Oxford Nanopore Technology – MinION

MinION is a portable device for molecular analyses that is driven by nanopore technology. It is adaptable for the analysis of DNA, RNA, proteins or small molecules with a straightforward workflow.

MinION

Scalability

The MinION can be run for minutes or days according to the experimental need. Users can adjust settings like the speed that the DNA passes through the nanopore. PromethION, which will soon be released into early access, is designed to be fully scalable so that users can operate between one or 48 flow cells at any one time.

Long read lengths

The Oxford Nanopore system processes the reads that are presented to it rather than generating specific read lengths. The longest read reported by a MinION user to date is more than 200Kb, but it can process the spectrum of read lengths.

身边的算法

  1. windows自带纸牌游戏(NP难)
    对于如何生成一副可被完成的组合,这是一个NP难问题;电脑每次随机生成一副牌,不保证一定有解。所以有时候,纸牌游戏无论如何都完成不了时,可能是这次真的完成不了,而不是你自己的问题。不过,判定到底是你的问题还是电脑的问题仍然是NP难的问题。可以编写一个程序,来算:当我们觉得已经无法前进时,出现了的所有牌,是否存在一种新的组合会使得出现新的翻牌希望。

Keywords of Genomics

Population genetics

Population genetics is the study of the distribution and change in frequency of alleles within populations, and as such it sits firmly within the field of evolutionary biology.

The main processes of evolution are natural selection, genetic drift, gene flow, mutation, and genetic recombination and they form an integral part of the theory that underpins population genetics.

Studies in this branch of biology examine such phenomena as adaptation, speciation, population subdivision, and population structure.

Population stratification

Population stratification refers to differences in allele frequencies between cases and controls due to systematic differences in ancestry rather than association of genes with disease.

It would be caused by systematic differences in the ancestry of cases and controls.

Diploid genome

Diploid genome refers to a genome that contains a balanced set of chromosomes derived equally from maternal and paternal sources.

Coalescent theory

Coalescent theory is a retrospective stochastic model of population genetics that relates genetic diversity in a sample to demographic history of the population from which it was taken.

That is, it is a model of the effect of genetic drift, viewed backwards in time, on the genealogy of antecedents.

GitHub

Repository

A repository is usually used to organize a single project. Repositories can contain folders and files, images, videos, spreadsheets, and data sets – anything your project needs. We recommend including a README, or a file with information about your project. GitHub makes it easy to add one at the same time you create your new repository. It also offers other common options such as a license file.

Branch

Branching is the way to work on different versions of a repository at one time.

By default your repository has one branch named master which is considered to be the definitive branch. We use branches to experiment and make edits before committing them to master.

Commit

On GitHub, saved changes are called commits.

Pull Request

When you open a pull request, you’re proposing your changes and requesting that someone review and pull in your contribution and merge them into their branch. Pull requests show diffs, or differences, of the content from both branches. The changes, additions, and subtractions are shown in green and red.

GitHub Pages

Nottwya

GitHub Pages are public webpages hosted and published through our site.

You can create and publish GitHub Pages online using the Automatic Page Generator. If you prefer to work locally, you can use the GitHub Desktop or the command line.

Pages are served over HTTP, not HTTPS, so you shouldn’t use them for sensitive transactions, like sending passwords or credit card numbers.

如何读文章?

  1. 读摘要
    通过摘要,我们能快速知道,这篇文章的主题、研究对象和实验结论等,这些能够帮助我们最终确定这篇文章是否含有我们需要的信息;
  2. 读图
    通过读图,我们能够迅速知道这篇文章比较凝练的信息,从而快速切入这篇文章的核心结论;此外,图片方便理解,通过图片能够帮助我们对文章建立初步认识;
  3. 选读
    在进行了上面两步以后,选定自己感兴趣的部分进行深入阅读。

J.Q. Liu

  1. Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions (2015)
    1. genome variation of wild and domestic yaks
    2. evolution
  2. Genome resequencing: 13 wild yaks and 59 domestic yaks

windows install and configure

如果是让电脑维修店的人重装系统,要注意找一家好一点的维修店。因为,重装系统看似一样,其实,每个店使用的安装镜像以及一些细节的配置是有出入的。去一家很差的店,重装的系统,会给自己后期的配置带来极大的困难。

