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Before you start, tell Bog where things are.

(setq bog-notes-directory (expand-file-name "./")
      bog-bib-directory (expand-file-name "../bibs")
      bog-file-directory (expand-file-name "../citekey-files")
      bog-stage-directory) (expand-file-name "../stage")

Now start Bog with M-x bog-mode or

(bog-mode 1)

The rest of this file is an example of how notes can be structured.

Books

dominik2010org

The Org Mode 7 Reference Manual - Organize your life with GNU Emacs

http://dl.acm.org/citation.cfm?id=1952135

The BibTeX files are stored in bog-bib-directory. You can open the file for the current heading with bog-find-citekey-bib (C-c " b).

Reproducible research

hinsen2011data

A data and code model for reproducible research and executable papers

doi:10.1016/j.procs.2011.04.061

A new BibTeX file for this citekey has been downloaded to bog-stage-directory. To prepare this file (and any other BibTeX file in that directory), run bog-clean-and-rename-staged-bibs.

The BibTeX mode settings below make the automatically generated citekey match Bog’s citekey format.

(setq bibtex-autokey-year-length 4
      bibtex-autokey-titleword-length nil
      bibtex-autokey-titlewords-stretch 0
      bibtex-autokey-titlewords 1
      bibtex-autokey-year-title-separator "")

schulte2011active

Active documents with Org-mode

doi:10.1109/MCSE.2011.41

A file associated with this citekey has been downloaded to bog-stage-directory. To associate that file with this heading, run bog-rename-staged-file-to-citekey (C-c " r).

That file is now stored in bog-file-directory and can be opened with bog-find-citekey-file (C-c " f).

schulte2012multi

A multi-language computing environment for literate programming and reproducible research

http://www.jstatsoft.org/v46/i03

After a title and URL (neither of which are necessary), there will usually be notes about the paper. To refer to another study, just insert the citekey name, such as dominik2010org. This is just normal text, but many Bog commands treat it as special. Put your point on dominik2010org, and run bog-open-first-citekey-link (C-c " l).

Notes do not have to be limited to a single file. name1990word is a study in another notes file. Place the point on name1990word and run bog-goto-citekey-heading-in-notes (C-c " H) to jump to that heading.

Look at the other commands by pressing C-c " C-h.