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This thesis presents Dibby, a program toolkit for disulphide bond mapping in proteins from tandem mass spectrometry data.

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A slightly improved thesis template

What's new:

  • modern packages (biblatex, cleveref, better fonts)
  • less confusing directory structure
  • slightly more useful examples (figures, diagrams, tables, code listings), structure hints, some goodies
  • autobuilding of abstract PDF/A files from metadata
  • multiple variants of the front page
    • MFF with the new logo
    • "traditional" UK variant
    • Nature faculty & bioinformatics
  • Czech localization with nicely named references
  • Dockerized & CI build options

See the pre-built version for details

CI configuration

The repository contains valid configuration for both GitLab CI and the GitHub actions. No matter what GIT hosting you use, you can always download latest version of your thesis right from the artifacts!

How-to

  1. Type make, check that everything compiles. You should get a thesis.pdf that passes the PDF/A validation. If not, complain.
  2. Fill in metadata.tex and all xmpdata files.
  3. Look at the example code (there are several hints), remember it, erase it.
  4. Write the thesis.
  5. Submit and defend the thesis.

Installing LaTeX

LaTeX installation may be hard (especially on various substandard operating systems). On most BSD and GNU-style Linux distributions, it should be sufficient to install some random texlive-* packages (and add more if non-standard TeX functionality is required); see e.g. a complete list for Debian.

Optionally, you can use a Docker container with TeX. You can either build the image yourself from the supplied Dockerfile:

cd docker
docker build -t betterthesis/latex .

...or get some pre-built one (which is usually much faster: image size )

docker pull aergus/latex

After that, you should be able to compile the thesis using this command (change the container name to betterthesis/latex in case you built it yourself):

docker run -u $UID -ti --rm -v $PWD:/th -w /th aergus/latex make

PDF/A

With a bit of luck, you should get a valid PDF/A right out of LaTeX.

A PDF/A validator that can point out exact problems is available here: https://github.com/mff-cuni-cz/cuni-thesis-validator

Common PDF/A problems include:

Solutions:

  • use pdfa.sh to convert the imported picture PDFs to PDF/A-compatible form the "hard way" (although this does not retain the PDF/A metadata mark, see comments in the script)
  • read the commentary by Martin Mareš (that describes most of the common problems) here: https://mj.ucw.cz/vyuka/bc/pdfaq.html
  • as a last resort if everything other fails, use pdfa.sh for the whole thesis.pdf

Ideas/improvements/more examples?

Pull requests welcome.

License?

Parts of the code (esp. the title page) are based on the original template (available from the faculty website) by Martin Mareš, Arnošt Komárek, and Michal Kulich. (Thanks!)

University and faculty logos are a property of the respective universities and faculties.

Everything else in this repository is released into the public domain, not encumbered by any kind of copyright at all.

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This thesis presents Dibby, a program toolkit for disulphide bond mapping in proteins from tandem mass spectrometry data.

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