Rex Godby’s Recommended Links

The third-party web sites listed here are mostly connected with scientific computing, scientific graphics or scientific writing, plus a few more general items. Star ratings (★-★★★★★) indicate my personal, subjective assessment of their design and usefulness. Listings are provided without warranty.

The symbol B indicates recommended starting points for beginners in the area. Consider searching for B or ★★★★★ using your browser’s Find command.

LaTeX (a document preparation system)

B My brief advice for beginners on getting started with LaTeX

Don’t bother to install LaTeX on your computer. Instead, set up a free account on Overleaf.com and use LaTeX through your web browser.
Try out some of the templates supplied by Overleaf, and/or some examples from the tutorials below.
As you gain experience, you may wish to install LaTeX locally for the occasional offline task, but Overleaf is the best choice for most things.
For handling references, use BibLaTeX if you can, though the less flexible BibTeX is mandated by many journals.

Tutorials

The LaTeX Wikibook ★★★★★
- including a helpful chapter on “Basics” ★★★★★ B
Phil Hasnip’s guide to LaTeX ★★★★
The Five-Minute Guide to LaTeX (PDF) ★★★★ B
Writing Scientific Documents Using LaTeX (PDF) ★★★
The Not So Short Introduction to LaTeX (PDF) ★★★
L2Tabu (LaTeX Taboos) (PDF) ★★★★
- also available as a more recently updated German original (PDF)
LaTeX for Complete Novices (PDF/HTML) ★★★★ B
25 tutorial videos on LaTeX from ShareLaTeX ★★★★ B
LaTeX Templates (large collection) ★★★★★ B
LaTeX Tutorials from ShareLatex ★★★★★ B
NEW! Several clear LaTeX Tutorials from Andy Roberts ★★★★ B
NEW! LaTeX for Beginners ★★★ B
NEW! Overleaf’s 3-part LaTeX tutorial ★★★★
NEW! LearnLaTeX.org Useful guide for beginners, linking to Overleaf.com examples. ★★★★ B

Documentation

LaTeX “cheat sheet” (2-page quick reference) ★★★★
NEW! A similar, but newer, LaTeX 2-page reference card ★★★★★
List of LaTeX symbols (PDF) ★★★★
Categorised list of LaTeX packages ★★★★ with direct links to documentation
CTAN (Comprehensive TeX Archive Network) for LaTeX packages ★★
The LaTeX Font Catalogue: fonts with math support ★★★★
NEW! TeXdoc Online - TeX and LaTeX Documentation ★★★
NEW! TeX User Group (TUG) FAQ (new location) ★★★

Some favourite LaTeX packages

(All these packages are available in TeXLive and in Overleaf.com. Place the relevant usepackage command in your document’s preamble.)

Font packages (to replace the default Computer Modern LaTeX font for both text and mathematics):
- mathpazo (based on Palatino) ★★★★★
- mathptmx (based on Times) ★★★★
Enhanced tables: longtable or array ★★★★
fancyhdr ★★
lastpage ★★
RevTeX mandatory for Physical Review journals ★★★★
TikZ / PGF for diagrams etc. (an alternative to drawing programs) ★★
Beamer for making presentation slides or posters (in PDF format) ★★★★
- Beamer User Guide ★★★★
showlabels (for temporarily printing the names of equations and Figures in margins to assist the writing process)
markdown ★★★ Allows use of the excellent lightweight markup language Markdown (see below) inside a LaTeX document.
tcolorbox ★★★★ (coloured boxes for examples etc.)

LaTeX editors

TeXStudio ★★★★★ (Linux, Mac, Windows)
TeXShop ★★★ (Mac: comes with MacTeX TexLive distribution)
TeXMaker ★★★★ (Linux, Mac, Windows)
TeXnicCenter ★★★ (Windows)
Gummi ★★★ (Linux, Windows) (includes live-update preview pane)
See also online LaTeX editors below, notably Overleaf.com ★★★★★ B

LaTeX distributions (to install on your own computer)

TexLive (Linux, Mac, Windows) ★★★★★ B

Bibliography tools for LaTeX

NEW! BibTeX ★★★★ The original, with somewhat inflexible styles, but required by many journals
NEW! BibLaTeX ★★★★★ More flexible bibliography styles
Note that both BibLaTeX and BibTeX read the same .bib files; they differ in how your references are processed into the printed bibliography.
See below for tools to edit .bib files, generate .bib files from Zotero, convert references to .bib entries (e.g. Crossref), etc.

