# Software Carpentry 2019-12-02/2019-12-03 @ ZB MED

## Day 1
- [x] Link tho this pad: https://hackmd.io/pfNXJI9dSSS6fZJatFAGiQ?view
- [x] Short link to pad: https://bit.ly/2pliIsw
- [x] Introduction of the instructors and helpers
- [x] Introduction of the participants
- [x] Who are the Carpentries
- [x] Motivation for the Carpentry workshops
- Automation
- Reproducibility / Transparency
- Empowerment
- [x] Life Long Learning
- [x] Ice breaker - Sort people by the following values:
- Sort by time time in research
- Group by research field
- Considering the course topic - how strong do you feel about knowing this already?
- [x] Sticky notes
- [x] If anything is not clear - please ask. There are no stupid questions
- [x] Code of Conduct https://software-carpentry.org/conduct/ => Be excellent to each other!
- [x] Photos and twitter
- [x] Wifi for external, options: eduroam and HOTSPOT.KOELN
- [x] Explain pad
- [x] Breaks
- [x] Coffee/Tea
- [x] Bathroom
- [x] Cheat sheet if provided
- [x] Installation and Github account
- [x] Exercise - add your name to the list of participants
- [x] Material of the course
- [x] Overview:
- Git: Software for tracking changes (versioning) of files/projects
- GitHub/GitLab: Online plattform for storing files/projects with Git
- Python: A programming language
- Shell/Bash: command line based user interface (for "talking" to the machine/computer)

## Participants:

1) Janko Sattler (X)

3) Alexander Kaczmarek (X)
4) Yanhong Hou (X) ([e-mail])
5) Andreas Scheel
6) Martin Höhne
7) Julia Désirée Mauz (X [e-mail])
8) Ksenia Kolesnikova
9) Erika Muratov (X) ([e-mail])
11) Xia LI (X)
12) Raphael Gries (X)
13) Daniele Civello (x)
14) Anna Cherianidou
15) Alba Filella Lopez de Lamadrid

## Day 2
- [x] Material of the course
- [x] Installation and Github account
- [ ] Feedback
- [ ] Plan for the afternoon
- [ ] [Link to our repo](https://github.com/foerstner-lab/Bits_and_pieces_for_the_carpentries_workshops)
- [ ] Comments in Python
- [ ] The Atlantic article - [The Scientific Paper Is Obsolete](https://www.theatlantic.com/science/archive/2018/04/the-scientific-paper-is-obsolete/556676/)
- [x] Book recommendations
- [ ] What to do after the workshop (see section below)

## Git

- [join_git](https://github.com/join)
- [picture](https://jdblischak.github.io/2014-09-18-chicago/novice/git/01-backup.html)

## Data

- [shell_data](https://github.com/swcarpentry/shell-novice/blob/gh-pages/data/data-shell.zip)
- Python GFF file: `ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Escherichia_coli/reference/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.gff.gz`

## Lessons

- [shell](http://swcarpentry.github.io/shell-novice)
- [git](http://swcarpentry.github.io/git-novice)
- [python](http://swcarpentry.github.io/python-novice-inflammation)

### Our Lessons:

- [pandas](https://github.com/konrad/Bits_and_pieces_for_the_carpentries_workshops/blob/master/python/)

### Python reading recommendations

- [Automate Boring stuff with Python](https://automatetheboringstuff.com/)
- Fluent Python (advanced)
- [Learning_python](oreilly.com/library/view/learning-python-5th/9781449355722/)
- online_courses
- [PEP-0008](https://www.python.org/dev/peps/pep-0008/)
- [pandas_cheat_sheet](https://github.com/pandas-dev/pandas/blob/master/doc/cheatsheet/Pandas_Cheat_Sheet.pdf)
- [python_cheat_sheet](https://github.com/ehmatthes/pcc/releases/download/v1.0.0/beginners_python_cheat_sheet_pcc_all.pdf)
- [The 35 Words You Need to Python](https://yawpitchroll.com/posts/the-35-words-you-need-to-python/)
- [Python built-ins worth learning](https://treyhunner.com/2019/05/python-builtins-worth-learning/)
- [Learning the Pandas Library](https://mcgillmsaa.files.wordpress.com/2018/05/learning-the-pandas-library-python-tools-for-data-munging-analysis-and-visual.pdf)
- [Schnellstart Phyton, german, free within uklan](https://link.springer.com/book/10.1007%2F978-3-658-26133-7)

## What to do after the LC-workshop

- Install Git Bash and Anaconda or you machine (ask the IT-department)
- Find a good text editor
1) [emacs](https://www.gnu.org/software/emacs/)
2) [vim](https://www.vim.org/)
3) [spider](https://www.spyder-ide.org/)
4) [atom](https://atom.io/)
5) [pycharm community edition](https://www.jetbrains.com/pycharm/)
- Go through the lessons and try to reproduce them alone
- Find small tasks you solve on a daily bases and try to solve them using the computation skills you have learned
- [Rosalind](http://rosalind.info/problems/locations/)
- [Intro_to_computer_science](https://www.udacity.com/course/introduction-to-python--ud1110)
- [Participate to the hacky-hour](https://hackyhour.github.io/Cologne/)

## Workaround if Anaconda doesn't work
Go to https://mybinder.org/ . Put the URL https://github.com/foerstner-lab/Bits_and_pieces_for_the_carpentries_workshops after "GitHub repository name or URL" and "write empty_jupyter_notebook_for_binder.ipynb" after "Path to a notebook file"

Click on "launch" .

import urllib.request
import pandas as pd
source_url = "ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Escherichia_coli/reference/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.gff.gz"
gff_file = "E_coli.gff.gz"
urllib.request.urlretrieve(source_url, gff_file)
gff_data = pd.read_csv(gff_file, sep="\t", comment="#", 
                       names=["seqid", "source", "type", "start", "end", "score", "strand", "phase", "attributes"])

### Links

- [Python 3 Quick Tip: The easy way to deal with file paths on Windows, Mac and Linux](https://medium.com/@ageitgey/python-3-quick-tip-the-easy-way-to-deal-with-file-paths-on-windows-mac-and-linux-11a072b58d5f)

- [Merging and Joining of Pandas Dataframes](https://chrisalbon.com/python/data_wrangling/pandas_join_merge_dataframe/)

### Heatmap

source_url = "https://raw.githubusercontent.com/foerstner-lab/Bits_and_pieces_for_the_carpentries_workshops/master/text_file_examples/Expression_comparison.csv"
table_file = "Expression_comparison.csv"

https://python-graph-gallery.com/100-calling-a-color-with-seaborn/