Tools We Love, Tools We Need

In a survey 22 people submitted their favorite tool that make their academic life more manageable. In an open floor session we all commented on tools and shared tricks.

Coding tools:

  • text editors: pycharm, Atom, sublime text
  • GitKraken, similar to github desktop interface. It gives an overview of all previous commits
  • Trick for git, –amend? Allows you to add things to previous commit, and allows to fix notes
  • Issue, how to comment out blocks in R? Solution: work in R-studio. There is also R-studio cloud.

Data tools (where do you store data? ):

  • google drive might be slow file by file, but big files are fast. Patient data(sensitive data) cannot be on google drive, but can be on OneDrive (microsoft)
  • some labs use google drive as their backup, constantly synching
  • Zenodo, 50 gb free data storage online
  • QUESTION: Do you have different data storage for current projects and published project? Lolo storage for data after publication. Requires lots of overhead. AWS is doable but expensive. Glacier (cold storage) is also expensive. Research credits program for 1 year by Google | Amazon, good for benchmarking, but expensive otherwise. Is OSF an option?
  • Issue: data online can only be accessed by scrambled URL’s. Dropbox had publicly accesed unscrambled URL’s for a while, but it is now gone. Scrambled URL’s a problem because you want to write software that points to data.
  • UW library might be an option for data storage(unlimited?!!), and might fix scrambled URLS? Look at Researchworks:

Do you preregister your studies?

  • What does pre-registering on OSF entail? A paragraph and questions one should answer about hypothesis etc.
  • advantage of preregistering: you would be more believable if you end up getting results you hypothesized before. It provides a paper trail.
    If you have a very specific hypothesis, preregistering would useful good to show that you are not p-hacking.
  • Issue: is it hard to change direction mid-study? Generally it’s ok to alter your direction a few times
  • Note: OSF preregistration is private until you publish the work

Presentation and Lecture Tools

  • is Reveal.js with an interface. It also allows you to fork from there. Note: there is a free plan).
  • Reveal also has latex plugin
  • Google slides has latex plugin also (but it creates an image, so requires retyping for alteration)
  • Poster software: Illustrator, Inkscape, latex
  • Polling sites:, Reveal.js allows you to write slides as you would websites (html, javasccript, markdown) google slides works.

Reference management tools

  • Mendeley
  • Endnote
  • Zotero+ZotFile
  • paperPile
  • RefWorks

From the discussion that followed it turns out most people do not really love their reference management tools, and that software is usually inadequate at extracting meta data from papers. Some of us just copy the .bibtex entry from googe scholar (it is consistent in it’s naming and much more likely to be correct). Sidenote from the discussion: Overleaf premium is free for .edu.

Note taking and wordprocessing

  • Google keep (also great for taking notes by talking to phone, saves text and audio file)
  • simplenote
  • Evernote for lab notebook
  • oneNote for lab notebooks
  • some labs push notes to lab repo

Time/Meeting Management

We appropriately ran out of time to address this.