Download and install Google Extension .crx file

  1. http://yurl.sinaapp.com/crx.php
  2. input 32-bit extension ID; for example:
    If we want to download this extension “https://chrome.google.com/webstore/detail/proxy-switchyomega/padekgcemlokbadohgkifijomclgjgif”, 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 (http://string-db.org) 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

System-wide:/usr/share/applications

user-only:/.local/share/applications

[Desktop Entry]
Version=1.0
Name=TopCoder Arena
Exec=javaws /path_to_thefile/ContestAppletProd.jnlp
Terminal=false
Icon=/pathtothefile/Topcoder_arena.png
Type=Application
Categories=Development

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
    link:http://www.oracle.com/technetwork/java/javase/downloads/index.html
  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):

    JAVA_HOME=/usr/local/oracle-java/jdk1.8.0_91
    PATH=$PATH:$JAVA_HOME/bin
    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!

linux常用权限

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:

750,755

能不能不可读但可写?

Ubuntu 常见问题

  1. txt乱码(windows下生成的文本在linux下打开)
    使用iconv解决。
    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
    使用dos2unix解决
    The Dos2unix package includes utilities “dos2unix” and “unix2dos” to
    convert plain text files in DOS or Mac format to Unix format and vice
    versa.
    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

    AVAHI_DAEMON_DETECT_LOCAL=0

  4. /boot空间不足:
    /boot是放置内核的地方,这时候就该删除多余的内核了。具体流程为:
    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
    20170312,尝试安装NVIDIA-Linux-x86_64-375.39.run,但是失败了,在网上发现,20170228时,有人也反映了这个问题。Ubuntu安装最新版的NVIDIA会有些问题,因为,Ubuntu跟Nvidia是两个机构,Ubuntu无法得到NVIDIA的源码,只能通过修改和调试让ubuntu兼容nvidia驱动,或者让用户使用ubuntu社区自己开发的驱动。在软件管理中心那里,有367.57版本的NVIDIA。
  7. 修改默认启动的内核
    sudo vim /etc/default/grub
    
    GRUB_DEFAULT=0
    #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.

from: faculty.washington.edu/leache/wordpress/2014/04/molecular-evolution-a-statistical-approach/

 

数学概率统计

课程大纲

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
集合、等势、确界、函数、映射、实数集、函数、函数的性质、初等函数
第2课 序列极限
序列极限的定义、ε-N语言、无穷小量、无穷大量、夹逼定理、极限性质、Stolz公式、重要极限
第3课 函数极限与连续函数
函数极限的定义、性质、序列极限和函数极限关系、极限存在定理、重要极限、连续函数的性质、闭区间上得连续函数
第4课 导数与微分
导数、求导数的方法、微分、高阶导数与高阶微分
第5课 微分中值定理
微分中值定理、洛必达法则
第6课 泰勒公式
泰勒展开、泰勒公式的余项、函数凹凸性、导数的应用
第7课 积分
不定积分、定积分、变上限定积分、微积分基本定理、换元与分部积分法、可积函数类、定积分的应用、广义积分
第8课 多元函数微分学(上)
多元函数概念、多元函数极限、偏导数、全微分、复合函数和隐函数的微分、方向导数、梯度
第9课 多元函数微分学(下)
多元函数微分中值定理及泰勒公式、隐函数存在定理
第10课 线性方程组和行列式
高斯约当算法、行列式的定义、行列式展开、向量空间、线性相关与线性无关、向量组的秩、矩阵的秩、线性方程组解集结构
第11课 矩阵运算
矩阵运算、矩阵乘积、可逆矩阵、分块矩阵、正交矩阵
第12课 矩阵的相似与合同
矩阵相似、特征值、特征向量、实对称矩阵的对角化、二次型、正定二次型与正定矩阵
第13课 矩阵分解
LU分解,Cholesky分解、QR分解、SVD分解
第14课 最优化问题
范数、凸函数、凸集、广义逆、秩一校正、共轭函数、线搜索
第15课 使用导数的最优化方法
最速下降法、牛顿法、共轭梯度法、拟牛顿法
第16课 对偶理论
KKT条件、线性规划、凸规划、拉格朗日乘子
第17课 二次规划

