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,
