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Tools for science and research

A science project – whether a simple seminar task, M.Sc. or Ph.D. thesis – requires tools to work efficiently. These tools depends on your personal preference and work styles, available budget and overall goals.

My recommended setup is geared towards open source, open format settings and I am/have been using this setup on Mac and Windoze in corporate and academic settings.

Writing

Editors

When using LaTeX for writing documents, a good editor is essential. There are a few nice ones around, again depending on preferences.

Reference management

Visualisation/Graphics

  • Vectorgraphics programs
    • (FOSS) Inkscape (open source, all platforms)
    • Corel Draw, Adobe Illustrator, Deneba Canvas
  • Raster graphics tools
    • GIMP The GNU Image manipulation tool - open source Photoshop®

Geographic/geophysical data

Data science

A bit of a crossover, but the Python ecosystem (Jupyter Notebooks, MatPlotLib etc) allows both, data analysis and visualisation in a notebook/browser.

Revisioning

When undertaking a science study, it is recommendable to set up a revision control system as used in software development. Nowadays, most of the products and workflows will be based on a digital toolchain, composed of input data, scripts/processing steps, visualisation steps and a documentation/text part. Each of these different steps will likely contain or result in a set of (intermediate) files which will evolve during the cause of the project. Having an ability to track, revert or branch at any case while maintaining a timeline of the project will not only sometimes help to save you but also provides an excellent automatic log.

Tools for revision control:

  • The Fossil Source Code management software: this is a very lightweight but powerful software which includes a forum, ticketing system and wiki, that runs from one executable across all OS.
  • GIT,
  • Webservices around version management tools
    • SourceHut purely FOSS-based hosting of GIT and Mercurial repositories, bug tracking, forum etc.
    • GitHub(owned by Microsoft)
    • BitBucket owned by Atlassian

Research (literature) databases and tools

Besides doing a general “Google search” for a specific topic, there are a number of webservices around that allow to specifically search for scientific papers/literature. The links below are just the most basic starting points for any research. The sprawling ecosystem of the internet and available services evolves on an almost daily base and you will need to find a way which suits your needs. So take these as starting points:

  • Google Scholar
  • Wikipedia's list of academic databases and search engines
  • GeoRef is a database now hosted on GeoScienceWorld and has been the key geoscience prior to the web. Quote from the website: “The GeoRef database covers the geology of North America from 1666 to the present and the geology of the rest of the world from 1933 to the present. The database includes references to all publications of the U.S. Geological Survey. Masters' theses and doctoral dissertations from U.S. and Canadian universities are also covered.”. Might require institutional access.

For years, I have been using two little tools from DevonTechnologies which help to search, organise and synthesise my private research library as well as scour the web. These are Mac-only tools:

There are of course more “Knowledge management tools” around, this is based on personal preferences, operating system, needs. Most likely, your setup and preferences will evolve over time.