  1. 操作系统重装
    win7
  2. 硬件驱动重装
    1.显卡驱动
  3. 软件重装
    1. DirectX
  4. 运行库
  5. 编程语言编译工具
    1. Java
    2. MinGW
    3. Strawberry Perl
  6. 小工具
    1. daemon tool lites
    2. pchunter
    3. xming+putty
  7. 123

NCBI 使用注意事项及技巧

  1. 关于序列标识join和complement:
    join:表示序列是模板链上的5′->3’;
    complement:表示序列是编码链上的5′->3’;
    example:
    join:
    现在(2016.4.5),似乎没有再标识join了。
    complement:
    我看到的素有gene类别下的序列都是给的complement。

    gene complement(2872..3195)
    /gene=” lacZ’ ”
    Sequence:NC_000913.3 (363231..366305, complement)

  2. 在指定的基因组检索目的序列:打开基因组,然后输入目的序列,开始检索。
  3. 对于蛋白质,NCBI提供了查看其CD(conserved domain),名字叫“Identify Conserved Domains”;

WordPress build & tips

  1. 连接数据库
    1. 在空间提供商处找到数据库的IP;
    2. 在网站根目录下找到WP的wp-config.php文件;
    3. 将DB_HOST的值,改为数据库的IP
  2. 备份
    1. 使用WP自带的工具中的导出工具,导出能被WP模板普遍识别的网站内容,方便在网站出现意外时,在任何一个新的WP木板上导入网站所有内容(不含图片)。
    2. 使用空间提供商的数据下载,直接下载整个网站,如若网站出现问题,直接从新上传整个WP;
  3. 防垃圾评论
    1. WP自身会要求管理者审核每一条评论;
    2. 使用Akismet,以后会自动过滤同一个邮箱的评论;
  4. 托管在国内的虚拟主机后,加载缓慢:
    原因:使用了google的fonts和ajax库
    解决方案:安装两个插件:Disable Google Fonts,WP Acceleration for China
  5. wordpress图片使用中文名称,会加载不出来,尽量使用英文名称
  6. wordpress整站迁移:需要修改配置文件。
  7. shift+enter: 回车以后的间距不会那么大
  8. 如果网站的域名改变了,要记得修改数据库的_options中的网站域名

Windows10 debug & optimize

 

五分法-如何读书或者文章

从Podcast-清华大学广播台-珊越拾穗-读书小贴士里听到的,觉得很有用。特此记录下来,不断加深巩固理解。

如何读书

  1. 历史化(historicize)
    了解这个书或者文章产生的背景。
  2. 对话式(dialogue)
    看一本书时,要有一个跟这本书相反意见的或者跟他相似意见的书,同时去看。看别的作家怎么讨论这个问题。然后就会发现作家的风格不同,读起来感觉不同。另外是读者跟作者的对话。
  3. 智性化(intellectualize)
    从读书过程中找到、发展自己的观点。
  4. 转化(transformative)
    通过阅读,有自己的发现和创新。

读文章

  1. 找到作者想要回答的问题
    作者通过写这本书,这篇文献,想要解决什么问题。
  2. 他有表述哪些竞争性的理论
    一个研究不可能是开天辟地,头一个的研究。这个问题肯定之前有被研究过,或者其他理论可以解释这个问题。在作者的作品中,他使用了哪些人的理论来解释这个问题,他是怎么解释的,这些理论在解释这个问题中是否有什么不足。
  3. 作者提出了他自己的什么观点
    除了前人的理论,他自己对这个问题的解读。
  4. 他用了什么东西,什么样的步骤,什么数据证明自己
    他是怎么证明自己的观点的。
  5. 他的长处和不足
    讨论他的文章的长处和不足。

写文章

  1. 我要解答什么问题;
  2. 别人是怎么解答这个问题的;
  3. 我和别人有什么不一样;
  4. 我怎么证明这个不一样是站得住脚的;
  5. 那我有什么不足或者我有什么新的发现或者我有什么优点。

特此向主播的导师,总结出这个方法的人,致以我的敬意。