create a list of blog topics...

[crmackay]

I'm just going to leave this here for now so I can remember to do this...

[crmackay]

Here is my list:

Ideas for blog posts on new website:

Categories:

• python
• unix
• R
• biotools
• stats/data analysis
• C/C++(golang?)
• julia?

note: you can have multiple “tags” and categories per article

Python 2

• topics we didn’t get to:
  • useful python modules:
  • pysam, biopython, etc.
  • better explanation on packages and modules
  • using a RDB instead of a dictionary(map)
  • the conundrum of parallel processing with python (you can do it...but should you?)
  • matplotlib - with ggplot flair, but easier syntax (depending on who you ask)
  • virtualenv's and dependency management
  • gzip’ed files
  • pandas!

Biotools

• bioinformatics in general
  • ??? people interested in diving into how these programs work…??
    • alignment algorithms, burrows wheeler transform, etc.
  • stats models:
    • hidden markov, dynamic bayesian networks, expectation maximization (a la RSEM), etc.
• running scripts on the cluster
  • apparently this works: https://gist.github.com/crmackay/6b21a03b299b8a111456

best practices

• source control (git and github)
• electronic lab notebook
• coding environment (eg “Hi I’m Jill/Arjen/Mike/Nick, and this is how I work”)
• getting a DOI for your code
• properly documenting code
• writing and using effective unit tests
• documenting pipelines and scripts --> facilitating the repeatability/reproducibility of your work...saying "in house scripts were used" in a manuscript and leaving it there is not okay (although apparently it is)
• continuous integration (Travis CI or others)

Other

• using public databases/datasets
• LaTeX tutorial and template walkthrough

feel free to add more in the comments