Download and install Google Extension .crx file

  2. input 32-bit exten­sion ID; for exam­ple:
    If we want to down­load this exten­sion “­lok­bado­hgk­i­fi­jom­clgjgif”, then the 32-bit exten­sion ID of it is “padekgcem­lok­bado­hgk­i­fi­jom­clgjgif”.
  3. Drop the .crx file into the chrome exten­sion page.

Gene-Gene\Protein-Protein Interaction Network — Tools

  1. Cytoscape — Agi­lent Lit­er­a­ture Search
  2. STRING:
    The many func­tion­al part­ner­ships and inter­ac­tions that occur between pro­teins are at the core of cel­lu­lar pro­cess­ing and their sys­tem­at­ic char­ac­ter­i­za­tion helps to provide con­text in mol­e­c­u­lar sys­tems biol­o­gy. How­ev­er, known and pre­dict­ed inter­ac­tions are scat­tered over mul­ti­ple resources, and the avail­able data exhibit notable dif­fer­ences in terms of qual­i­ty and com­plete­ness. The STRING data­base ( aims to provide a crit­i­cal assess­ment and inte­gra­tion of protein–protein inter­ac­tions, includ­ing direct (phys­i­cal) as well as indi­rect (func­tion­al) asso­ci­a­tions. The new ver­sion 10.0 of STRING cov­ers more than 2000 organ­isms, which has neces­si­tat­ed nov­el, scal­able algo­rithms for trans­fer­ring inter­ac­tion infor­ma­tion between organ­isms. For this pur­pose, we have intro­duced hier­ar­chi­cal and self-con­sis­tent orthol­o­gy anno­ta­tions for all inter­act­ing pro­teins, group­ing the pro­teins into fam­i­lies at var­i­ous lev­els of phy­lo­ge­net­ic res­o­lu­tion. Fur­ther improve­ments in ver­sion 10.0 include a com­plete­ly redesigned pre­dic­tion pipeline for infer­ring protein–protein asso­ci­a­tions from co-expres­sion data, an API inter­face for the R com­put­ing envi­ron­ment and improved sta­tis­ti­cal analy­sis for enrich­ment tests in user-pro­vid­ed net­works.
  3. 1

GDB error

  1. PC reg­is­ter is not avail­able” (“Sus­pend­Thread failed. (win­err 5)”)
    MS Win­dows
    GDB may fail with this mes­sage. This is due to it .If you get this issue you may want to down­grade to GDB 7.2.
  2. 1
  3. 1

Ubuntu Desktop Entry



[Desk­top Entry]
Name=TopCoder Are­na
Exec=javaws /path_to_thefile/ContestAppletProd.jnlp

Gnome/Unity  Menu edi­tor: menuli­bre

Linux — Installation of Oracle Jave JDK/JRE

  1.  check OS archi­tec­ture: 32-bit or 64-bit?

    file /lib/systemd/systemd

  2. check if we have Java installed on our OS

    java –ver­sion

    if we should unin­stall Open­JDK if we have one installed on our OS.

    sudo apt-get purge open­jdk-\*

  3. cre­ate a direc­to­ry to hold our Ora­cle Java JDK bina­ries.

    sudo mkdir –p /usr/local/oracle-java

  4. Down­load Ora­cle Java JDK for lin­ux
  5. copy the file we down­load to the direc­to­ry we cre­ate

    sudo cp –r jdk-8u20-linux-i586.tar.gz /usr/local/oracle-java/
    cd /usr/local/oracle-java/

  6. unpack the com­pressed file we down­load

    sudo tar xvzf jdk-8u91-linux-x64.tar.gz

  7. Edit the sys­tem PATH file /etc/profile and add the fol­low­ing sys­tem vari­ables to your sys­tem path.

    sudo vim /etc/profile

    then add the fol­low­ing lines below to the end of the file pro­file (final­ly save and exit):

    export JAVA_HOME
    export PATH

  8. Inform our OS where our Ora­cle Java JDK is locat­ed.

    sudo update-alter­na­tives –install “/usr/bin/java” “java” “/usr/local/oracle-java/jdk1.8.0_91/bin/java” 1
    sudo update-alter­na­tives –install “/usr/bin/javac” “javac” “/usr/local/oracle-java/jdk1.8.0_91/bin/javac” 1
    sudo update-alter­na­tives –install “/usr/bin/javaws” “javaws” “/usr/local/oracle-java/jdk1.8.0_91/bin/javaws” 1

