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As a researcher, I use a variety of software tools on a regular basis, and I’d like to share this list of tools here.

Writing and Collaborating on Papers

For writing papers, I use Sublime Text 3 with the LaTeXTools package installed. This allows me to edit and compile the document directly from ST3. I have the same setup with the Atom editor as well, and both work well.

For collaborating on papers, I prefer to use GitHub and host the source files (e.g., tex,bib) in a repository dedicated for the paper. I believe this gives each co-author the freedom to choose and set up their own work environment and tools (as opposed to something like ShareLaTeX).

Typically when starting to work on a paper, we use Google Docs to draft out an outline for the paper and reach an agreement on the direction of the paper. The commenting mechanism on Google Docs works well and supports brainstorming.

Other tools I typically use:

  • LatexDiff, a command line tool, for generating visual diffs between compiled documents. Useful when outlining changes to reviewers between revisions. Similarly, Git-LatexDiff aims to generate a diff and simplify the process even further
  • AbstractFormater for formating text. Very useful, especially for paper submissions
  • BibTex normalizer for cleaning up the bibtex file
  • EZProxy plugin for accessing academic papers from outside of the university’s network
  • Octobox for managing GitHub notifications
  • Draft: a writing tool that I find helpful in overcoming writer’s block

Preprints and Study Data Sharing

  • Zenodo: for sharing data from our studies (e.g., replication package)
  • arXiv: for preprints or papers that are not archived elsewhere

English Prose

  • Grammarly: is an English-language writing aid for the browser
  • Proselint: works well with text and markdown files in Sublime Text and Visual Studio Code (no Latex support though)
  • Write-good: a prose linter extension for developers

Team Communication

  • Slack: most of our group’s communication happens on Slack, though we may switch to Mattermost later this year
  • Keybase: it’s like a combination between Slack and Dropbox, that also leverages cryptography.
  • Skype: video calls when we’re not co-located
  • Email

Schedule and Time Tracking

Keeping Up To Date

Knowledge Management and To-Dos

Presentation Slides


  • In the past I used PowerPoint to create conference posters, but I’m trying to switch to Inkscape

Collecting Data from Surveys and Interviews

Data Analysis

  • Google Sheets and R Studio: for data exploration and analysis
  • RQDA: for qualitative data analysis (coding, memoing, generating themes)
  • Tidyverse: a set of packages for data science with R
  • DataGrip: when data-mining large SQL data sets

Creating Visualizations

Coding Tools / IDEs

App / Tool Design

  • Balsamiq: for low-fidelity mockups
  • InVision: for interaction design
  • UX Check: for identifying usability issues using Neilsen’s heuristic evaluation

Creating Video Demos

  • Shotcut: cross-platform video editing (works great in combination with OBS).

User Analytics




  • Duplicity: for encrypted local and remote backups

Running a Research Seminar

Course Teaching and Learning Management System

Tools I wish I could use, but they’re Mac-only

What tools do you use?
Any recommendations for other tools I should try?

P.S. I’d love to meet you on Twitter.

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Alexey Zagalsky



Alexey Zagalsky

Software Engineering Researcher

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