Other tools for use with LaTeX

lacheck LaTeX checker ★★★★★ B for clear help tracking down problems (LaTeX’s own error messages can be obscure even for simple errors)
ChkTeX LaTeX checker ★★★★ B for further help tracking down problems. (Works best with short lines, so recommended usage is fold -s document.tex | chktex .)
latexdiff ★★★★ for producing a marked-up LaTeX document showing changes (see also online version below). May fail on complex documents.
LibreOffice Writer’s “Compare Documents” feature (also available in other word processors) is handy for producing an easy-to-absorb display of changes to the LaTeX source
The Pandoc document converter ★★★★★ (e.g. HTML or Markdown to/from LaTeX or Beamer)
Zotero reference manager ★★★★★
plus Zotero’s BetterBibTeX add-on ★★★★★ for smart import/export of BibTeX .bib files
See also section on Publication references, DOIs, BibTeX, etc. below
NEW! MathPix ★★★★ Mac and iOS apps that convert (using Mathpix’s servers) an image of a handwritten or PDF equation into LaTeX! Works very well.
latexmk command for automating LaTeX / BibTeX compilation ★★★★

Online LaTeX tools

Overleaf.com online LaTeX compiler ★★★★★ B (formerly WriteLatex)
Codecogs “live” equation editor ★★★★★ B
Another LaTeX “live” equation editor ★★
LaTeX “live” table editor ★★★
TablesGenerator LaTeX “live” table editor ★★★★★
BibTeX .bib bibliography-entry editor ★★★
Online version of the Pandoc document converter ★★★★ (see above)
Detexify symbol lookup ★★★★★ B (handwritten symbol to LaTeX)
Online latexdiff tool ★★★★ Generate a comparison document
LaTeX word count tool ★★ B

Forums and blogs

LaTeX StackExchange forum (active, questions and answers) ★★★★★

Graphics and PDF tools

B My brief advice for beginners on preparing scientific graphics:

Prepare each Figure as a stand-alone PDF (with cropped margins: see pdfcrop below), and include it in your LaTeX document.
For graphs etc., use matplotlib or Plotly in Python.
For diagrams, use LibreOffice Draw or draw.io.
Geogebra is handy for producing geometrical or mathematical parts of a diagram which can easily be imported into a diagram in SVG or PDF format.
Note that the Codecogs LaTeX equation editor can now export an image of an equation in SVG format.
If you prefer to draw diagrams “programmatically” rather than with a mouse, consider TikZ.
LibreOffice Draw is notably adept at editing PDFs (e.g. joining two PDFs into a single Figure).

Graphics tools

Draw.io - excellent online drawing program ★★★★★ B Excellent for scientific diagrams. Also has a huge amount of clip art built in.
LibreOffice Draw ★★★★ B is a good drawing programme e.g. for scientific diagrams. It is notably capable for cropping and joining PDF drawings (e.g. making a two-part Figure from two PDFs)
B Geogebra.org ★★★★★ excellent online supercharged “graphing calculator” to make graphs, animations, etc. of functions, as “applets”, which can also be combined into “Activities”. Symbolic capabilities too. In the cloud, with good export capabilities.
Ipe drawing editor ★★★★ (lightweight editor, suitable for scientific diagrams)
Inkscape drawing editor ★★★ (heavyweight)
Desmos.com ★★★ Graphing calculator, very slick and professional to use, but less sophisticated than Geogebra, However, can export graphs in SVG as well as PNG.
See also the TikZ package ★★★★ (under LaTeX above: script-driven graphics)

