Tools, hacks, and software for your PhD thesis.
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Inbox Zero
Inbox Zero is a method amongst others to manage your email workflow. If you consider your Inbox being what you actually have on your mind at a certain time, Inbox Zero aims at having a clear view, processing/tagging/archiving your emails as soon as possible in order to always stay up-to-date.
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org-mode
Org-mode is a tool to write notes, todo lists, keep track of deadlines, and much much more, in an efficient matter. You can e.g. implement GTD (Get Things Done) with org-mode.
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LaTeX
LaTeX is the de-facto tool to write high-quality scientific articles. It respects standards and provides packages for almost everything you'll need, for example to write complex mathematic formulas.
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ShareLatex - Write and compile LaTeX online
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OverLeaf - Another tool for online LaTeX
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Beamer - A package to create LaTeX presentations
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Zotero
Zotero organises your articles collection. You can then easily tag them, in order to find later what you need to cite.
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CiteULike
CiteULike is a platform to share references.
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Graphics and plots
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matplotlib - Python library
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tikz - Graphics in LaTeX
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draw.io - Browser-based tools to draw graphics
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Org-mode (again) permits to write research notebooks, in order to document for instance experiments and data analysis. You can embed code (and run it interactively), data tables, plots, etc. You can also export your content to many kinds of formats, includinh LaTeX and HTML.
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Jupyter is a tool to create notebooks in more than 40 programming languages. Like with org-mode, you can embed many types of interactive data, through a web interface.