Month: June 2016

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.

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

1. wine QQ
   安装后无法输入用户名；
   通过二维码扫码进入后，无法发出消息；
   后台程序混乱；
   结语：还是用WebQQ。
2. 1
3. 1

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

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!

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

Often used:

750,755

能不能不可读但可写？

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

   1 2 3 4 5 6

   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

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).

1. Biostars https://www.biostars.org/

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/

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

   1	sudo apt-get install fcitx-table-wbpy

2. baobab,synaptic: Disk Usage Analyzer
   
   sudo apt-get install baobab synaptic

   1	sudo apt-get install baobab synaptic

3. upgrade ubuntu:
   
   sudo update - manager -c -d

   1	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

   1 2 3

   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

   1	sudo apt-get install kolourpaint4

7. Process Viewer：Htop
   an interactive process viewer for Unix systems.
   
   sudo apt-get install htop

   1	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

   1 2 3

   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

   1	gsettings set com.canonical.Unity.Launcher launcher-position Bottom

10. foobar

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