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.

  • 263 tools listed
  • 20 categories
  • 224 free or open source

263 tools

Consano

A crowdfunding platform for individuals to donate to medical research projects.

FundingPlanningFREE
New2026
Consensus logo

Consensus

AI Evidence Search Engine for Scientific Claims

AI Research AssistantDiscoveryFREE, SUBSCRIPTION

CORE

Aggregator of open access research papers for researchers and repositories.

DiscoveryPublishingOPEN SOURCE

Crossmark

Quick and easy access to the current status of an item of content. 

PublishingFREE

CrossRef

Search metadata records for journal articles, field-specific, for software.

DiscoveryPublishingFREE

Crossref Funder Registry

DiscoveryFundingOPEN SOURCE
New2026
CryoSPARC logo

CryoSPARC

Cryo-EM Structure Determination

AnalysisBioinformaticsFREE FOR ACADEMIC USE

Crystal

General-purpose program for the study of crystalline solids.

DiscoveryFREE

Cytoscape

Network Data Integration, Analysis, and Visualization in a Box.

AnalysisVisualizationOPEN SOURCE

Data One

Find data from affiliated member repositories

DiscoveryPlanningFREE

DataBank

An analysis and visualisation tool that contains collections of time series data.

DiscoveryOPEN SOURCE

Dataverse

Open source research data repository software

AnalysisCodeFREE OPEN SOURCE

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?

Tell us what your lab runs on. Listing is free and we do not take payment for placement.

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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.