I am currently working on a paper in the field of image reconstruction, or computational biology if you will. Now matter how I slice or dice it, it is one of these stories that cannot be told in 3500 words or so. Not only are there several equally important methodological points that need to be discussed to get a complete story, there is also quite a bit of background required to point out the subtle flaws in the currently popular ways of approaching this particular problem; and it takes some words to clearly point out what may appear to be a subtle problem from a distance, especially while making sure to be fair to everyone.
I don't intend to butcher what I feel is a solid and profound story for the sake of cramming it into some word budget. I am no fan of needless verbosity, but I really am going to need about 20 pages to do this right. I strongly prefer to publish in an open access journal. And I would imagine that an open access online journal does not have as much of an incentive to be stingy with word counts, no? PLOS computational biology would be a logical choice, yet they do have a restrictive word count. I can't find any open access journals that appear to be sympathetic to my plight.
Am I missing something? Or should I just write the whole article first, make that into the supplement, and then write a 3000 word teaser with nonstop references to the supplement to substantiate my claims? I am somewhat afraid that people will actually miss the point without an explicit disclaimer at the start of the 'article', along the lines of 'hey, if you want to read the actual story with a good flow to it, you need to start reading the supplement. this is basically just a drawn out abstract.'. If you are referring to the supplement, the convention is to refer to a figure of secondary importance; not to three pages of text you kind of have to read first to understand the rest of the article.
Does anyone have a helpful perspective on such a situation?