ActivePapers: a platform for publishing and archiving computer-aided research

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.

Bringing Molecular Dynamics Simulation Data into View

“…We believe a particularly important step will be the integration of interactive visualization of MD trajectories into reviewing processes and ultimately journal policies that have a major impact on the research behavior of individual scientists [48]. Recently established journal formats such as ActivePapers [49] or the Living Journal of Computational Molecular Science (https://www. livecomsjournal.org/) already foster interactive web-based publications.…”

Best practice data life cycle approaches for the life sciences

“…Other tools can act as or be combined to produce notebooks for small standalone code-based projects (see 66 and update), including Jupyter Notebook, Rmarkdown, and Docker. However, it remains a challenge to implement online laboratory notebooks to cover both field/lab work and computer-based work, especially when computer work is extensive, involved and non-modular 51 . Currently, no best-practice guidelines or minimum information standards exist for use of electronic laboratory notebooks 6 .…”

Storing Reproducible Results from Computational Experiments using Scientific Python Packages

“…Several tools for keeping track of provenance and aiding in adhering to best practices for reproducible research already exist, e.g. Sumatra [Dav12], ActivePapers [Hin15], or Madagascar [Fom15]. Tools like Sumatra, ActivePapers, and Madagascar generally function as reproducibility frameworks.…”

“…Thus, one may ask: How are the results and the metadata stored, and how may they be accessed later on? For example, Sumatra by default stores all metadata in a SQLite database [Dav12] separate from simulation results (which may be stored in any format) whereas ActivePapers stores the metadata along with the results in an HDF5 database [Hin15]. The idea of storing (or "caching") intermediate results and metadata along with the final results has also been pursued in another study [PE09].…”

“…A plethora of related alternative tools exist for aiding in making results reproducible. We have already discussed ActivePapers [Hin15], Sumatra [Dav12], and Madagascar [Fom15] which are general reproducibility frameworks that allow for wrapping most tools -not only Python based computations. Such tools are definitely excellent for some workflows.…”