  9. Inform our OS that Ora­cle Java JDK must be the default Java.

    sudo update-alter­na­tives –set java /usr/local/oracle-java/jdk1.8.0_91/bin/java
    sudo update-alter­na­tives –set javac /usr/local/oracle-java/jdk1.8.0_91/bin/javac
    sudo update-alter­na­tives –set javaws /usr/local/oracle-java/jdk1.8.0_91/bin/javaws

  10. Reload our sys­tem wide PATH /etc/profile

    source /etc/profile

  11. test if we hava Java installed

    java –ver­sion
    javac –ver­sion

  12. Suc­cess­ful­ly!


read­able? writable? exe­cutable?
7 1 1 1
6 1 1 0
5 1 0 1
4 1 0 0
3 0 1 1
2 0 1 0
1 0 0 1
0 0 0 0

4=readable 2=writable 1=executable
1=yes 0=no

Often used:



Ubuntu 常见问题

  1. txt乱码(windows下生成的文本在linux下打开)
    The iconv program reads in text in one encoding and outputs the text in
    another encoding. If no input files are given, or if it is given as a
    dash (-), iconv reads from standard input. If no output file is given,
    iconv writes to standard output.
    iconv [options] [-f from-encoding] [-t to-encoding] [inputfile] > [outputfile]
    iconv -f gb2312 -t utf8 [inputfile] -o [outputfile]
  2. windows下编写的Perl程序不能在Linux下运行
    The Dos2unix package includes utilities "dos2unix" and "unix2dos" to
    convert plain text files in DOS or Mac format to Unix format and vice
    In DOS/Windows text files a line break, also known as newline, is a
    combination of two characters: a Carriage Return (CR) followed by a
    Line Feed (LF). In Unix text files a line break is a single character:
    the Line Feed (LF). In Mac text files, prior to Mac OS X, a line break
    was single Carriage Return (CR) character. Nowadays Mac OS uses Unix
    style (LF) line breaks.
    Besides line breaks Dos2unix can also convert the encoding of files. A
    few DOS code pages can be converted to Unix Latin-1. And Windows
    Unicode (UTF-16) files can be converted to Unix Unicode (UTF-8) files.dos2unix [options] [FILE ...] [-n INFILE OUTFILE ...]
  3. Network service discovery disabled
    Your current network has a .local domain, which is not recommended and incompatible with the Avahi network service discovery. The service has been disabled.

    sudo vim /etc/default/avahi-daemon

    Make the parameter below from 1 to 0


  4. /boot空间不足:
    1. 确定自己使用的内核编号

    uname -a

    2. 确定自己安装过哪些内核

    sudo dpkg --get-selections | grep linux-

    3. 删除多余内核
    sudo apt-get purge 后面跟上两类文件,一类是“linux-headers”,另一类是“linux-image”,这两者是成对的。当前使用的内核不能删除。
    4. 清理deinstall (这是一条组合命令,先得到标识为deinstall的名称,再purge。)

    dpkg --purge `dpkg --get-selections | grep deinstall | cut -f 1`

    5. 更新grub

    sudo update-grub

  5. 用户A编辑文件file.txt,这时,用户B向file.txt追加输入字符,能够成功输入。不过,具体顺序,有待探究。
  6. 安装最新版的NVIDIA驱动
  7. 修改默认启动的内核
    sudo vim /etc/default/grub
    #GRUB_DEFAULT="Advanced options for Ubuntu>Ubuntu, with Linux 4.10.0-041000-generic"
    sudo update-grub
  8. foobar

