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Applied Bioinformatics from PennState 适合初学者

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发表于 2016-9-1 14:59:26 | 显示全部楼层 |阅读模式
本帖最后由 happylittlepig 于 2016-9-1 17:09 编辑

主要内容:Linux操作的基本命令;生物信息的基本概念及常用的数据格式介绍;常用软件的安装及使用;最后有具体的RNA-seq数据处理例子(可以学习里面的shell脚本和项目工作目录安排)。
该教程讲的内容挺全面,适合生信初学者入门学习,极力推荐。推荐指数5星。

BMMB 852:Applied Bioinformatics (Fall, 2016)Lecture Notes
Lectureswill appear below as they are presented. Homework are specified in eachhandout.
Lecture 1
Courseinformation, homework and project information, introduction to computing,setting up you computer, basic unix command line usage, organizing yourprojects. Homework 1.
· Otherrelevant blog posts on Designingprojects and research workflow based on github.
· Biostarquote of the day from VeryBad Things:
I've been doing bioinformatics for about 10years now. I used to joke with a friend of mine that most of our work wasconverting between file formats. We don't joke about that anymore.
Lecture 2
Dataformats, data analysis concepts, basic Unix commands: wc, grep, cut, sort,redirecting input and output streams, piping commands, processing a tabularfile with UNIX tools. Homework 2.
· Datasetfor this lecture, the latest yeast genome feature file: SGD_features.tab and its corresponding README obtained from the SGDCurated Data page
· Possiblyuseful: unix flags explained: Explain Shell
· Suggestedreading: Unixfor Biologists
"Invent a new, weakly defined,internally redundant, ambiguous, bulky fruit salad of a data format.Again."*
Lecture 3
Whatdo words mean? Sequence Ontology and Gene Ontology, Gene Set Enrichment,homework 3.
· Abrowser for Gene Ontology terms and annotations: Quick GO see also QuickGO:a user tutorial for the web-based Gene Ontology browser
· Ourcurrent favorites: standalone: ErmineJ and web based: AgriGO - GO Analysis Toolkit and Database forAgricultural Community
· Notreally science but amusing: categorizing the world is a daunting task see: Celestial Emporium of Benevolent Knowledge
"I'm new to GO terms. In the beginningit was fun, as long as I stuck to one algorithm. But then I found that thereare many out there, each with its own advantages and caveats (the quality ofgraphic representation, for instance). [...] As a biologist, what should Itrust? Deciding on this or that algorithm may change the wholestory/article!"
Lecture 4
Accessingdata from scientific publications, the GenBank format, automated download ofdata from NCBI, installing and using Entrez Direct. Homework 4.
.


BioinformaticsConsulting Center at Penn State
I serve as the director of the BioinformaticsConsulting Center (BCC) at Penn State. Our center offers bioinformatics dataanalysis services that cover multiple application domains of high throughputsequencing. Services range from routine data manipulation steps to developingnovel, domain specific methodologies. Our center is also in charge ofdistributing and managing the sequencing data produced by the Penn StateGenomics Core Sequencing Facilities.
                                                                                                                                                                                         ---------- Dr. IstvánAlbert






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发表于 2016-9-8 17:33:35 | 显示全部楼层
从哪里上这个课啊?
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 楼主| 发表于 2016-9-12 14:12:43 | 显示全部楼层
深藏功与名 发表于 2016-9-8 17:33
从哪里上这个课啊?

直接点进去下载就好了
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发表于 2016-9-27 00:05:23 | 显示全部楼层
请问这个需要翻墙吗? 第一个链接打不开啊
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发表于 2016-10-4 22:09:20 | 显示全部楼层
视频资料在哪里下载啊?
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发表于 2017-2-7 13:20:42 | 显示全部楼层
你好,这个我进去了只看到要收费的电子档资料。找到了一个链接
http://www.personal.psu.edu/iua1/courses/2014-BMMB-852.html
但是没有找到相关的视频资料。请问一下,这个课程有视频资料吗?
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