第二部分:数据科学中的概率论 28小时
第1课:事件与概率
概率导论,事件及其运算,古典概型与几何概型,主要介绍概率论发展历史上主要研究的两种概率模型和概率论公理化体系
第2课:条件概率与统计独立性
条件概率,贝叶斯公式,统计独立性
第3课:随机变量与分布函数
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
第4课:数字特征与特征函数
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5课:极限定理
极限定理基础,大数定律,中心极限定律
第6课:随机过程
随机过程基础,马尔可夫链,高斯过程
第7课:统计模拟
统计模拟基础,统计模拟应用,MCMC

第三部分:数据科学中的统计基础 26小时
第1课:数理统计学的基本知识
第2课:估计
参数估计的方法(最大似然,矩估计),估计的优良性标准(最小方差无偏估计),置信区间,分布函数与密度函数的估计
第3课:假设检验
问题描述,似然比检验,单参数情形的假设检验,广义似然比检验,p值,拟合优度检验,非参检验
第4课:抽样调查的意义与作用(主要应用)
第5课:抽样调查的基本概念
总体与样本,几种基本的抽样方法,简单随机抽样(详细),分层抽样,整群抽样,二阶与多阶抽样,系统抽样,不等概率抽样,误差与精度的表示方法
第6课:试验设计简介
试验设计问题的提法与数学模型,正交表与正交设计
第7课:多元统计分析的意义与作用
第8课:多元正态分布及参数的估计
随机向量,多元正态分布的定义与基本性质,条件分布和独立性,随机阵的正态分布,多元正态分布的参数估计
第9课:多元正态总体参数的假设检验
几个重要统计量的分布,单总体均值向量的检验及置信域,多总体均值向量的检验,协方差阵的检验,独立性检验,正态性检验
第10课:判别分析(与支持向量机的联系)
距离判别,Bayes判别法及广义平方距离判别法,Fisher判别,判别效果的检验及各变量判别能力的检验,逐步判别
第11课:聚类分析
聚类分析的方法,距离与相似系数,系统聚类法,系统聚类法的性质及类的确定
第12课:主成分分析
总体的主成分,样本的主成分,主成分分析的应用
第13课:因子分析
因子模型,参数估计方法,方差最大的正交旋转,因子得分
第14课:简单线性回归
建立简单回归模型,最小二乘估计,估计sigma2,最小二乘估计的性质,模型的比较:方差分析,测定系数,R2,置信区间和检验,残差
第15课:多元回归
在简单回归模型上增加一个自变量,回归的矩阵表示,方差分析,附加变量图,通过原点的回归
第16课:结果分析
解释参数估计值,抽样在回归中的作用,含测量误差的自变量
第17课:诊断一:残差及影响
第18课:诊断二:症状与治疗
散点图,非常数方差,非线性,变换响应变量,变换自变量,正态性假设
第19课:建立模型一:定义新的自变量
多项式回归,虚拟变量:二分类/多分类,比较回归直线,变量的尺度,线性变换及主成分
第20课:建立模型二:共线性与变量选择
什么是共线性,为什么共线性是一个问题,共线性的度量,变量选择,假设和记号,根据实际意义选择子集,求子集:逐步回归,选择一个子集的准则,求子集:所有可能的回归,求子集:LASSO;求子集:LARS
第21课:非最小二乘估计
ridge,主成分回归,偏最小二乘回归
第22课:线性回归的推广
广义线性模型(logistic、poisson),非线性回归,统计决策与bayes统计,统计决策问题概述,什么是bayes统计(著名的三羊问题),共轭分布
第24课:马氏模型
基本概念,隐马氏模型,隐马氏模型理论,隐马氏模型应用

FreeCell

1~999999

916343,

1000000~1999999

 

2000000

2416098

3000000

3963289

4000000~4999999

4562572

5000000~5999999

 

6000000~6999999

6523718

……

8000000~8999999

8283851

Ensemble and Entrez

Ensemble

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.

Entrez

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.

他们之间ID的互相转换可以通过蛋白质序列或者核苷酸序列的比对来实现,但是这种比对得到的结果可能不唯一,因为,相似度很高的比对结果可能有多个。

https://www.biostars.org/p/16505/

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:
    http://www.oracle.com/technetwork/java/javase/downloads/index.html
  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