---
# System prepended metadata

title: Advanced Sequencing Technologies & Bioinformatics Analysis

---

# Advanced Sequencing Technologies & Bioinformatics Analysis

### Introductory Python and other useful skills
---

**Jason Williams, CSHL**
(e) williams@cshl.edu 
(t) @JasonWilliamsNY 

**Zoom** (for screensharing): [ link](https://cshl-dnalc.zoom.us/j/99181036435)


## Resources

### Data/knowledge management 

\* - FOSS [Data Management intro](https://cyverse-foss.readthedocs-hosted.com/en/latest/03_managing_data.html#)
- See also: https://cyverse.org/foss

- Markdown: [Cheatsheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet)
- ReadTheDocs/mk-docs: [Documentation](https://readthedocs.com/), [https://mkdocs.readthedocs.io/en/stable/](https://mkdocs.readthedocs.io/en/stable/)
- FairSharing: [FAIR sharing](https://fairsharing.org/)
    - [FAIR Principles paper](https://www.nature.com/articles/sdata201618)
- Data Stewardship: [Wizzard](https://ds-wizard.org/)
    - Example [DMPs](https://www.lib.ncsu.edu/do/data-management/elements-of-a-dmp)

### Reproducibility

- GitHub: [github.com](github.com/)
- Conda: [Conda](https://docs.conda.io/en/latest/)
- Bioconda: [Bioconda](https://bioconda.github.io/)
- Docker: [Docker](https://www.docker.com/)
    - Ten Simple Rules on [Dockerfiles](https://journals.plos.org/ploscompbiol/article/comments?id=10.1371/journal.pcbi.1008316)
- Biocontainers: [Biocontainers](https://biocontainers.pro/)
- Jupyter: [jupyter.org](https://jupyter.org/)
- Snakemake: [snakemake](https://snakemake.readthedocs.io/en/stable/)


### Software and coding skills 



- Software Carpentry: [SWC](https://software-carpentry.org/)
- Data Carpentry: [DC](https://datacarpentry.org/)
- Bioconductor: [bioconductor.org](http://bioconductor.org/)


### Computational resources

- CyVerse: [https://cyverse.org/](https://cyverse.org/)
- JetStream2: [https://jetstream-cloud.org/](https://jetstream-cloud.org/)
- Galaxy: [https://usegalaxy.org/](https://usegalaxy.org/)

### Community resources 

- Biostars: [https://www.biostars.org/](https://www.biostars.org/)
- StackOverflow: [https://stackoverflow.com/](https://stackoverflow.com/)
- Twitter Bioinformatics: [Bioinformatics Community](https://twitter.com/i/communities/1506791236987879425)
- LifeSciTrainers: [LifeSciTrainers.org](http://lifescitrainers.org)

---


## Notes 

### Objectives 

- Prepare you with the basic Python for later in this course 
- Understand basic data management skills and resources 
- Learn about learning resources and how to focus your future learning


### Plotting and Programming in Python 

- Software Carpentry [Plotting and Programming in Python](http://swcarpentry.github.io/python-novice-gapminder/)
- Google Colab [Colab](https://colab.research.google.com/)

- [New Google account instructions](https://support.google.com/accounts/answer/27441?hl=en)

### Jupyter Instructions 
(Thanks My!)

[Launch jupyter notebook on instance]

- Step 0: Connect to your instance via SSH:
`ssh -i [student-key].pem ubuntu@[public.ip.address]`

- Step 1:  Launch jupyter notebook app: Type in the command line:
`jupyter-lab`
(Note : dont type ‘jupyter notebook’. )
(this will generate a very long message in the terminal)Step 
- 2: Access Jupyter Notebook
There are 2 ways to do this:
    -  1 way: type in browser:
http://[your_instance_public_ip_address]:8888
eg. http://54.162.98.35:8888
then paste the token in or create a password
    - another way:  type in browser
http://[your_instance_public_ip_address]:8888/tree?token=[token]
Eg. http://54.162.98.35:8888/tree?token=xxx where xxx is in the token in the message generated while running ‘jupyter nbclassic’))You should then see the notebook interface.

To stop jupyter notebook, press Crtl + C (in the command line). (edited) 
PDF 


### Set up commands 

    
    #Get the dataset
    !wget http://swcarpentry.github.io/python-novice-gapminder/files/python-novice-gapminder-data.zip
    
    #Check the download 
    !ls
    

    #Unzip the dataset 
    !unzip python-novice-gapminder-data.zip
    
    

#### [Variables and assignment](print("fractional string to int:", int("3.4")))



#### [Built in and types](http://swcarpentry.github.io/python-novice-gapminder/03-types-conversion.html)

#### [Libraries](http://swcarpentry.github.io/python-novice-gapminder/06-libraries.html)

#### [Tabular data](http://swcarpentry.github.io/python-novice-gapminder/07-reading-tabular.html)

### Help code

    data_oceania_country = pd.read_csv('data/gapminder_gdp_oceania.csv', index_col='country')
print(data_oceania_country)



#### [Pandas](http://swcarpentry.github.io/python-novice-gapminder/08-data-frames.html)


#### [Plotting](http://swcarpentry.github.io/python-novice-gapminder/09-plotting.html)


    
## Survey questions 

- How much (if at all do you use Python)
    - Never: ++++++++++
    - Once in a while:++ + + + +
    - Everyday:+