This is an updated list of tools and resources and bookmarks that I use and find helpful for research. It’s based on this blog post but updated when I find the time (or a new toy) and is aimed at helping my students (and me) get going in projects and writing papers. Many of these tools are free, some of them are not, and some require setting up an account. In the spirit of Open Research, Open Science and FLOSS/FOSS standards, I’ve tried to stay away from the corporate walled gardens as much as possible in this list.
- I use Zotero.org for reference management when writing papers, but also keeping track of interesting articles that I want to read some day. It’s wonderful. Check it out.
- Some useful open Zotero Groups that I’m a member of, there are probably more I should make open and add here too.
- Firn on ice sheets
- Publications from my colleagues at DMI
Literature searching is an art in itself. I do occasionally use google scholar for some basic literature searching, and I have a researchgate account, which can be useful for getting access to otherwise paywalled articles. I have now also started using the Internet Archive’s scholar search as my primary source. Helpfully they will find you pdfs wherever possible. Given the problem of paywalls in academic research, the openaccess button which will email the authors on your behalf if there is nothing available online is porbably worth knowing about too.
I was recently alerted to OpenAlex which I haven’t used very much yet but which appears to be another open science tool for literature reviews. It’s made by OurResearch, a non-profit organisation that specialise in developing useful tools to open up science publishing, notably including the successful unpaywall, a tool that scours the web to find open and free pdf articles of paywalled papers.
And similarly, the German Bielefeld University search engine BASE is another alternative to google scholar that is very well reputed and which I intend to start testing further,
I’ve also been exploring other options which it turns out I like much better than traditional search, at least when going into a new field for the first time:
- Research Rabbit and Connected Papers have been revolutionary in terms of finding relevant scientific articles
- Inciteful is a similar tool which I am still exploring
- Obsidian is a note-taking app with brilliant possibilities for tagging, back and forward linking and the ability to visualise your notes as a graph to see connections. It’s in markdown langugae and just saved as a bunch of text files on your computer, unless you choose a cloud back up version.
Adapting the philosophies behind Getting Things Done and Cal Newport‘s Deep Work have revolutionised my ability to feel in control while attempting to do too much. We should probably recognise the enormous privilege of these guys though, I can’t help wondering who is keeping things running in the background (I’d be lost without the contribution of my spouse). In practice I use ToDoist to track my To Do lists, though I don’t always keep them up to date..
Over on mastodon, Nika Shilobod shared this truly awesome list on github curated by PhD student Helena Hartmann which she urges others to contribute to as well. I haven’t checked everything out but there are some really incredibly useful looking tools, not just for research but also careers.
“All the resources I wish I knew when starting my PhD. This repository is aimed to be a living, constantly developing resource where everybody can contribute with new resources!”
Helena Hartmann
Programming Tools
Github and Gitlab. Obviously.
Python: In transitioning from Matlab, I found Jupyter helpful, but also Datacamp‘s quick and easy to follow online courses got me up to speed reasonably quickly, especially useful for learning xarray and dask
Pangeo: Superb suite of tools for dealing with big geoscience datasets and climate model outputs. Also a lively online community. Start here: https://pangeo.io/
We now have an AI/Deep learning network at the office and as I now have a deep learning project to think about I’ve been attending it. The notable app came up as an interesting snippet. I haven’t explored it much yet but it looks very cool 😎. It’s a plugin for ChatGPT to help you write code and analyse data.
Julia: I am not (yet) using Julia but I can see it is really and up and coming language with a lot of applications in machine learning and as more and more climate modelling starts to migrate to using GPUs. (See e.g. https://dj4earth.github.io)
This list of resources on Julia was compiled by Patrick Heimbach at University of Texas and is awesome. I will dive into these at some point.
https://julialang.org/learning/getting-started/
https://julialang.org/learning/tutorials/
https://julialang.org/learning/
Henri Drake & Alan Edelman
https://github.com/ClimateMARGO/ClimateMARGO.jl
https://eartharxiv.org/repository/view/214/
Climate Modelling unit for MIT’s “Introduction to Computational Thinking”
Gael Forget – ClimateModels.jl
https://gaelforget.github.io/ClimateModels.jl/dev/
https://github.com/JuliaClimate
Julia Academy
https://juliaacademy.com/p/intro-to-julia
Martin D. Maas (MatecDev)
Julia Programming: a Hands-on Tutorial
https://www.matecdev.com/posts/julia-tutorial-science-engineering.html
Outreach
I made these little webcomics for kids when on fieldwork the last couple of years. It is quite a lot of extra work which probably explains why I never finished the second one (one day!) But it was actually quite simple to do. I used the Comic strip app on my android phone and uploaded the images using the wordpress app. Given we were out of range of any signal at all during the trip I uploaded most of them when we got back to base.
Sterna Paradisaea 