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생물학 연구를 위한 컴퓨터 사용기술 제 6강

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Computational Skill for Modern Biology Research

Computational Skill for Modern Biology Research Department of BiologyChungbuk National University6th Lecture 2015.10.13Ipython Notebook, Pandas, Matplotlib

Syllabus1Introduction : Why we need to learn this stuff?2Basic of Unix and running BLAST in your PC3Unix Command Prompt II and shell scripts4Basic of programming (Python programming)5Python Scripting II and sequence manipulations6Ipython Notebook and Pandas7Tutorial and Basic of Next Generation Sequencings8Next Generation Sequencing 910Next Generation Sequencing Analysis 11R and statistical analysis12Bioconductor I13Bioconductor II14Network analysis

Python scripting and research..BioinformaticSoftwareExtract InformationsUsing scripts..RepeatsDuring multistep analysis, several scripts and resulting files is generated..

Data

ExtractedDataBioinformatic analysis is multistep processUsing python scripts, we can analysis various dataset..

Results

Python Scripts(Sometime we need to modify scripts slightly)

Original dataVarious output

Sometime it may be difficult to tracks what I did before

Notebook in Experimental Research

1. Protocols..

2. Experimental Procedures..

3. Resulting Data..

4. Analysis.......

Should be summarized in the notebook.How about computational experiments?

iPython Notebook (Jupyter)Electronic Notebook for Python scripts and results

Run in web browser

Like in Python Interpreter, You can test small code snippet and see the results

6

Long script can be executed

Results are stored in the same file with scripts

Documentations along with results and scripts

Documentations

codeData & Results

You can distribute iPython Notebook and share code and results simultaneously

You can send .ipynb file with colleagues

And share them!

You can even publish notebook in webs

Installing iPython Notebook and Other PackagesYou can install iPython in your current PythonBut It is more convenient to install all of them as single installs

http://www.continuum.io/downloadsPython + iPython Notebook + many scientific packages

OrAnd Install them!You can install in Windows

Anaconda PythonIf installation is done correctly,

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