> so I try the viki script, which works fine
> [...]
> What I don't like with viki is the inability to make a real wiki
> editable with a browser from the files, and vice-versa.

IMHO you have 3 options:

#1
Put all text files on a shared folder both you and your director/
supervisor have access to and edit them with vim. In this scenario,
viki (or a similar plugin) would be ok.

#2
Use a plain text server-based wiki like dokuwiki. You could then sync
the plain text files on the server with your local copies but still be
able to edit them via a browser. There are a few dokuwiki plugins
around that convert dokuwiki markup to something else.

#3
Use a web-based wiki only. If you use firefox, you could use
extensions like ViewSourceWith to edit the file with vim -- and use an
appropriate syntax style.

> and after that, I write a paper using latex, and need to cite the
> different that I read (I use latex + bibtex for this).

If you use viki, you could also use the deplate converter which
converts viki markup to html/latex/dokbook etc. and is capable of
handling citations via bibtex, footnotes etc. For math, you could
still use embedded latex markup.

> - Do you know some guide to organize your work

I personally use option #1. I use custom bibtex fields to link to the
summaries writting in viki markup and to the pdf documents etc. --
those fields are ignored by the usual bibtex styles. VikiMinorMode
makes those links clickable. I search the bibtex file for appropriate
keywords etc. The summaries are collected in a directory (the filename
is the bibtex key) so that they can be easily searched with grep etc.
I don't use the web-browser to edit those files. Usually I carry
around some device (laptop, netbook, handheld etc.) that contains all
those files. I use unison to sync all those text files between
different computers/devices.

Disclosure of interests: I'm the author of viki & deplate.


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