在他的实验中得到了重要结果，希望科学史上能留下你的一笔！恭喜你们！

尽管我一直在坐井观天中，但我也一直在不懈努力，而且要更加努力了！

Great clouds

2009-05-11T09:48:00.000-07:00

I love watching clouds -- that is, literally anything in the sky.

Here in College Station we have a climate that always changes drastically, and a sky usually full with turbulent clouds. Just now towards noon this day, I stood outside the building to enjoy the air, and saw those majestic clouds there. I instantly took a few pics, but the effect was poor -- partly due to mist air this day, a lot of moisture. After a while, the battery was drained, and I had to get back.

祝妈妈母亲节快乐！

2009-05-10T11:19:00.000-07:00

祝亲爱的妈妈母亲节快乐！

照片老早就照了，是在borlaug center旁边的一个什么楼，忘记名字了。楼前有一座老模老样的雕像，挺有派头的老牛仔，仔细一看，腰上怎么还挎个鸟巢？里面还蹲着个小家伙？？哈，原来有个斑鸠在很合适的位置筑巢育雏了，真有意思

发现college station的斑鸠真是多啊，一个个胖乎乎的，也不是很怕人。哪天专门讨论一下。

The picture: a dove made a nest in a fine position in a statue, in front of a building near my office. I took the picture when I'm running one afternoon (in May 1st?)

Happy Mother's Day, my dear mother!

三言两语

2009-04-26T08:27:00.000-07:00

最近过得还凑合，出来跟大家冒个泡。

我的韩国朋友Gangman要回国了，去和家人做短暂的团聚。他做的课题的几个任务还在我旁边那间屋子里的服务器上呜呜的跑着。他说程序跑完了文章就出来了，我于是就这么帮他守着。我把我带来的那套礼品筷送给了Gangman，他特高兴！我比他还开心，因为带来的礼物总算派上合适的用场了。之前在国内买的另一套作为新婚礼物送了武师姐，用途基本一样吧，呵呵

在国内的最后几天，一个好朋友要回家了，回那个``烟花三月''的城市。离别前留给我了一对很漂亮的小海螺，我用伞兵绳把它挂车里了。每次我进车，它都会晃一晃，就好像好朋友在向我招手似的。

My friend Gangman will go back home soon, to reunite with his wife and family. I gave him as present the chopsticks I brought here, and glad that he was really happy about it. Some time ago I gave the other one to Haiyan, as wedding gift. So this is basically the same.

The photo shows that I hung a pair of little seashells in my car, which is a gift from my good friend back in China. Every time it swings, it seems like my friend is waving to me. God knows when we can see each other again.

Driving test passed!

2009-04-16T08:49:00.001-07:00

I passed the driving test this morning. Hooray!

The computer system in Department of Public Safety office is down today so I did not get my temporary permit instantly, and thus I keep the record paper with me and will bring it back later. Here shows it!

First ticket in US

2009-04-09T06:33:00.000-07:00

As usual, I was riding on a bike leisurely from apartment to office this morning. When I was about to get off and walk the remaining distance, I noticed a police officer in black uniform was riding after me and blowing his horn at me. I was wondering what happened when he said "Stop!"

Oh my god... I suddenly realized what has happened, before the officer gently told me why I was stopped for... I didn't stop at the stop sign.

Thus I got a WARNING ticket, it is my first ticket in US, and I will keep it.

今天早上因为我违章骑车（忽略停车标志）而吃了一张ticket。

当时我已经骑到实验室旁边准备下车了，忽然发现后面跟了个胖警察，穿着制服（短衣短裤:)），骑着自行车追我，还朝我鸣笛。我马上反应过来是犯事了，赶快停下来。警察先向我说明我哪里违章了，然后例行索要证件。我的学员驾照还给要了去看看。然后就是在这张ticket上一通写。这当我瞥见他腰上装备真不少，还有一支手枪...不敢瞎看了赶紧目视前方....

也幸好只是个警告，没有经济损失。不过我以后一定会注意啦！

写到这里不由得想起本科时候也有类似经历：在北京颐和园路东口那里因为骑车带人被一位交警拦下来，要证件没带，然后被告诫不要违章，并被罚了二十块。

My jogging route

2009-04-06T12:10:00.000-07:00

I took my camera with me when jogging yesterday afternoon. It was Sunday and there's quite big wind blowing from north-west. Not a dust in the air, the sky was crystal blue. Very cool temperature too.

Basically, the pictures shows my daily jogging route.

An old tree seen on the playground, quite near to my apartment.

Near the George Bush Library.

Still near the Bush Library. You can see on the grass field a piece of land was intentionally left untouched for the wild flowers to bloom.

The George Bush Library. My friend Clay told me that before the library was built, here used to be a farm where livestocks were kept.

The small pond in the research park.

Near Bush Library, on the route back.

When serious industry gets absurd

2009-04-01T08:11:00.000-07:00

今早adug同学推荐我看的...谷歌的技术精英们，天才般的整了个``谷鸽''。

“思想有多远，山寨就有多远”，google高举全民山寨的大旗，雷啊！！！

（...心想，这么牛X的鸽子一天得吃多少谷子呢？？）

============
Or, when a bunch of absurd people control it..

Anyway, I like to be absurd. Occasionally, that is.

Random photos (2)

2009-03-31T08:08:00.001-07:00

The street lights besides Callaway building.

Two young Aggies were busy putting up a board on the green grass field. I walked there and asked what's that for. They explained a lot but I could not understand much -_-|| Seemed that was a campaign for student president election.

A red VW Beetle on the empty car park besides Reed Arena. It was spring break and a peaceful, bright afternoon.

Python-C software installation

2009-03-16T13:10:00.000-07:00

I've been trying to install xMAN software, named for "extreme mapping of oligonucleotides". This software is a new kind to me: C-extended Python. And its installation tends to be different.

First install prerequisite:

sudo yum install swig.x86_64
sudo yum install python-numarray.x86_64

The package comes along with a setup.py, run as suggested:

sudo python setup.py install

Got error:

error: Python.h: No such file or directory

Looked through Google, saw that python-dev needs to be installled:

sudo yum install python-devel.x86_64

Then the installation worked just fine!