Evaluating a novel cloud-based software platform for linking data and structured experimental designs
Year: 2018
Type: supplementary-materials
Abstract: ‘Open data’ science requires precise definition of experimental procedures used in data generation, but traditional practices for sharing protocols and data cannot provide the required data contextualization. Here, we explore implementation, in an academic research setting, of a novel cloud-based software system designed to address this challenge. The software supports systematic definition of experimental procedures as visual processes, acquisition and analysis of primary data, and linking of data and procedures in machine-computable form. The software was tested on a set of quantitative microbial-physiology experiments. Though time-intensive, definition of experimental procedures in the software enabled much more precise, unambiguous definitions of experiments than conventional protocols. Once defined, processes were easily reusable and composable into more complex experimental flows. Automatic coupling of process definitions to experimental data enables immediate identification of correlations between procedural details, intended and unintended experimental perturbations, and experimental outcomes. Software-based experiment descriptions could ultimately replace terse and ambiguous ‘Materials and Methods’ sections in scientific journals, thus promoting reproducibility and reusability of published studies. The tested software is Riffyn, and this dataset contains 1) the JMP scripts used for automatic data analysis, 2) PDF printouts of the shake-flask and batch bioreactor as well as chemostat processes designed in Riffyn, 3) all experimental data gathered as processed and extracted with Riffyn and 4) an export of the complete process descriptions as JSON objects for computable use by external software applications, as exported from Riffyn.
Source: Figshare
Language: English
Subfield: Information Systems and Management
Field: Decision Sciences
Domain: Social Sciences
Open Access status: green
OpenAlex ID: W6902554630