Memories

贴上一些散乱的照片，记录我研究生期间的生活（自2004年秋至2008年冬）。
Some of the past photos in my graduate years, from fall 2004 to winter 2008.



当时第一学期我的桌子就是这模样的。当时Ms. Eve正在我右手边忙活，闪光灯让她很惊讶！这可能是我第一次用数码相机。
I entered Dr. Zhen Su's lab on September 2004, and here's what my desk looked like by that time. Ms. Eve who was busy working beside me was surprised by the flash light, and gave me some comments I forgot.
This was literally my first time using a digital point-and-shoot.



哈佛大学的刘小/晓乐博士于2005年夏来访，很兴奋的与她在实验室内合影。当时尽管我懂得很少，但还是明白Dr. Liu是个牛人。最左边的就是小江同学啦，我一直这么称呼他，呵呵。
Dr. Shirley Liu at Harvard University paid a visit to our lab on summer of 2005, and it's my honor to have a photo with her, as I already knew she was a great scientist.



2005年夏，去昆明参加全国植物基因组学大会，然后去石林玩了一趟。总之感觉那时石林里的人比石头多，我差点儿被挤扁了...
In summer 2005, I visited Shilin (the stone forest) in Kunming on a national conference for plant genomes. Tourists there seemed to be more abundant than stone...but luckily, we were able to find a corner to have a nice pic.



2005年7月，在导师夫妇的带领下，实验室所有人去大觉寺游玩，真是个宁静美丽的好地方。
All of our lab went to Da Jue Temple to enjoy its beauty (July 2005). It's in north part of Haidian district, just a few km from CAU campus. Great place to visit!
当大家都玩够了，坐下讨论serious stuff的时候，我和yyliu悄悄走开，一起去寻找古寺中尚未被发现的僻静角落。
While everyone's talking about serious business, Yunyan and I went to a quiet corner in search for more beauty there.




2006年4月28日，张子丁老师招待了我们几个人大吃一顿！当时我们还给张老师买了束鲜花来着，记性不错吧:-) 我让服务员给我们拍照留念。
On April 28, 2006, we had a pleasant lunch together with Dr. Ziding Zhang, who recently joined China Agricultural University as a new faculty.




我与前女友在06年劳动节去了趟红螺寺...总之觉得去那个地方实在是浪费时间。
I together with my ex-girlfriend went to Hongluo Temple, around Labor's Day, 2006. Not at all a good place to visit :-(


06年夏天，工作餐（可能是欢送yyliu兼欢迎lidaof入伙?)
This could be a ``farewell to yyliu & welcome for lidaof'' lunch? Obviously we were not so focused on the dishes. (summer 2006)



06年夏天比较能折腾，去了数次博奥公司。那儿还见到在NIBS的赵杨，我的老同学。他帮我照了张相。
I was on a leave for CapitalBio Inc. on July 2006, and I met my buddy Zhao Yang there, who was struggling like me in National Institute of Biological Sciences (NIBS).



我们这些搞bioinformatics的就这样子... 于2006十月，实验室的老成员们。
How we bioinformatics guys looked like: (October 2006)



不会吧？2007年就照了这么一张相？
The year 2007 was so peaceful that I only had one photo... in December:



2008年三月来了场沙尘暴。当时的天空让我有点抑郁。
Beginning of 2008 was so bad! Look we had a terrible sand storm on a March day. I remembered on that day Chinese government held a face-to-face meeting with world-wide journalists and media.



幸好的是，天气很快转好了，而且相当不错。
四月底的某一天那个薄雾笼罩的美妙清晨，老于同学拎着照相机在校园里散步...
Luckily, the weather quickly turned fine. Yu took a walk on campus on a beautify morning (Apr 29, 2008), and took those equally-nice photos...
来到实验室时，我当然正在埋头苦干啦，于是来一张吧～睡眼惺忪的样子是闪光灯搞的！
Of course, I was in the lab that time, the ``golden morning'', busy with my stuff.



08年劳动节，在实验室里给邸超过生日。奶油蛋糕一年才见一次，抢～...阿，真tm难吃
We celebrated Di Chao's birthday on May 1, 2008, right in lab. But the cake was terrible...



C刘第一个毕业啦！我们都很怀念和他在一起的日子...
On June 2008, cliu was the first student to graduate from this lab. We all feel so happy to be with him!


2008年7月，某人要求我请大家吃涮锅，名曰庆祝文章接收，于是就又在实验室里小折腾了一番^_^
We ate hotpot (do westerners know what is that??) on July 20, 2008, on demand of adug to ``celebrate'' acceptance of my manuscript...


我真的太喜爱爬山了，连下雨的时候也愿意去...而且不止我一个人这样，哈哈！
The thing I would like to do most for recreation is walking in hills and forests, so even in rainy days (July 31, 2008).



最后我就很高兴的毕业了！光荣阿，尽管没学位服穿了...
And finally I graduated, happily :-D

Severe errors that might ruin a project

I have recently ran into a severe error that would have spoiled a project... and luckily I got to know a bit why.

