Philippe's Expérience Note

參考了很多 Mac Ruby 更新的文章，大部分的人還是傾向直接用 MacPorts 更新，趁著更新的同時也記錄一下更新的筆記
首先如果你的 Mac 還沒裝 MacPorts 先到官網下載 MacPorts-1.9.2.pkg
安裝完後進行更新
$sudo port -d selfupdate 
MacPorts command:
port -d selfupdate #=> 升級 macport
port install xxx  #=> 安裝 xxx 軟體
port upgrade outdated #=> 升級所有軟體
port installed   #=> 列出已經安裝軟體
port search xxx  #=> 列出與 xxx 條件相符的軟體


我的 Macbook 藍芽當機今天算起來已經是第二次了
也不知道是什麼原因引起的...

還好有解決方法步驟 

剛剛在執行一個簡單的 Rails 範例 (base on win7)，一直出現 系統遺失 sqlite3.dll ，以為是沒安裝 SQLite3 (gem install sqlite3-ruby) ，重新安裝後還是不行....
爬文之後才知道安裝完 sqlite3 不會在系統產生 sqlite3.dll 檔案
解決方法：
到 SQLite 官網上，下載 sqlitedll-3_7_2.zip 並解壓縮，將 sqlite3.dll sqlite3.def 丟到 \windows\system32 就可以了！
本文章同步於 Tumblr

小技巧 - 第一招
如何去除在文件中的出現的 ^M 符號
使用 tofrodos 套件
OS: ubuntu
先檢查一下 ubuntu 中是否有安裝 tofrodos 套件

筆記另類觀點


筆記成功術：升級你的大腦創意與效率

(圖片來源：博客來網路書店)

在css中 加入下面code
用這個方法來做programming的筆記真的很方便
ps. 還有另一個不錯的方法syntaxhighlighter，我目前使用上還會有程式碼斷行的問題，等問題解決了在放上來

code{

display: block; /* fixes a strange ie margin bug */

font-family: Courier New;
font-size: 11pt;

overflow:auto;

background: #f0f0f0 url(http://chenkaie.googlepages.com/Code_BG.gif) left top repeat-y;

border: 1px dashed #333;

padding: 5px 5px 5px 20px;

max-height:200px;

line-height: 1.2em;
margin: 5px 5px 0 15px;

}

We currently have room in the lab for more graduate students. Before you apply to this lab or any other, there are a few things to keep in mind. First, be realistic about graduate school. Graduate school in biology is not a sure path to success. Many students assume that they will eventually get a job just like their advisor's. However, the average professor at a research university has three students at a time for about 5 years each. So, over a career of 30 years, this professor has about 18 students. Since the total number of positions has been pretty constant, these 18 people are competing for one spot. So go to grad school assuming that you might not end up at a research university, but instead a teaching college, or a government or industry job. All of these are great jobs, but it's important to think of all this before you go to school.
Second, choose your advisor wisely. Not only does this person potentially have total control over your graduate career for five or more years, but he/she will also be writing recommendation letters for you for another 5-10 years after that. Also, your advisor will shadow you for the rest of your life. People will always think of you as so-and-so's student and assume that you two are somewhat alike. Finally, in many ways you will turn into your advisor. Advisors teach very little, but instead provide a role model. Consciously and unconsciously, you will imitate your advisor. You may find this hard to believe now, but fifteen years from now, when you find yourself lining up the tools in your lab cabinets just like your advisor did, you'll see. My student Alison once said that choosing an advisor is like choosing a spouse after one date. Find out all you can on this date.
Finally, have your fun now. Five years is a long time when you are 23 years old. By the end of graduate school, you will be older, slower, and possibly married and/or a parent. So if you always wanted to walk across Nepal, do it now. Also, do not go to a high-powered lab that you hate assuming that this will promise you long-term happiness. Deferred gratification has its limits. Do something that you have passion for, work in a lab you like, in a place you like, before life starts throwing its many curve balls. Your career will mostly take care of itself, but you can't get your youth back.
If, after reading this, you want to apply to this lab, we would love to hear from you.
source: The Johnsen Lab, Duke University, Department of Biology

phosphorylation sites
‧serine (Ser, S) 絲胺酸

Beta-hydroxyalanine, an amino acid with an aliphatic hydroxyl side chain, non-essential in human diet, constituent of protein, and which is also an important intermediate in phosphatide synthesis.