How to Write a Peer Review for an Academic Journal: Six Steps from Start to Finish by Tanya Golash-Boza

PhD2Pub­lished has sev­er­al infor­ma­tive posts about writ­ing jour­nal arti­cles, and more recent­ly has fea­tured a post out­lin­ing a poten­tial­ly rev­o­lu­tion­ary col­lab­o­ra­tive peer review process for this kind of pub­lish­ing. Todays post offers an alter­na­tive per­spec­tive; that of the jour­nal arti­cle peer review­er. Doing peer reviews pro­vides impor­tant expe­ri­ence for those writ­ing their own papers and may help writ­ers con­sid­er what they should include based on what peer review­ers are look­ing for.

At some point in your schol­ar­ly career, you like­ly will get asked to review an arti­cle for a jour­nal. In this post, I explain how I usu­al­ly go about doing a peer review. I imag­ine that each schol­ar has their own way of doing this, but it might be help­ful to talk open­ly about this task, which we gen­er­al­ly com­plete in iso­la­tion.

Step One:  Accept the invi­ta­tion to peer review. The first step in review­ing a jour­nal arti­cle is to accept the invi­ta­tion. When decid­ing whether or not to accept, take into con­sid­er­a­tion three things: 1) Do you have time to do the review by the dead­line? 2) Is the arti­cle with­in your area of exper­tise? 3) Are you sure you will com­plete the review by the dead­line? Once you accept the invi­ta­tion, set aside some time in your sched­ule to read the arti­cle and write the review.

Step Two: Read the arti­cle. I usu­al­ly read the arti­cle with a pen in hand so that I can write my thoughts in the mar­gins as I read. As I read, I under­line parts of the arti­cle that seem impor­tant, write down any ques­tions I have, and cor­rect any mis­takes I notice.

Step Three: Write a brief sum­ma­ry of the arti­cle and its con­tri­bu­tion. When I am doing a peer review, I some­times do it all in one sit­ting – which will take me about two hours – or I read it one day and write it the next. Often, I prefer to do the lat­ter to give myself some time to think about the arti­cle and to process my thoughts. When writ­ing a draft of the review, the first thing I do is sum­ma­rize the arti­cle as best I can in three to four sen­tences. If I think favor­ably of the arti­cle and believe it should be pub­lished, I often will write a longer sum­ma­ry, and high­light the strengths of the arti­cle. Remem­ber that even if you don’t have any (or very many) crit­i­cisms, you still need to write a review. Your cri­tique and acco­lades may help con­vince the edi­tor of the impor­tance of the arti­cle. As you write up this sum­ma­ry, take into con­sid­er­a­tion the suit­abil­i­ty of the arti­cle for the jour­nal. If you are review­ing for the top jour­nal in your field, for exam­ple, an arti­cle sim­ply being fac­tu­al­ly cor­rect and hav­ing a sound analy­sis is not enough for it to be pub­lished in that jour­nal. Instead, it would need to change the way we think about some aspect of your field.

Step Four: Write out your major crit­i­cisms of the arti­cle. When doing a peer review, I usu­al­ly begin with the larg­er issues and end with minu­ti­ae. Here are some major areas of crit­i­cism to con­sid­er:

–          Is the arti­cle well-orga­nized?

–          Does the arti­cle con­tain all of the com­po­nents you would expect (Intro­duc­tion, Meth­ods, The­o­ry, Analy­sis, etc)?

–          Are the sec­tions well-devel­oped?

–          Does the author do a good job of syn­the­siz­ing the lit­er­a­ture?

–          Does the author answer the ques­tions he/she sets out to answer?

–          Is the method­ol­o­gy clear­ly explained?

–          Does the the­o­ry con­nect to the data?

–          Is the arti­cle well-writ­ten and easy to under­stand?

–          Are you con­vinced by the author’s results? Why or why not?

