Skip to content

Latest commit

 

History

History
631 lines (562 loc) · 11 KB

Badges.org

File metadata and controls

631 lines (562 loc) · 11 KB
Raw

Training Badges

Badge should help make sure that group members have a certain knowelge or set of skills . They do not indicate masterhood but a basic understanding of the topic and related sources for further learning.

Begin with the end in mind: Write some questions/aims for each badge.

  • States [Active] / [Draft] / [Obsolete]
  • Tags/Categories:
    • Group organisation
    • General Data Science
    • High throughput sequencing
    • Software Develeopment
  • “TT” stand for training topic

TT0001 - Code of conduct

  • Also refer to ZB MED’s person for this

TT0002 - Mentoring agreement

TT0003 - Start with your document now

If you start a project thesis … start writing it already at the beginning..

TT000X - Server-“Seepferdchen” (server seahorse)

  • tmux
  • ssh
  • mosh
  • remote file editing
  • top / htop
  • df
  • store in data folder not home
  • ansible
  • Anacondo for software
  • Docker / singularity

TT000X - Lab journal

TT000X - FAIR data

Reading recommendations

Questions:

Task

TT000X - Git (+ GitHub/GitLab) basics

Reading recommendations

Questions:

  • What are version control systemy?
  • What are distributed version control
  • What is git?
  • Which other?

Task

  • Generate dummy article Markdown file and put put under version control with git. Make changes.
  • Share this it on Github

TT000X - Project data organisation

TT000X - Projekt organization and documentation

Reading recommendations

TT000X - Text editors

TT000X - Text files

TT000X - Unix shell - basics

TT000X - Unix shell - advanced

  • shell scripts
  • for loops
  • & and while
  • unnamed pipes

TT000X - Unix shell - advanced

File in /etc, /proc and other

  • systemd

TT000X - Hash sums

TT000X - Writing dates

-**** TT000X - Storing data in tables

https://www.tandfonline.com/doi/full/10.1080/00031305.2017.1375989

TT000X - SSH (and Mosh)

TT000X - Short read mappers

  • Tool for HTS (samtools, bedtools, cutadapt, FASTQC) - maybe merge with mappers

TT000X - Good practices for programming

TT000X - Making Software Citable

TOO00X - Important persistent identifiers

  • DOI
  • ORCID
  • ROR

TT000X - Python beginner

  • [ ] scripts, REPL (python and ipython), Jupyter notebook
  • [ ] variables
  • [ ] literal
  • [ ] data structures (list, tubles, dictionaries)
  • [ ] conditionals
  • [ ] for loops
  • [ ] functions
  • [ ] PEP008

Questions

  • What are conditionals
  • What is an iterator
  • What does “pythonic mean?

TT000X - Python - black

TT000X - Python - object oriented programming

  • classes

TT000X - Python - list comprehension

  • What is list comprehension?
  • What are generators

TT000X - Python - linting

pylint

TT0000 - Python - type hints

TT000X - Python testing (unit test, pytest, CI)

  • pytest
  • code coverage

TT000X - Python debugging

TT000X - Python visualisation packages

TT000X - Python bioinformatics packages

TT000X - Python pandas

TT000X - Python packaging/projects

Questions

  • Which files belong into a Python project and what is their function?

TT000X - Python type checking

TT000X - Refactoring

TT000X - R basics

TT000X - R tidyverse

TT000X - Rstudio

TT000X - HTML and CSS

TT000X - Static site generator

TTOOOX - Python web programming

  • static vs. dynamic
  • flask vs. Django

TT000X - Python flask

TT000X - Python Django

TT000x - Python - Bioservices

TT000X - Opens Science

  • Research Cycle

TT000X - Copyright and Creative commons licenses

TT000X - Open Source and open software licenses

  • Cathedral and Bazaar
  • copyleft vs. permissive
  • Research software

TT000X - Markup languages overview

TT000X - Markdown

TT000X - LaTeX

TT000X - Preprints

TT000X - Genome browsers

TT000X - tmux

TT000X - Academic carreer paths

TT000X - Basic Statistics

Questions

  • What is a t-test?
  • What is a p-value
  • What is correction for multiple testing?

TT000X - Peer reviewing

TT000X - Samtools

TT000X - Bedtools

TT000X - Continious Integration

TT000X - Continious Delivery

TT000X - Using Docker containers

TT000X - Creating Docker containers

TT000X - Using Singularity

TT000X - Creating Singularity containers

TT000X - Rsync

TT000X - Good scientific practice guidelinder of the DFG

TT000X - Semantic Versioning

TT000X - Making a poster

TT000X - Research Data Repositories

https://www.re3data.org/

  • Zenodo
  • SRA
  • GEO

TT000X - Meetings

TT000X - Packing and compressing

  • tar
  • zip
  • gzip, bzip2, xz
  • pgzip, pbzip2, pzx

tar cf myfile.tar.bz2 –use-compress-prog=pbzip2 dir_to_compress/

TT000X - Password management

TT000X - Differential Gene expression anlysis

  • DESeq2
  • EdgeR
  • READemption
  • Liu et al.

TT000X - READemption

TT000X - Genome annotations with ANNOgesic

TT000X - Functional enrichment analysis

ClusterProfiler

  • with standard organisms (enrichKEGG or enrichGO)
  • with non-standard organims (enricher or GSEA)

TT000X - Wikidata

TT000X - Writing documentation

TT000X - zsh

TT000X - VPN

  • openconnect

TT000x - P-values

https://twitter.com/wetlabsucks/status/1192037932481294337?s=09

TT000x - RSS

https://twitter.com/wetlabsucks/status/1192037932481294337?s=09

TT000x - Backups

  • rsync
  • restic

TT000x - Backups

Working collaborative