Abstract
Computational models and methods take an ever more important place in modern scientific research. At the same time, they are becoming ever more complex, to the point that many such models and methods can no longer be adequately described in the narrative of a traditional journal article. Often they exist only as part of scientific software tools, which causes two important problems: (1) software tools are much more complex than the models and methods they embed, making the latter unnecessarily difficult to understand, (2) software tools depend on minute details of the computing environment they were written for, making them difficult to deploy and often completely unusable after a few years. This article addresses the second problem, based on the experience gained from the development and use of a platform specifically designed to facilitate the integration of computational methods into the scientific record.
Highlights
In the course of a few decades, computers have become essential tools in scientific research and have profoundly changed the way scientists work with data and with theoretical models
The challenge for future ActivePapers developments is to facilitate the transition of computational methods from subroutines hidden inside software tools to precise specifications that become part of the scientific record
As I have pointed out earlier[21], today’s scientific software fulfills two distinct roles: it is a tool that permits doing computations, and the only precise and complete description of the models and methods applied in these computations
Summary
In the course of a few decades, computers have become essential tools in scientific research and have profoundly changed the way scientists work with data and with theoretical models. Each publication has one or more ActivePaper files deposited as supplementary material, but all the files are available in digital repositories with DOIs. Among the published ActivePapers, there are software libraries[50,51], a database of protein structures[52], and combinations of datasets and code that document computational studies[53,54,55]. The alternative would have been to publish each MD trajectory separately as an ActivePaper, and use DOI-based references in the analysis step to refer to this data Because such references are nearly transparent to the user (the dependencies are downloaded automatically when needed), file size limits apply in practice only to individual HDF5 datasets. The challenge for future ActivePapers developments is to facilitate the transition of computational methods from subroutines hidden inside software tools to precise specifications that become part of the scientific record
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