Bate-羥丙胺酸，一種帶有脂族羥基側鏈的胺基酸，在人類食物中為非必需，是蛋白質的成分，也為磷脂合成的重要中間體。

(the graph from wiki)

‧threonine (Thr, T)蘇胺酸

An amino acid, aminohydroxybutyric acid, constituent of protein, essential in human diet.

一種胺基酸，氨基羥丁酸，為蛋白質的成分，人類飲食中必須。

(the graph from wiki)

‧tyrosine (Tyr, Y)酪胺酸
Amino acid with aromatic side chain, constituent of protein, also important as a precursor of adrenaline and noradrenaline, and of thyroxine and melanin.

具芳族側鏈的氨基酸，是蛋白質成分，也是腎上腺素和去甲腎上腺素、甲狀腺素和黑色素的前體，因而重要。

(the graph from wiki)
‧Histidine (His, H) 組胺酸
Amino acid with a basic side chain, constituent of protein, possibly essential in the human diet, precursor of histamine.

帶有一個鹼基側鏈的胺基酸，蛋白質的分組，在人類食物中可能是必需的，為組織胺的前體。

(the graph from wiki)

‧phosphoserine 磷酸絲胺酸

Phosphorylated derivative of the amino acid serine in proteins, modified after incorporation into the protein chain. Enzymatic phosphorylation and dephosphorylation of serine by serine-threonine protein kinases is a mechanism for regulating the activity of certain proteins.

是絲胺酸參入蛋白質鏈之後受到修飾的氨基酸絲胺酸的磷酸化衍生物，通過絲胺酸-蘇胺酸蛋白激酶催化的蘇胺酸磷酸化及去磷酸化作用是某些蛋白質活性的調節機制。
‧phosphothreonine 磷酸蘇胺酸

Phosphorylated derivative of the amino acid threonine in proteins, modified by protein kinases after incorporation into the protein chain. Enzymatic phosphorylation and dephosphorylation of threonine by serine-threonine protein kinases is a mechanism for regulating the activity of certain proteins.

蛋白質中的蘇胺酸(一種胺基酸)的磷酸化衍生物，結合到蛋白質鏈後受到蛋白激酶修飾。絲胺酸-蘇胺酸蛋白激酶催化的蘇胺酸磷酸化及去磷酸化作用是某些蛋白質活性的調節機制。
‧phosphotyrosine 磷酸酪胺酸
Phosphorylated derivative of the amino acid tyrosine in proteins, modified after incorporation into the protein chain. Enzymatic phosphorylation and dephosphorylation of tyrosine residues by tyrosine protein kinases is a mechanism for regulating the activity of some proteins. Phosphorylation of tyrosine in the cytoplasmic tails of a class of receptor proteins is a means of signalling their activation by ligand.

蛋白質中的酪胺酸(一種胺基酸)的磷酸化衍生物，結合到蛋白質鏈後受到蛋白激酶修飾。酪胺酸蛋白機酶催化的磷酸化及去磷酸化作用是某些蛋白質活性的調節機制。酪胺酸的磷酸化在一種受體蛋白胞質尾中是一種發送其被配體激活的信號的方式。

最近在念一些phosphorylation相關的paper，碰到很多不懂的生字，感覺這些生字都很像...真的不好記
‧kinase 激酶
Any enzyme that transfers a phosphoryl (phosphate) group from ATP or other high-energy phosphates to an acceptor molecule.

哈佛大學分子與細胞系的學生和Xvivo動畫製作公司，合作的影片-The Inner Life of the Cell
內容是白血球如何感覺周圍環境，並對外部刺激迅速做出回應，動畫做得很細膩
(上面這部動畫是沒有說明的部分，如要聽說明，請點選下面連結)