Demonstration on writing a paper with a reference data base

Biologists writing papers and grants not only use word processors, they use reference data bases. Consider the differences in how citations appear [a] in the paper and [b] in the references. Examples:
(1) J. Biol. Chem., [a] (author, date), [b] numbered, alphabetized, most information but not title.
(2) The FASEB J., [a] (number), [b] numbered, but in order of appearance, all information.
Also, there are many variations on style, like whether the date is in parentheses and whether the volume is bold.

Suppose that for 5-10 years, a PI (principal investigator) is working in a sufficiently restricted area that (s)he cites many of the same papers in the references of many papers or grants. Suppose also that these are submitted to several journals and agencies. Or even considder, perish the thought, that J. Biol. Chem. rejects your paper but you want to try to publish it in the FASEB Journal. You could spend a lot of time re-typing the references in a different specific format. In order to avoid this tedious chore, references are typed one time and maintained in a reference data base where the program (here we will demonstrate Endnote) can be used to set the style for a particular journal. It is also possible these days (though we will not demonstrate it this time) to obtain the reference from the National Library of Medicine (and thus not to have to type it into your data base at all). If the style of a particular journal of interest is not in the menu, you can make your own.

Demo: Write a little text using Word. In the old days, people always typed The phrase "The quick brown fox jumps over the lazy dog" to test typewriters because it used all the letters in the alphabet. Go to EndNote. Click on a reference. Pull down under edit and copy. Click over to Word and pick a place you want to paste this reference. Note that all that shows up is author, year, and a #number identifying the data base entry, all in parentheses. The parentheses signal the program that that is a reference. Save the Word. Go to Endnote. Pick a style under styles. Under paper, pull down to scan and get a window. The number 1 is good, 0 means you have used parentheses for something other than a reference which is no real problem, 2 or more means that Endnote cannot determine which reference you mean (and that is a problem). Pull down under paper to format and it will default to save a Word file with your name followed by the journal you selected. Now click to WordPerfect and open this new paper and note that the references are added at the end and, in the text, the citations are made in a way that is used for that journal.

A mini-PhotoShop demo

The following will be demonstrated:
Open, select, copy, new (defaults to the right size), paste
Change the size (For web, 700 or les wide or 500 or less high is good.)
Move
Free transform, apply
Background, layers, flatten
Type tool, color, size, etc


This page was last updated 8/23/06

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