GOSH Community Forum

Digital tools for a "academia starter" bootcamp

Hi folks,

Here in Brighton we’ve been thinking more and more about offering starting grad students (and whoever is interested really), a “digital tools bootcamp” to introduce tools that make life easier in the long run and help people adhere more to open science principles. I would like to know if you have tools/suggestions that you think would be good for this!

We would like to create curriculum for intensive 2 weeks where people get the chance of learning or at least get introduced to good tools and practices

some examples:

  • version control
  • R and python
  • How to setup a landing page/website
  • How to keep lab notes when you’re coding/running automated experiments
  • Arduino and physical computing
  • Open Science MOOC
  • PrePrints
  • making things citable with Zenodo
  • making things useful with documentation
  • How to pick good (open) file formats e.g. for data, documents, etc.
  • Latex
  • Open Source packages (libreoffice, GNU/Linux distros)
  • Open leaders programs
  • Markdowns

This is a wiki! please feel free to add/modify

@jcm80, @julianstirling, @rbowman, @jc2450, @nanocastro, @jarancio, @vektor, @pazbernaldo, @maxliboiron, @ffederici, @regfade


Sounds great!
Check https://kumu.io/access2perspectives/digital-open-science for some other suggestions and happy to co-design the training series with tasks and learning materials.


Definitely something that I think folks would find useful. I recently found https://missing.csail.mit.edu/ and have been slowly making my way through it. Not sure if it would make a good supplement, or may not work closely enough with the tools you have in mind though.


I’d love to participate! So much to learn and share! Great initiative! It’d be so good to replicate it all over!


For lab notebook and everyday science documentation check: https://www.elabftw.net/
The creator is in my lab !

I would love to participate too :slight_smile:


I put it in Twitter but copying it here too https://raoofphysics.github.io/phd-starter-kit/ is a good guide, or at least one I found useful.

I think the open science mooc has, in each module, tools listed. Or at least some of them I’ve seen for sure.

Ah! And all the carpentries stuff I feel is super useful too.


Hi. I’m new to GOSH, but have been lurking for a while. I currently have a fellowship to develop a new course sequence here called “Open Science Instrumentation and Data Collection”. I’m developing a set of lessons using the Software Carpentry curriculum model (and templates) that will lead students through setting up a Raspberry Pi (and python) for data logging and to use it to connect to — and program — an Arduino for physical computing. There has been a proposal for a while to create a “Hardware Carpentry” that I think these materials might fit with.

Here’s the link to the thread about hardware carpentry: https://github.com/carpentries-incubator/proposals/issues/8


Sounds exciting @amchagas , let us know in what other ways we can help.

@jarancio beat me to suggesting the Open Science MOOC, which I also think looks pretty good.

A few more resources off the top of my head, some pretty specific:

  1. Coding Club - Uses datasets from environmental/ecological monitoring as examples, but the tools and community-developed tutorials they have are generically applicable to other cases. I’ve met the founder, and Coding Club is being actively developed.

  2. REUSE Guidelines - A proposed standard for how to clearly indicating the license for a project by Free Software Foundation Europe. One of my pet peeves is how often people don’t think about licensing, and these guidelines make the process much easier. I strongly suggest this for your course!

  3. Write a standards-compliant README for source code or datasets - This is a crucial part of good documentation, so try to make README files useful and step in the shoes of someone completely new to your project with zero prior knowledge.

  4. Guides to Better Science - Published by the British Ecological Society, but again, is widely applicable to scientists. Full disclosure/shameless plug: I am one of the editors of the Guide to Reproducible Code in the series which was well-received in the Twitter-verse.

  5. Open Science Framework (OSF, developed by the Centre for Open Science), Research Ideas and Outcomes (RIO), and Zenodo (supported by CERN) - Web platforms/journals for publishing all material from the scientific process, from data, presentations, general files, source code, pre-prints, etc. A bonus is that AFAIK these platforms are themselves hosted on open source software.

  6. Publish registered reports on OSF, RIO, or PLOS - These are peer-reviewed, and often pre-accepted for publication in a journal, plans for research. The idea is for peer review to happen before research is conducted, which I think has lots of potential to overhaul the aging and increasingly inefficient peer review system currently in place.

For general open source replacements for closed sourced software/services, I often look at switch.software, Framasoft’s De-google-ify Internet, or PrivacyTools for comprehensive lists organised by category.

BTW, I’ve drafted a list of open source replacements for commonly used/seen closed source software in this git repository. Everyone please feel free to critique, fork, and improve!

Oh, and here are a some more-ethical replacements for common web tools:

Whew, this post is longer than I thought. Hope it is useful! Curious what others would suggest.

P.S. Also don’t forget that contributing to Wikipedia, the Wikipedia Commons or other Wikimedia projects is a great way to publish, too! Happy to chat more about this.

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