Step Five: Write out any minor crit­i­cisms of the arti­cle.  Once you have laid out the pros and cons of the arti­cle, it is per­fect­ly accept­able (and often wel­come) for you to point out that the table on page 3 is mis­la­beled, that the author wrote “com­pli­ment” instead of “com­ple­ment” on page 7, or oth­er minu­ti­ae. Cor­rect­ing those minor errors will make the author’s paper look more pro­fes­sion­al if it goes out for anoth­er peer review, and cer­tain­ly will have to be cor­rect­ed before being accept­ed for pub­li­ca­tion.

Step Six: Review. Go over your review and make sure that it makes sense and that you are com­mu­ni­cat­ing your cri­tiques and sug­ges­tions in as help­ful a way as pos­si­ble.

Final­ly, I will say that, when writ­ing a review, be mind­ful that you are cri­tiquing the arti­cle in ques­tion – not the author. Thus, make sure your cri­tiques are con­struc­tive. For exam­ple, it is not appro­pri­ate to write: “The author clear­ly has not read any Fou­cault.” Instead, say: “The analy­sis of Fou­cault is not as devel­oped as I would expect to see in an aca­d­e­mic jour­nal arti­cle.” Also, be care­ful not to write: “The author is a poor writer.” Instead, you can say: “This arti­cle would ben­e­fit from a close edit­ing. I found it dif­fi­cult to fol­low the author’s argu­ment due to the many styl­is­tic and gram­mat­i­cal errors.” Although you are an anony­mous review­er, the Edi­tor knows who you are, and it nev­er looks good when you make per­son­al attacks on oth­ers. So, in addi­tion to being nice, it is in your best inter­est.

RNA-seq — wikipedia

RNA-seq (RNA sequenc­ing), also called whole tran­scrip­tome shot­gun sequencing(WTSS), uses next-gen­er­a­tion sequenc­ing (NGS) to reveal the pres­ence and quan­ti­ty of RNA in a bio­log­i­cal sam­ple at a given moment in time.

RNA-Seq is used to ana­lyze the con­tin­u­al­ly chang­ing cel­lu­lar tran­scrip­tome. Specif­i­cal­ly, RNA-Seq facil­i­tates the abil­i­ty to look at alter­na­tive gene spliced tran­scripts, post-tran­scrip­tion­al mod­i­fi­ca­tions, gene fusion, mutations/SNPs and changes in gene expres­sion. In addi­tion to mRNA tran­scripts, RNA-Seq can look at dif­fer­ent pop­u­la­tions of RNA to include total RNA, small RNA, such as miR­NA, tRNA, and ribo­so­mal pro­fil­ing. RNA-Seq can also be used to deter­mine exon/intron bound­aries and ver­i­fy or amend pre­vi­ous­ly anno­tat­ed 5’ and 3’ gene bound­aries.

Pri­or to RNA-Seq, gene expres­sion stud­ies were done with hybridiza­tion-based microar­rays. Issues with microar­rays include cross-hybridiza­tion arti­facts, poor quan­tifi­ca­tion of low­ly and high­ly expressed genes, and the knowl­edge of the sequence. Because of the­se tech­ni­cal issues, tran­scrip­tomics tran­si­tioned to sequenc­ing-based meth­ods. The­se pro­gressed from Sanger sequenc­ing of Expressed Sequence Tag libraries, to chem­i­cal tag-based meth­ods (e.g., seri­al analy­sis of gene expres­sion), and final­ly to the cur­rent tech­nol­o­gy, NGS of cDNA (notably RNA-Seq).

Molecular Evolution: A Statistical Approach

Ziheng Yang’s new book, “Mol­e­c­u­lar Evo­lu­tion: A Sta­tis­ti­cal Approach” is on sale at Ama­zon. The cov­er pho­to, a west­ern fence lizard (Scelo­porus occi­den­tal­is), was tak­en by Charles Linkem dur­ing our col­lect­ing trip to Ore­gon last sum­mer. Some peo­ple think that the lizard is beau­ti­ful, while oth­ers (Ziheng includ­ed) think that it looks ter­ri­fy­ing. The book cov­ers the sta­tis­ti­cal and com­pu­ta­tion­al foun­da­tions of mol­e­c­u­lar evo­lu­tion, phy­lo­ge­net­ics and phy­lo­geog­ra­phy. It pro­vides expla­na­tions and exam­ples using real data analy­sis. The data and com­put­er pro­grams are avail­able on the web, and course mate­ri­als are pro­vid­ed at the end of each chap­ter. This will make it easy to use the book for teach­ing, per­haps in a grad­u­ate sem­i­nar course.