I have utilized the tgicl (TIGR sequence assembling software) to make one assembling job. The tgicl called formatdb to build index of all the sequence reads, and there's .nhr, nin, .nsq files been produced.

After assembling, I want to get sequences for all singletons, so I used fastacmd to fetch them from the database formated by tgicl. Everything is usual... but the output is unusual: identifiers of the sequences thus fetched are strange names like following:

>gnl|BL_ORD_ID|10 000067_0726_3676 ...descriptions...

The second word is indeed sequence name, and I have no idea how the first strange name came here. This would cause serious trouble in further processing if the name change were not considered.

Anyway, I found that if I do formatdb using following parameters:

$ formatdb -i xxx.fasta -p F

The produced file xxx.fasta.nhr contains all name correspondance, which uses only one line to hold the very big contents! And this indirectly saved my ass in this nasty issue, especially when I was running to meet the deadline!

Ubuntu for Lenovo Thinkpad X61

I have got a X61 and now I want to use Ubuntu on it.

A partition of 40 GB was made for /home, and 15 GB for /, and 300 MB for /boot
(peculiarly, my lab PC which runs Ubuntu 8.03 gets a lot of stuff in /boot and the tiny space of 100 MB is used up, and the update manager refuses to work!!)

** The system is in English.

** Enable Chinese input

I have previously installed scim-chinese, but this won't help.

I followed this link, and its quite easy: go to System > Administration > Language support, and select Chinese. Ubuntu will download a lot of stuff. After that, select "allow input complex characters". Finally select OK. Log-out will be required.

http://www.blog.highub.com/linux/ubuntu-install-chinese-input/

现在我可以输入中文了 :-)
(Now I can input Chinese!)


** Adjust bash prompt appearance

Edit ~/.bashrc, around line 55, make following replacement:

old: PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
new: PS1='${debian_chroot:+($debian_chroot)}[\u@\h \W]\$ '

I have no ideas what that's about -_-||


** Personalize Vim

Vim is my favorite unix software...

$ sudo apt-get install vim

And I created a .vimrc file with following contents:
set hls
set nonumber
set ts=4
" use indent of 4 spaces, and have them copied all around
set shiftwidth=4
set shiftround
set expandtab
set autoindent
syntax on

A more comprehensive (and old) .vimrc sample file is here:
http://www.stripey.com/vim/vimrc.html


** Personal data for Firefox

The personal data on my lab PC was built into a tarball, and transfered to X61.
Original contents in ~/.mozilla/firefox/ were back-upped and deleted, where my personal data was used to make the replacement.

And Firefox happily accepts my personal data and new configurations.


** Install following goodies (and problems)

$ sudo apt-get install dia
xxxxxxxxxx
xxxxxxxxxx
The following packages have unmet dependencies:
dia: Depends: dia-common (= 0.96.1-5ubuntu2) but 0.96.1-7ubuntu1 is to be installed
Depends: dia-libs (= 0.96.1-5ubuntu2) but 0.96.1-7ubuntu1 is to be installed
E: Broken packages

I'm using Chinese version of sources.list (locates at /etc/apt/), and I changed it to a "western" version I found online.

$ sudo apt-get update
## finishing update
$ sudo apt-get install dia

Then Dia 0.96.1 was installed successfully.

千里之外（续1）

好几天前锻炼身体的时候做了三组推举，完后没有充分放松，结果导致后两天胸肌疼的象被大象踩过...

还好，签证算是顺利拿到了，可是我留在北京的时间也因此迅速缩减。我将不得不“按原计划”在几天后回家，订月底的机票，然后奔赴美利坚！

一个人在那里生活也没什么不好的，多少年的日子我都单独过来了，而且在那里不用忍受宿舍的不方便，可以早起早睡、自己做饭伺候自己的胃口、弄个破车时常擦擦洗洗...也可以去跟系里的同事们胡扯了～

日子一天天过去，我的感冒几乎也完全好了。我又开始正常的早起、午睡、闷在空气污浊的实验室里忙活，然后下午顶着寒风去慢跑，注视国旗班的同学举行降旗仪式，有时会想象一下Texas的空气会不会这么清冽...

就仿佛什么都没有发生一样。

昨天我去了研究所里，开父亲的车去的。重走在那条道路上，心仿佛回到一周前。在所里的大厅中，我凝视着PI们的照片和简介，又看了那张大合影，捕捉着可能跟我有那么一丝关系的一切...

千里之外

元旦一直在感冒...唉

今天晚上，准备签证已经非常疲倦了，就开始听歌曲，《牡丹江》，《青花瓷》，最后是《千里之外》

当听到 我送你离开/千里之外/你无声黑白/沉默年代/或许不该/太遥远的相爱 时，眼泪竟然抑制不住的流了下来！


我送你离开，千里之外，你无声黑白，沉默年代/或许不该/太遥远的相爱


我送你离开，千里之外，琴声何在，生死难猜，用一生等待...



I'm leaving, you without me, I without you
A thousand miles beyond reach

Love between
May not be expected
in those silent days