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

Day 1

  • Link tho this pad: https://hackmd.io/pfNXJI9dSSS6fZJatFAGiQ?view
  • Short link to pad: https://bit.ly/2pliIsw
  • Introduction of the instructors and helpers
  • Introduction of the participants
  • Who are the Carpentries
  • Motivation for the Carpentry workshops
    • Automation
    • Reproducibility / Transparency
    • Empowerment
  • Life Long Learning
  • 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?
  • Sticky notes
  • If anything is not clear - please ask. There are no stupid questions
  • Code of Conduct https://software-carpentry.org/conduct/ => Be excellent to each other!
  • Photos and twitter
  • Wifi for external, options: eduroam and HOTSPOT.KOELN
  • Explain pad
  • Breaks
  • Coffee/Tea
  • Bathroom
  • Cheat sheet if provided
  • Installation and Github account
  • Exercise - add your name to the list of participants
  • Material of the course
  • 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)

  2. Alexander Kaczmarek (X)

  3. Yanhong Hou (X) (yh_hou@163.com)

  4. Andreas Scheel

  5. Martin Höhne

  6. Julia Désirée Mauz (X juliadesiree.mauz@gmail.com)

  7. Ksenia Kolesnikova

  8. Erika Muratov (X) (erika.muratov@dlr.de)

  9. Xia LI (X)

  10. Raphael Gries (X)

  11. Daniele Civello (x)

  12. Anna Cherianidou

  13. Alba Filella Lopez de Lamadrid

Day 2

  • Material of the course
  • Installation and Github account
  • Feedback
  • Plan for the afternoon
  • Link to our repo
  • Comments in Python
  • The Atlantic article - The Scientific Paper Is Obsolete
  • Book recommendations
  • What to do after the workshop (see section below)

Git

Data

  • shell_data
  • 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

Our Lessons:

Python reading recommendations

What to do after the LC-workshop

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"])

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/

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