第一部分:数据科学中的数学基础 35小时
第1课 基本概念、函数
第2课 序列极限
第3课 函数极限与连续函数
第4课 导数与微分
第5课 微分中值定理
第6课 泰勒公式
第7课 积分
第8课 多元函数微分学(上)
第9课 多元函数微分学(下)
第10课 线性方程组和行列式
第11课 矩阵运算
第12课 矩阵的相似与合同
第13课 矩阵分解
第14课 最优化问题
第15课 使用导数的最优化方法
第16课 对偶理论
第17课 二次规划

第二部分:数据科学中的概率论 28小时
随机变量及其分布,离散型随机变量,连续型随机变量, 随机变量的联合分布和边际分布, 随机变量的条件分布, 随机变量的独立性,随机变量的函数及其分布,共轭分布,次序统计量
期望与方差,协方差与相关系数,条件期望及预测, 熵与不确定性,特征函数

第三部分:数据科学中的统计基础 26小时



















Ensemble and Entrez


The Ensem­bl project was start­ed in 1999, some years before the draft human genome was com­plet­ed. Even at that ear­ly stage it was clear that man­u­al anno­ta­tion of 3 bil­lion base pairs of sequence would not be able to offer researchers time­ly access to the lat­est data. The goal of Ensem­bl was there­fore to auto­mat­i­cal­ly anno­tate the genome, inte­grate this anno­ta­tion with oth­er avail­able bio­log­i­cal data and make all this pub­licly avail­able via the web.


Sin­gle search engine of NCBI. Entrez is not a gene data­base. It’s the name of the NCBI infra­struc­ture which pro­vides access to all of the NCBI data­bas­es. One of those is the Gene data­base, so you would say “Entrez Gene”.

there is not nec­es­sar­i­ly an one-to-one map­ping between Entrez Gene and Ensem­bl Gene IDs.


ubuntu software

  1. Fcitx: a input method framework with extension support, which provides an interface for entering characters of different scripts in applications using a variety of mapping systems.
    sudo apt-get install fcitx-table-wbpy
  2. baobab,synaptic: Disk Usage Analyzer
    sudo apt-get install baobab synaptic
  3. upgrade ubuntu:
    sudo update - manager -c -d
  4. Install Oracle Java:
  5. wine1.8
    sudo add-apt-repository ppa:ubuntu-wine/ppa
    sudo apt-get update
    sudo apt-get install wine1.8
  6. 做图工具:Kolourpaint
    sudo apt-get install kolourpaint4
  7. Process Viewer:Htop
    an interactive process viewer for Unix systems.

    sudo apt-get install htop
  8. Indicator-SysMonitor
    sudo add-apt-repository ppa:fossfreedom/indicator-sysmonitor
    sudo apt-get update
    sudo apt-get install indicator-sysmonitor
  9. Move launcher to bottom
    gsettings set com.canonical.Unity.Launcher launcher-position Bottom
  10. foobar

DAVID new version: 6.8

DAVID 6.8 (cur­rent beta release) May. 2016

– The DAVID Knowl­edge­base com­plete­ly rebuilt
— Entrez Gene inte­grat­ed as the cen­tral iden­ti­fier to allow for more time­ly updates
while still incor­po­rat­ing Ensem­bl and Uniprot as inte­gral data sources
— New GO cat­e­go­ry (GO Direct) pro­vides GO map­pings direct­ly anno­tat­ed by the source data­base (no par­ent terms includ­ed)
— New anno­ta­tion cat­e­gories
— New list iden­ti­fier sys­tems added for list upload­ing and con­ver­sion
— A few bugs fixed