Tools of the Trade

A curated directory of the software researchers actually use - from literature discovery and reference managers to electronic lab notebooks, analysis pipelines, imaging and the new generation of AI research tools. Every entry is written by hand, and every outbound link is checked.

  • 254 tools listed
  • 20 categories
  • 214 free or open source

254 tools

Annotated Books Online

A digital archive of early modern annotated books.

DiscoveryReference ManagementFREE, OPEN SOURCE

Annotation Studio

An open-source, a suite of collaborative web-based annotation platform.

DiscoveryPublishingFREE ,OPEN SOURCE

Aperio ImageScope

View and annotate digital pathology images.

DiscoveryPublishingFREE

Arrowsmith

Identify biologically meaningful links between two sets of Medline articles.

AnalysisDiscoveryFREE OPEN SOURCE

arXiv

arXiv is a repository of electronic preprints approved for posting after moderation, but not full peer review

PublishingFREE

Arxiv Sanity

Browse recent arXiv papers based on semantic similarity.

DiscoveryPlanningOPEN SOURCE

AsPredicted

Generates a short, time-stamped pre-registration document that is easy to share.

AnalysisDiscoveryFREE

Atomic Simulation Environment

Set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.

AnalysisPublishingOPEN SOURCE

Authorea

Online collaborative writing, citing, hosting of data and publishing.

DiscoveryReference ManagementFREE

Avogadro

Avogadro is an advanced molecule editor and visualizer

AnalysisVisualizationFREE OPEN SOURCE

Baidu Scholar

Baidu Scholar aims to become the biggest, most comprehensive research platform in China.

DiscoveryPlanningOPEN SOURCE

BASE (Bielefeld Academic Search Engine)

BASE provides more than 150 million documents, from more than 7,000 sources.

DiscoveryPlanningFREE

Built something researchers should know about?

We add tools on reader suggestions, and we list open-source projects and one-person side projects on the same terms as funded platforms. Listing is free, there is no paid placement, and we write the entry ourselves after trying the tool.

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Missing a tool?

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How entries are chosen

  • It has to be alive. Links are verified, and tools that die or get acquired into irrelevance are retired rather than left to rot.
  • Researchers have to actually use it. Adoption in real labs matters more than a polished launch page.
  • Cost is stated plainly. Free, open source, freemium or paid - including when "free for academics" comes with conditions.
  • No paid placement. Nobody buys their way onto this list, and there are no affiliate links.
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What is in here

The directory covers the whole research workflow: planning and funding, literature discovery, reference management, lab notebooks and inventory, analysis and computation, figures and visualisation, writing, publishing, and data sharing. Alongside the long-established tools you would expect, it tracks the AI workbenches and foundation models now reshaping how computational research gets done.