crmackay
commented
9 years ago 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
I'm just going to leave this here for now so I can remember to do this...