PDF tools

PDF-Arranger ★★★★★ B GUI tool for combining, splitting or reordering PDFs. Formerly known as PDF Shuffler. (Linux)
PDF Toolkit (pdftk) ★★★ command-line tool for combining, splitting or reordering PDFs
NEW! pdfcrop ★★★★★ command-line tool for cropping white space from the edges of a PDF Figure (comes with e.g. TeXLive)
Okular PDF reader ★★★★ B a good all-round PDF viewer for Linux which can be used to annotate PDFs
The Evince PDF reader ★★★ B (the built-in Document Viewer in Gnome/Ubuntu) is also a fairly good PDF viewer for Linux which can now annotate PDFs
On Macs, the built-in Preview viewer ★★★★ B is a great PDF viewer and annotation tool
NEW! Easy PDF ★★★★ Online PDF conversion to editable Excel, Word, etc.
LibreOffice Draw ★★★★ is very capable for cropping and joining PDF drawings (e.g. making a two-part Figure from two PDFs)

Python (a programming language)

B My brief advice for beginners on getting started with Python

Install and use the Anaconda distribution of Python 3 on your computer, even if your operating system comes with its own version of Python: Anaconda properly sets up everything you need for scientific computing in Python 3, including python, numpy, scipy, matplotlib, ipython, jupyter and spyder. Anaconda uses the conda package manager (rather than pip).
Try working with Python in a Jupyter Notebook (see below)
Try some examples (focusing on NumPy and Matplotlib) from the tutorials below.
Use Python 3. Python 2 is obsolete.

Official web site

The Python language ★★★★

Python distributions

The Anaconda Python distribution Comprehensive, easy to use and fast ★★★★★ B Uses the conda package management system (in preference to pip)
Python and associated libraries and tools are also available as Ubuntu packages ★★★★

Python code development tools

The IPython “shell” (optimised for numerical and graphical Python use from the terminal) ★★★★
Also the closely related Jupyter console and Jupyter qtconsole ★★★★ which are more advanced versions of iPython
The Spyder development environment (works well with IPython) ★★★★
Visual Studio Code editor ★★★★ comes with excellent Python extensions and is very popular for general Python code development. Open-source, originally from Microsoft. Can read and write Jupyter notebooks directly, to some extent.
See also Jupyter (Notebooks and JupyterLab) below (Jupyter comes from the IPython people)

Jupyter Notebooks and Jupyter Lab

Jupyter notebooks for Python ★★★★★ B (great for recording research, experimenting with code, and for tutorial use). The Anaconda Python distribution has it all set up nicely for you. The newer JupyterLab (which is replacing the older Jupyter Notebook user interface) is particularly recommended; the notebook file format is common to both.
NEW! Video guide to JupyterLab ★★★★★ B
NEW! Google Colab online hosting of Jupyter Notebooks ★★★★★ B (also known as Google Colaboratory). Works with your Google Drive. Collaborative editing.
NEW! Microsoft Azure online Jupyter Notebook hosting ★★★★ Similar to, but not quite as good as, Google Colab.
NEW! Example Jupyter notebooks from Google Colab ★★★★★ Excellent. (A few things, such as widgets, are specific to Google Colab, but most are general.)
NEW! Binder ★★★★★ online Jupyter Notebook hosting for GitHub repositories. Allows users to run Jupyter notebooks from GitHub repositories in the cloud, without Python installed locally.

Some favourite Python libraries, modules and add-ons

NumPy numerical libraries ★★★★★ B Very important huge library for fast numerical calculations. Also includes useful links to other major packages for scientific computing.
- Official NumPy tutorials ★★★★★ B
SciPy numerical libraries ★★★★
MatPlotLib scientific graphics ★★★★★
Numba ★★★★★ (wonderful automatic generation of fast compiled C code from Python functions)
Pandas ★★★★★ Excellent library for reading, analysing, plotting and writing data (including spreadsheet and CSV read/write)
Cython ★★★★ (generates fast compiled C code from Python with some manual modification)
F2py ★★★ for calling fast, compiled Fortran subroutines from Python(part of SciPy)

