tips：safari浏览器切换快捷键 cmd+shift+左/右，ctrl+shift+tab向左切换页面；ctrl+tab向右切换页面。边看教材边google必备。

tips2：随手查到的一篇小心得，希望也能记录自己的学习过程。https://mp.weixin.qq.com/s/RhbRwsWDflpNMga1D0R2kw?

               1  Introduction

    The Biostar Handbook introduces readers to bioinformatics, the scientific discipline at the intersection of biology, computer science, and statistical data analytics that is dedicated to the digital processing of genomic information.

    The Handbook has been developed, improved and refined over more than a half decade in a research university setting and is used in an accredited PhD level training program. The contents of this book have provided the analytical foundation to hundreds of students, many of whom have become full time bioinformaticians and work at the most innovative companies in the world.

1.1.1 How is this book different?

    这本书的编写采用了基于问题（problem-based）的方式，让读者学习起来更有效率。

1.1.2 What is the book based on?

    这本书是怎么来的呢？作者在大学教了很多年生信和编程相关的课程了，也是生信届“知乎”，著名问答网站 Biostars的创始人。基于这些经验，本书的写作对于初学者来说非常友好，能够帮助他们快速入门。

1.1.3 What is a Biostar?

什么是biostar，集三者之大成

1.2 How to use the handbook

1.2.1 what is currently covered in the book

本书主要内容：

1. Bioinformatics foundations 生信基础

        #Data formats and repositories.数据格式和存储

        #Sequence alignments.序列比对

        #Data visualization. 数据可视化

        #Unix command line usage. Unix命令行用法

2. Bioinformatics data analysis protocols 数据分析方法

        Genome variation and SNP calling.  

        RNA-seq and gene expression analysis 

        Genome Assembly (coming in 2017) 基因组组装

        Metagenomics (coming in 2017) 宏基因组

        ChIP-Seq analysis (coming in 2017) 

3. Software tool usage

        Using short read aligners    

        Using quality control tools

        Manipulating sequence data

1.2.2 Is there a theme to the book?

    The book explains most concepts through the task of analyzing the genomic data obtained from the 2014 Ebola virus outbreak in Africa. 采用的2014年埃博拉病毒的基因组数据。

1.2.3How long will it take me to learn bioinformatics from this book?

    约100小时，书籍配合网站课程资源（根据PSU的线下课程applied bioinformatics转化的在线课程）。

    本书的目标就是让那些充分投入本书的学习的学生在学习结束后，能够达到发表级别的数据分析能力。

1.3 What is bioinformatics

    DNA sequencing was initially valued for revealing the DNA content of a cell. It may come as a surprise to many, however, that the greatest promise for the future of bioinformatics might lie in other applications. In general, most bioinformatics problems fall under one of four categories:

        Assembly: establishing the nucleotide composition of genomes 组装

        Resequencing: identifying mutations and variations in genomes 重测序（对测序结果的解析）

        Classification: determining the species composition of a population of organisms 分类（分型）

        Quantification: using DNA sequencing to measure the functional characteristics of a cell 量化分析

    并非循规守矩的套用protocol和pipeline，创造力和对多学科知识的深刻理解亦为关键。

       https://www.nature.com/news/core-services-reward-bioinformaticians-1.17251

    No project was identical, and we were surprised at how common one-off requests（独一无二的要求） were. There were a few routine procedures that many people wanted, such as finding genes expressed in a disease. But 79% of techniques applied to fewer than 20% of the projects. In other words, most researchers came to the bioinformatics core seeking customized analysis（定制分析，个性化分析）, not a standardized package.