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.

翻译：科学的进步不仅依赖于事实的积累，更源自工具的演进。关键的是，工具极少被孤立使用，它们形成工具组合——由学科工作流程与分析需求共同塑造的配置组合。软件作为现代研究中近乎无处不在、且可通过已发表文献追溯的要素，为研究科学中的工具使用提供了独特视角。本文通过分析2004年至2021年间130万篇出版物中提及的软件，绘制了科学领域的软件空间图谱。我们构建了一个包含520个软件工具的网络，这些工具通过学科共同使用关系相连接，连接强度依据显性比较优势测算的邻近度进行加权。该网络揭示出一个具有清晰结构的景观：工具聚类为8个功能群落，包括计算与统计学、湿实验室仪器设备以及多个生物信息学专业领域，每个学科因其特有的工具组合而占据独特位置。学科工具组合的广度由其研究工作流程的性质决定：融合实验与计算任务的领域会跨越多重群落，而方法论需求较窄的领域则集中于单一群落。这些结构差异在整个观测期内保持稳定。与此同时，在所有宏观学科类别中，各学科的工具组合正逐步结晶固化，趋向于一致的工具集。