Tutorials and books

The (official) Python tutorial ★★★★ B
List of numerous Python tutorials ★★
Python “cheat sheet” (quick reference) ★★★
NumPy/MatPlotLib “cheat sheet” ★★★★
NEW! MIT Computer Science “The missing semester” ★★★★ Tutorials on practical computing, including version control, debugging and profiling
Dive into Python (free e-book) ★★★
NEW! Effective MatPlotLib ★★★★
NEW! The book “Elegant SciPy ★★★ Free text and examples of this book
Whirlwind Tour of Python (free e-book, registration required) ★★★ …
- … with its associated Jupyter Notebooks ★★★
Commercial books on Python for science (Amazon UK links):
- Effective Computation in Physics: Field Guide to Research with Python ★★★★★ B
- High Performance Python ★★★★ (2nd editiion 2020)
- Python in a Nutshell: A Desktop Quick Reference ★★★
Lectures on scientific computing using Python (based on Jupyter notebooks) ★★★★★ B
- including (among others) Excellent tutorial on Matplotlib in Jupyter Notebooks ★★★★★ B
Matplotlib (scientific graphics) tutorial (2-hour video) ★★
Comparison of NumPy commands with Fortran and MATLAB ★★
Ben Dudson’s Python course ★★★
Python: Introduction for Absolute Beginners (course notes) ★★
Python: Introduction for (scientific) Programmers (course notes) ★★
Python: Interoperation with Fortran ★★ (course notes)
High Performance Python I tutorial ★★ (3-hour video)
High Performance Python II tutorial ★★ (3-hour video)
Using the Python profiler, cProfile (to identify performance bottlenecks) ★★★
The Python Programming Wikibook ★★★★ B
UPDATED! SciPy lecture notes ★★★★ B
Software Carpentry tutorials ★★★
Python course (Cambridge Engineering) via online Microsoft Azure Jupyter Notebooks ★★★★
Python course at CodeAcademy (Not yet star-rated)
The book “Python Data Science Handbook“ (O’Reilly) in the form of free online Jupyter Notebooks ★★★★★ including excellent chapters on MatPlotLib and NumPy
NEW! Effective Computation in Physics GitHub site ★★★★★ Much excellent material (tutorials, exercises, code examples from the book) associated with the splendid Python-based book Effective Computation in Physics (see above)
NEW! The Hitchhiker’s Guide to Python ★★★★ A substantial web site with lots of helpful content and links
NEW! Video lectures on Python (principally aimed at economists) ★★★★
NEW! YouTube channel Python Programmer (Giles McMullen) ★★★★
NEW! The Modern Lab Notebook: Scientific computing with Jupyter and Python ★★★★ Clear YouTube video tutorials totalling 2 hours (2019), including NumPy and Pandas.
NEW! Tips on Interactive High Performance Computing ★★★★
NEW! Pandas introductory guide (official) ★★★★★
NEW! Pandas cheat sheet (official) ★★★★★
NEW! Python Practice Problems for Beginner Coders (from UC Berkeley) ★★★★ (plus links to further resources)

Forums and blogs

Python (tag on StackOverflow) ★★★
Matplotlib graphics library (tag on StackOverflow) ★★★★
NumPy numerical libraries (tag on StackOverflow) ★★★★
SciPy numerical libraries (tag on StackOverflow) ★★★

Linux (an operating system)

B My brief advice for beginners on getting started with Linux:

Download Ubuntu and make a bootable USB stick
Use the USB stick to try out Ubuntu, and if you like it, to install Ubuntu on your computer (either alongside or in place of the existing operating system)
For less powerful computers (e.g. more than 5 years old), I recommend you try Lubuntu, a lightweight version of Ubuntu

Official sites

Ubuntu ★★★★ B
Ubuntu packages site ★★★★
GNU Bash shell reference manual ★★★★

Some favourite Ubuntu packages (details in the Ubuntu packages site above and, in some cases, elsewhere on the present page)

abiword asymptote geany geany-plugins gfortran glabels grace gufw ipe latexdiff latexmk meld okular pandoc pdfarranger pdftk retext texlive-full texmaker w3m openssh-server
Install with “apt-get install …” or using the Ubuntu Software Centre

