Another blog about academic workflow I’m afraid – not that I’ve blogged on this before but I’ve finally nailed down my preferred “pipeline” for producing papers, reports and what-have-you and felt I’d share mine.
Mendelay has it’s flaws, but it’s my preferred citation/pdf manager. It automatically parses an internal database of my citations and references into a bibtex file that I can then use when writing. Simple. But there are some irritations and complications with this approach when you try to use the bibtex file for a proper paper, report or thesis such as the meta-info extraction returning poorly formatted conference and Journal titles.
Standardised Journal/Conference names
Mendelay has had this on it’s “todo” list for a long time now. Jabref amongst others, allow you to define abbreviated journal names for it to scan for and replace with the full title you specify. Perfect for ensuring your references are in order. But since Mendelay regenerates my master bib file on the fly whenever a change is made (or I delete it), I wrote a small batch file for Windows that concatenates my abbreviations list with the bibtex file, into a newly useable version.
Abbreviations in Jabref work by first defining the abbreviation in the bibtex file, then referencing the abbreviation by placing #ABBR# in the relevant field when editting an entry. The #’s are rather important it appears, and you can use this method presumably in different field types, not just “booktitle” or “journal”.
For example, here’s an example entry of an abbreviation in a bibtex file, particularly note the curly braces:
@STRING{ACCV = {Asian Conference on Computer Vision}}The problem is this stuff has to be IN the bibtex, and Mendelay regenerates that file every time it updates it, removing your additions.
In my workflow, I ignore Mendelay’s (often spurious) meta-data extraction for the Journal or conference proceedings field and enter #ACCV# directly in the using Mendelay. This ensures that the abbreviation is propagated to the mid-level bibtex file (you must tell Mendelay not to escape LaTeX chars otherwise you’ll end up with more slashes than necessary). I get around having to manually insert all my abbreviations by keeping an abbreviation text file next to the bibfile and using this code to join them and generate a new file I work from.
more abbrevs_v2.txt > temp.txt type temp.txt library.bib > new_library.bib del temp.txt
So now I’m left with this, much nicer method of writing:
Edit stuff in Mendelay, read, review, add citations etc; >> Run batch file to generate abbreviation friendly file >> use new file in TeXworks.
command for a particular symbol, try 
. Good to know.
means:
)-ish calc notation
means:
and 
denote A is a subset of B. However, 
is more properly used to denote a proper subset. (
should refer to a vector of values for x indexed at 1 and of m length, that is a subset of real numbers. However, 
would refer instead to the Cartesian product of n copies of R, i.e. essentially an n-length cartesian coordinate describing a point in n-dimensional space. That is to say, when used in the context of the above example, we are now looking at a vector of coordinates in n-dimensional space, where i is a number between 1 and m, and 
is a cartesian coordinate describing a point in space.
means:
where the value of 
is between 1 and 10.
means:
and you multiply each value instead of summing it.
means:
means:
refers to:
means:
means:
means:
means:
are used to denote a Matrix. Lowercase roman letters denote variables or vectors, such as in: 
means the probability that y is equal to 1, given x parameterised by theta, is 0.7
x is distributed as N(params).