biology.md

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/subject-guide/biology/	RSE Toolkit - Subject Guide	Subject Guide	single

Biology

Bioinformatics

Major languages:

for tools and also web-development efforts

• Python
• R
• Java
• minor c++
• lately some poeple are big advocats of Rust

for web development,a lot of different web technology stacks are used ranging for older stacks to the latest and greatest with React.js, Vue, etc Q: should we try to get some ideas on what is used most? I'll check if I can find some overview publication (eWorkbench?)

A lot of emphasis is put on enabling Reproducible Research lately. This includes container technologies like Docker and workflow systems like Nextflow, snakemake which are the most popular ones.

Typical journals

A lot of work is published in the following journals:

• Bioinformatics
• NAR
• PLoS
• eLife
• JOSS

Furthermore, an enormeous amount of articles about bioinformatics software are published on bioarxiv before actual publication via the said journals.

Resources

• https://github.com/danielecook/Awesome-Bioinformatics
• https://www.reddit.com/r/bioinformatics/
• https://global.oup.com/academic/product/introduction-to-protein-science-9780198716846
• https://web.stanford.edu/~hastie/ElemStatLearn/
• https://www.biostars.org/
• an overview of curated tools from the literature https://bio.tools/

Python

• pypi
• (bio)conda
• https://biopython.org/

R

• CRAN/MRAN
• Bioconductor

Java

• mvn
• https://biojava.org/

C++

• conan.io
• http://biocpp.sourceforge.net/

Rust

Introductory books

• https://global.oup.com/academic/product/introduction-to-bioinformatics-9780198794141

Communities

• ELIXIR

commercial companies

• Qiagen
• 10X Genomics
• https://en.wikipedia.org/wiki/List_of_bioinformatics_companies

Bioimaging

Major languages:

for tools and also web-development efforts

• Java

• Python, more specifically Machine Learning and Deeplearning

• web development

Typical journal

• Nature Methods
• Journal of Microscopy
• computer science journals for algorithmic approaches

main topics and challenges

• big data and performance

• bioformats / open and closed source image file formats

• open-source tools centered around ImageJ (Fiji)

  • plugins
  • centralised repo

specific skill sets

• image processing
• image analyis
• general algoritms for Machine Learning and Deeplearning

specific tools list

• Cell Profiler

• cytomine

• qpath

• ilastik

• imageJ/Fiji

    commerical tools imaris,
  
    microscope vender software
  

communities

• Euro BioImaging
• Global Bioimaging
• Neubias http://eubias.org/NEUBIAS/ or follow-up conference series
• https://www.youtube.com/channel/UC-oy7UpEhRfHQ-5ePCviKFg
• https://forum.image.sc/about

general tips

• not scared if you do not have biology background
• strong need for RSEs in the field at the moment