Tutorials

Phil Hasnip’s Introduction to Linux ★★★★
Linux command line reference (brief) ★★★
PC World beginners’ guide to Linux ★★★★ B
Wikibooks Linux Guide ★★★
Linux.com Beginners’ Guide ★★★ B (very brief)
I’d like to list more tutorials here, especially for beginners: I’d welcome suggestions

Forums and blogs

Ask Ubuntu (StackExchange) ★★★★
Linux (tag on StackOverflow) ★★★
Linux Today ★★★

Online tools

Regular expression visualiser for grep, perl, etc. ★★★
NEW! Regular expression analysis/testing online ★★★★★

Miscellaneous

Bibliography tools, DOIs

doi.org: resolve a DOI into the online publication ★★★★★ (edit the URL to replace the DOI 10.1103/PhysRevB.99.161102 with yours)
Crossref.org tool to convert a list of references to their DOIs ★★★★★
Crossref.org flexible search for references (returns DOIs, BibTeX .bib, etc.) ★★★★
DOI2Bib: DOI to BibTeX .bib conversion ★★★★
A Python API to convert DOI to BibTeX .bib ★★
NEW! Bibtex.com ★★★★★ (A clear guide to BibTeX .bib and .sty files and how to use them)
NEW! Bibliography converters from Bibtex.com ★★★★★ A useful set of online tools for converting e.g. DoIs to .bib entries)
See also BiBTeX- and BibLaTeX-related items in LaTeX section above

Writing

Online RSS readers (“news-feed” readers)

Feedly ★★★★ B

Online text tools (occasionally useful from phones and tablets)

TextMechanic ★★★ Sort, extract columns, etc.
Mergely ★★★★ B Online diff/meld to compare/merge two texts
Online Text Tools ★★★★ Sort, merge columns, etc.
IDEone ★★ Online coding environment: execute small programs (Awk, Sed [via bash], Perl, Fortran, Python, etc.) online
(See also Online LaTeX tools above)

Online HTML tools

HTML link checker ★★★★
HTML Tidy ★★★★
HTML validator ★★★
HTML editor ★★★★ B
HTML Instant editor ★★
URL decode/encode tool ★★★★ Useful for converting all those “%20”s into spaces, etc.
LaTeX word count tool ★★★★ Various options for choosing what/how to count

Lightweight markup languages (for later conversion to HTML or LaTeX), and associated tools

Markdown
- Extended Markdown (as supported by Pandoc) ★★★★ a very good basic markup language
- Markdown guide from GitHub ★★★★★ B
- GitHub Markdown documentation ★★★★
reStructuredText (RST) ★★★ a less lightweight markup language
The Pandoc document converter ★★★★★ for converting between Markdown, RST, LaTeX, HTML, Word, etc.
ReText editor ★★★★ for editing Markdown/RST on Linux
VS Code editor ★★★★ B this general-purpose editor has a Markdown preview mode
IA Writer editor ★★★★ for editing Markdown/text on iPhone, iPad or Mac and converting to HTML etc. (commercial)
Markdown LaTeX package ★★★★ permits direct inclusion of Markdown text in a LaTeX document.
NEW! Stackedit.io online Markdown editor ★★★★★ Supports LaTeX math. Excellent.
NEW! Hackmd.io online collaborative Markdown editor ★★★★ Supports LaTeX math. Simultaneous collaborative editors.
NEW! Dillinger.io online Markdown editor ★★ OK but LaTeX math support uses unusual double-dollar syntax

