1.Setup
工欲善其事,必先利其器

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Learn how to do our jobs efficiently and reproducibly.

0) Get an OS

  • 由于历史原因,就生物信息数据分析而言,linux操作系统的软件生态比windows好得多,有很多生物信息的工具只支持linux系统。所以熟悉linux操作系统的使用对于学习生物信息是很有必要的。
  • 除了需要linux环境,在我们的学习中还会遇到各种软件的依赖。鉴于在自己的笔记本上使用linux环境的同学不多,为了给大家提供linux的操作环境,并且节约一些软件安装的时间,我们提供了两种解决方案:
1.1 Working on Docker
1.2 Working on Cluster

1) Learn an editor

  • linux有一些桌面版是带有图形界面的,我们可以像在window和mac上一样使用类似记事本的工具进行文本编辑。然而并不是所有的linux发行版都有图形界面,所以了解在各种linux环境下都适用的终端文本编辑工具是有必要的。我们这里主要介绍两种,VimAtom

A. Vim

You can start from a simple version of Vim, like MacVim.
Then, you can learn vim progressively, and it will be your last text editor. There isn’t any better text editor that I know of. It is hard to learn, but incredible to use.I suggest you teach yourself Vim in 4 steps:
  1. 1.
    Survive
  2. 2.
    Feel comfortable
  3. 3.
    Feel Better, Stronger, Faster
  4. 4.
    Use superpowers of vim

B. Atom

A hackable text editor for the 21st century. See how to use Atom.

2) README

Always document your project. We suggest always having a README.md file in your project DIR.

3) Backup your data regularly

It's necessary to backup data regularly.
  • Here is a tutorial for data backup methods and tips: How to backup

4) Homework

  • Install and use docker
  • Learn and use an editor like Vim

5) Teaching Videos (link)

  • Part I: 1.1 How to use Docker
  • (Advanced) Part I: 1.2 How to use cluster - submit jobs to the queue