Ask HN: Whats you're ideal PhD workflow

• zotero

  254 9,225 9.9 JavaScript

  Zotero is a free, easy-to-use tool to help you collect, organize, annotate, cite, and share your research sources.

  

If you're Emacs savvy (Spacemacs user myself) why not use the org-mode tools to work the LaTeX?

Also, references in Zotero => https://www.zotero.org/

There is a good Android client for Zotero, so toting around research on a tablet is a cheap approach.

• org-ref

  27 1,338 7.6 Emacs Lisp

  org-mode modules for citations, cross-references, bibliographies in org-mode and useful bibtex tools to go with it.

Since you’re an emacs user, I highly recommend org mode and org-ref for technical writing. For collaborative writing I’ll export to overleaf, but I’ve never found anything quite as good as org mode for organizing, building, and revising research writeups.

You don’t have to go all in on org for notes and TODO tracking (I’ve tried and haven’t made it stick).

https://github.com/jkitchin/org-ref

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• reproducible_papers

  1 15 6.5 Python

  Automate computations, plotting, and LaTeX with Makefiles.

My main workflow improvement over the course of my PhD has been making my papers reproducible. This means: I can clone a github repo and in a single command, re-run all computations, re-generate all figures and tables, and compile the final paper.

Any manual step like "resize the figure window until the proportions look good" or "run script A, then run script B", or "upload this file to Overleaf" creates an opportunity for your results (figures and tables) to become out of sync with your source code. This can cause big problems.

I use Makefiles to accomplish this [1], but the exact techniques don't matter. The main point is the end goal.

More broadly, in research it's always tempting to do things quick and dirty. Conference deadlines loom. Code bases are usually small and short-lived. But in my experience, your 4-months-later future self will appreciate tests, documentation, etc. just as much as your 4-years-later future self.

You can still be quick and dirty when it comes to project scope. This is where you get most of the speedup anyway. Go ahead write a function that doesn't handle edge cases, but add a comment about it!

[1] https://github.com/jpreiss/reproducible_papers

• sioyek

  88 5,859 5.5 C

  Sioyek is a PDF viewer with a focus on textbooks and research papers

I wrote a research-oriented PDF viewer during my own PhD. The ability to be able to quickly find and search references proved invaluable to me (obviously I am biased though :) ). Here it is:

https://github.com/ahrm/sioyek

• dendron

  28 6,415 6.3 TypeScript

  The personal knowledge management (PKM) tool that grows as you do!

  

would recommend checking out https://wiki.dendron.so

it’s an open source, local first, markdown based note taking tool that is integrated with vscode/cli

(full disclosure: i’m the creator and happy to answer any questions as well on our discord: https://discord.gg/NDYd9nYkM3)

• SaaSHub

  www.saashub.com featured

  SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

  

Suggest a related project