https://github.com/irskep/thesis_papers

Don't mind me, I'm just Steve's thesis work.
https://github.com/irskep/thesis_papers

Last synced: 2 months ago
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Don't mind me, I'm just Steve's thesis work.

• Host: GitHub
• URL: https://github.com/irskep/thesis_papers
• Owner: irskep
• Created: 2011-01-24T05:07:25.000Z (over 14 years ago)
• Default Branch: master
• Last Pushed: 2012-01-17T21:48:52.000Z (over 13 years ago)
• Last Synced: 2023-04-13T11:42:27.889Z (over 2 years ago)
• Language: Python
• Homepage:
• Size: 5.6 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

          
Steve Johnson's Amazing Thesis Report

=====================================

Requirements

------------

* XeTeX (pretty version only, otherwise use `make simple`)

* `listings`

* `xspace`

* `hyperref`, `color`, `xcolor`, `xltxtra`, `xunicode`, `graphicx`, `fixltx2e`

Compiling the PDF

-----------------

Everything (3 iterations of `xelatex` and one of `bibtex`):

    > make

Just one iteration of `xelatex`:

    > make once

Use vanilla LaTeX and Computer Modern instead of Garamond/Gill Sans/Inconsolata:

    > make simple

Structure

---------

TeX basics:

* `stevejohnson_thesis.tex`: Combine all files into one document

* `formatting/`

    * `doxygen.sty`: Required for producing the iPathCase-KEGG source code

      documenation appendix

    * `setup.tex`: Import packages, configure formatting

    * `commands_and_style.tex`: define commands, configure `listings` package

* `bibliography.bib`: Information for citations and bibliography section

Content:

* `fig/`: All figures

* `background/`: Background chapter sections (`main.tex` combines them into a

  chapter)

* `basic/`

    * `abstract.tex`: Abstract. Also contains macro definitions for different

      PathCase databases because for some reason they didn't work in

      `setup.tex`.

    * `conclusion.tex`, `introduction.tex`, `literature_survey.tex`: Top-level

      chapters corresponding to their file names

    * `title.tex`: Title page

* `kegg/`: iPathCase-KEGG chapter sections (`main.tex` combines them into a

  chapter)

* `kegg_doc/`: Source code documentation appendix for iPathCase-KEGG (`all.tex`

  combines them into a chapter)

* `kegg_manual/`: Source files for generating the iPathCase-KEGG manual in both

  HTML and LaTeX format

    * `generate_html.py`: Python script to generate HTML version (LaTex version

      is generated by the third party tool MultiMarkdown)

    * `template.html`: Basic HTML template with style information

    * `template_index.html`: HTML template with manual contents inheriting from

      `template.html`

    * Various images

* `smda/`: iPathCase-SMDA chapter sections (`main.tex` combines them into a

  chapter)