The software space of science

TL;DR

This study maps the landscape of scientific software use across disciplines by analyzing 1.3 million publications, revealing structured communities of tools and their disciplinary clustering.

Contribution

It constructs a network of software tools based on co-usage in research, identifying functional communities and disciplinary patterns over time.

Findings

Tools cluster into 8 functional communities.

Disciplinary tool portfolios are stable and distinct.

Fields with mixed workflows use multiple tool communities.

Abstract

Science advances not only through the accumulation of facts but also through the evolution of tools. Crucially, tools are rarely used in isolation. They form tool portfolios, combinations shaped by a discipline's workflows and analytical demands. Software, near-ubiquitous in modern research and traceable across the published literature, offers a unique window to study tool use in science. Here, we map the software space of science by analyzing mentions to software from 1.3 million publications from 2004 to 2021. We construct a network of 520 software tools linked by disciplinary co-usage, with link strength weighted by proximity based on revealed comparative advantage. This network reveals a structured landscape in which tools cluster into 8 functional communities, including computing and statistics, wet lab instrumentation, and several bioinformatics specializations, with each discipline occupying a distinct position reflecting its characteristic tool portfolios. The breadth of a discipline's tool portfolio is shaped by the nature of its research workflow: fields combining experimental and computational tasks draw on multiple communities, while those with narrower methodological demands concentrate in one. These structural differences are stable across the observation period. At the same time, across all broad disciplinary categories, disciplinary tool portfolios are crystallizing, settling on a common set of tools.