Here's the academic reference on outlines: PDF Courtesy of Purdue University, formerly at http://owl.english.purdue.edu/handouts/general/gl_outlin.html
Use an outline to organize your ideas and writing. I suggest you adopt this approach (I liked the status report on the sections). Excerpted from Notes on Writing Papers and Theses, by Ken Lertzman, Simon Frasier University, http://aerg.canberra.edu.au/pub/aerg/edulertz.htm#nine, which has moved, but we can't find to where.
When you first start a writing project, make an outline of the major headings. List the key ideas to be covered under each heading. Organize your thinking and the logic of your arguments at this level, not when you are trying to write complete, grammat ical, and elegant sentences. Separate out the three tasks of: (1) figuring out what you want to say, (2) planning the order and logic of your arguments, and (3) crating the exact language in which you will express your ideas.
Many people find it useful when making an outline to attach page lengths and time lines to each subsection. For instance, section 2.4 may be "Evidence for differential use of canopy gaps by Clethrionomys." To this you might append, '3 more days analysi s, 4 days writing; 10 pages." Such time estimates are usually inaccurate, but the process of establishing them is quite useful.
It is very easy to write and expand outlines with word processors. When starting a writing project, I create a file in which I first develop an outline as described above. I save a copy of the outline separately and then commence the writing by expandi ng the outline section-by-section. I usually get ideas for later sections while writing earlier ones and can easily page down and write myself notes under later section headings. This is especially useful for filling out the structure of a Discussion whil e writing the Results. (For instance, "When discussing the removal experiment, don't forget to contrast Karamozov's 1982 paper-- his Table 3--with the astonishing results in Figure 7.") By the time I get to writing the Discussion, the outline has usually been fleshed out substantially and most of the topic sentences are present in note form.
Here's an outline you might want to start with. PDF Courtesy of Craig Jones, formerly posted at http://mri.brechmos.org/wp-content/uploads/2010/01/22/how-to-organize-a-paper/paper_outline.pdf
Here's a template in Microsoft Word, with section headings and some reminders (you'll like using Document Map, if you haven't before): http://www.esf.edu/for/yanai/publishing/paper_template.doc
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