Computer algebra and symbolic graphing calculators

B Wolfram Alpha ★★★★ Highly intelligent engine for doing calculus, plotting (static) graphs, etc. Free version can sometimes run out of steam.
SymPy ★★★★ Python’s symbolic algebra package. Now rather powerful. Like Mathematica and Maple, there is something of a learning curve, but the combination of symbolic algebra with Python’s numerical libraries and familiar programmability make for a useful combination. A good choice for users for whose problems Wolfram Alpha has run out of steam, especially those with prior experience of Python.
Geogebra.org ★★★★ Excellent super-powerful graphing calculator including animated graphs, extensive symbolic capabilities, LaTeX, SVG export. Online in the cloud, or apps available for iOS, Mac, etc.
Wolfram Development Platform ★★★ Intermediate between Wolfram Alpha and Mathematica. Powerful, though documentation chaotic. Note “free-form” input is flexible, like Wolfram Alpha. Requires free registration.
Symbolab ★★★ Basic graphing plus some symbolic capabilities.
See also the well-known (and very complex) commercial packages Mathematica and Maple available on UoY Windows PCs (and also via the UoY browser-based York Desktop Service).

Development tools

Geany editor ★★★★★ B (code/text editor and lightweight integrated development environment with excellent plugins)
VS Code editor ★★★★ comes with excellent extensions and is very popular for general code development. Open-source, originally from Microsoft.
For Python-specific development environments, see earlier, e.g. Spyder.

Funding of Open Source software

NumFOCUS.org ★★★★★ Charitable funding of significant open-source projects. Their lists of sponsored and affiliated projects signify Python libraries that are likely to be around for a while.

Version control

The Git home page ★★★★ for code development
The “Pro Git” book ★★★★ free online
Version Control with Git ★★★★ tutorial from Software Carpentry
Git Quick Reference ★★★★ from Software Carpentry
Note the gitk and git-gui visual tools ★★★★ B (part of the Git installation, for browsing and committing, respectively)
A list of further visual tools for Git ★★★

Connectivity tools

SSH secure shell terminal connection ★★★★ B (Built into Linux and MacOS; ssh -X recommended)
SFTP/SCP secure shell file transfer ★★★ (Built into Linux and MacOS)
SFTP/SCP secure shell file transfer via Nautilus file browser ★★★★★ B (Built into Linux)
Cyberduck SFTP/SCP file transfer app ★★★★★ B (for MacOS)

Online network tools (DNS etc.)

NEW! DNSchecker ★★★★ Get all DNS records for a domain, presented in a clear, convenient list
NEW! MX Toolbox ★★★★ Query many different aspects of an internet domain or computer
NEW! Whois.com ★★★ Look up “whois” info about an internet domain

General references on numerical methods

NAG Fortran Library manual ★★★★ (HTML and PDF formats; see in particular the excellent Chapter Introductions which are relevant to all numerical computation)
Numerical Recipes books ★★★ (including Fortran versions of the book available free of charge)

Awaiting categorisation and/or analysis

None at present

LaTeX (a document preparation system)

B My brief advice for beginners on getting started with LaTeX

Tutorials

Documentation

Some favourite LaTeX packages

LaTeX editors

LaTeX distributions (to install on your own computer)

Bibliography tools for LaTeX

Other tools for use with LaTeX

Online LaTeX tools

Forums and blogs

Graphics and PDF tools

B My brief advice for beginners on preparing scientific graphics:

Graphics tools

PDF tools

Python (a programming language)

B My brief advice for beginners on getting started with Python

Official web site

Python distributions

Python code development tools

Jupyter Notebooks and Jupyter Lab

Some favourite Python libraries, modules and add-ons

Tutorials and books

Forums and blogs

Linux (an operating system)

B My brief advice for beginners on getting started with Linux:

Official sites

Some favourite Ubuntu packages (details in the Ubuntu packages site above and, in some cases, elsewhere on the present page)

Tutorials

Forums and blogs

Online tools

Collaboration and communication tools

Collaborative editing tools

Project management tools

Videoconferencing

Miscellaneous

Bibliography tools, DOIs

Writing

Online RSS readers (“news-feed” readers)

Online text tools (occasionally useful from phones and tablets)

Online HTML tools

Lightweight markup languages (for later conversion to HTML or LaTeX), and associated tools

Computer algebra and symbolic graphing calculators

Development tools

Funding of Open Source software

Version control

Connectivity tools

Online network tools (DNS etc.)

General references on numerical methods

Awaiting categorisation and/or analysis