So far, I puplished a paper (literature review) using the "classical" structure: Introduction-Method-Results-Discussion-Conclusion.

At the moment I am writing another paper which presents the result of our developments of a simulation approach. The paper should contain the following parts:

  1. Literature study
  2. Description of the mathematical theory behind some methods
  3. How we implemented (2) into the actual modeling language
  4. Use cases

My question: How would you structure (+ name) the sections? My first idea was:

  • Introduction (including lit-review)?
  • Method (does the description of the mathematical theory belong to that section?)?
  • Implementation?
  • Results?
  • Conclusion?

Two more specific questions:

  1. In which section would you place the description of the tool (f.i. a certain Matlab package)? In the "Introduction/lit-rev" section? Or in the "Implementation" section?
  2. It is necessary to compare two fundamental modelling approaches (in order to motivate why we use one of them): Where would you place this section? In the section method, or lit-rev?

Thank you very much for your help!

closed as off-topic by gman, Brian Tompsett - 汤莱恩, Bob Brown, Scott Seidman, Buzz Nov 1 '16 at 0:56

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It depends on your target audience, but my inclination would be to say that unless you're specifically targeting an audience that would be interested in the detailed implementation (say, computer science), the means by which you implemented the theoretical model may not be sufficiently interesting to include in the main text. With that in mind, I'd recommend the following structure:

  • Introduction
  • Methods
    • Theoretical Model
      • Reference to the appendix for implementation details
    • Use Cases
  • Results of use cases
    • Confirmation of model validity with use cases
    • Novel findings produced by the model
  • Conclusions
  • Appendix (or supplemental material, depending on the journal's requirements)
    • Details of implementation
    • Public location where source code will be available following publication

This structure comes with the caveat that I work in a field where models are valued for their ability to generate new findings, and are of lesser interest when they don't advance the state of knowledge within the field. If your field is more interested in the implementation details you may want to go with your original layout and place the implementation description within the main text.

As for the other questions, I would describe the model in detail in the methods section, and compare the modelling approaches broadly in the introduction (with the bare minimum amount of detail to justify your new approach), and specifically in the methods, with an emphasis on why your approach addresses a weakness of the previous approach.

  • I like the detail in @significance 's answer, I'd recommend accepting that response. – Adam Bosen Nov 1 '16 at 0:42

As an editorial board member of a modelling journal, I broadly agree with @Adam_Bosen. I'd structure it something like this:

  • Introduction
    • Why it matters
    • Use cases
    • Lit review
    • Existing mathematical theory that you are using
  • Methods
    • New mathematical theory that you are developing
    • Description of your model (including all equations if there aren't too many, or with any but the most novel equations relegated to an Appendix if it is a complicated model). Mention the language of implementation if it is a modelling journal, but not the actual code. If it's for a disciplinary science journal, less detail here.
    • Details of testing procedures (e.g. how you compare it with other models, sensitivity analysis, performance characterisation methods).
    • Technical details of use cases (e.g. scenarios)
  • Results
    • Results of testing procedures
    • Results of use cases
  • Discussion
    • What you learnt about the use cases
    • Strengths and limitations of your new approach
    • Next steps and remaining challenges
  • Conclusion
    • How good is your model and what does it add to the stat of the art?
  • Appendices (optional)
    • Full equations
    • Model code
    • Data used

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