Table of Contents
Index
Glossary
Table of Contents
Index
Glossary

  
m3 METHODS

In the Methods module, an account is given of the response of the authors to the problem described in the module Central problem: `tools' have been selected or developed, and applied to that problem. The Methods section of linear articles in the domain of experimental sciences predominantly deals with the experimental methods, particularly with the set-up. The Methods module defined in the modular model provides an account of all methods that were used:

The module METHODS contains a description and discussion of the different (experimental, numerical and theoretical) methods used to solve the central problem in the article, including their restrictions.

Authors have at their disposal `toolboxes', which contain the theoretical, experimental and numerical methods and tools available at the time they did the research. Consequently, they can apply existing methods, with or without adaptation, to the situation at hand. The information on these existing methods may have been published elsewhere. In that case, a Methods module can just provide a link to that published module, instead of repeating the description and discussion of the method represented in that existing module.

When a new method that is likely to be used in later research is presented in an article, the information should be represented in such a way that the module can easily be used in subsequent articles, by the same authors or by other authors. For example, a report on an experimental set-up is provided elsewhere, in a module designed for multiple use, and included in the article at hand by link. However, the article-specific measurement parameters are described in the individual article itself.

When more than one method is used in the article, which is generally the case, the Methods module is a complex module consisting of constituent modules focusing on those different methods. The typology by the conceptual function of the information distinguishes between experimental, numerical and theoretical methods. The different methods can be the components of an aggregate `complete method', in which case the complex Methods module is a  compound module. In the case that various specific types of methods are used in parallel, the Methods module is a  cluster module.

In the Methods module, sufficient information is made available to allow in principle even the least informed members of the target audience to understand, accept and reproduce the methods. That implies that the restrictions of the methods must be included.

m3a Experimental methods  

The module EXPERIMENTAL METHODS contains:

• a report on the experimental set-up (general scheme and specific instrumentation) used in this work;
• a report on the measurement procedure for generating experimental data using the set-up;
• a report on the restrictions of the experimental methods, e.g. with respect to the range and precision of the measurements;
• optional argumentation on the reliability and on the relevance of the experimental methods.

The general modular model allows for a further distinction, for specific domains, of this module into a constituent module focusing on the set-up and one focusing on the measurement procedure. In the domains of biochemistry and medicine, for instance, measurements are often carried out following highly standardised protocols, which are explicitly given in  journals like Bioorganic & Medicinal Chemistry.

m3b Numerical methods 

The module NUMERICAL METHODS contains:

• a report on the tools from the `numerical toolbox' that were used in this work (i.e. the computer hardware and software and the algorithms);
• a report on the parameters and procedures used to generate the data using the numerical tools;
• a report on the restrictions of the numerical methods, e.g. pertaining to the precision and speed;
• optional argumentation on the reliability and on the relevance of the numerical methods.

Numerical methods can be used to do `experiments on the computer', or to approximate other calculations, like integrations, that cannot be executed analytically.

m3c Theoretical methods  

The module THEORETICAL METHODS contains:

• a report on the tools (e.g. models and theories) from the standard `theoretical toolbox' used in this work;
• a report on the calculations performed using these theoretical tools to generate theoretical data;
• a report on the restrictions of the theoretical methods, e.g. with respect to higher-order terms;
• optional argumentation on the reliability and on the relevance of the theoretical methods.

In response to the central problem at hand, theoretical methods can be used to provide a qualitative explanation of observed phenomena or to calculate quantitative theoretical results. The `theoretical toolbox' contains the existing theories and models, theoretical assumptions and approximations. We consider data analysis techniques to be part of the theoretical toolbox.

The module Theoretical methods gives an account of the theoretical methods, including their restrictions, which pertain to the assumptions made in the model and the calculations, such as neglecting higher order terms. Apart from a report on the theoretical methods, the choices that were made can be justified in this module, in order to convince the reader of the reliability of the theoretical methods and their applicability in the situation at hand or in other situations.