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

Before the Abstract

A science communication blog and podcast by Springer Nature

PublishingFREE

BenchFly

Create and host unique science videos.

Lab WorkPAID

Benchling

Transform your R&D with the industry's most widely adopted Life Sciences R&D Cloud.

AnalysisDiscoveryFREE

Bibliogo

Free reference management and collaboration tool that allows users to search an online catalog of millions of documents.

FundingPlanningFREE

BibSonomy

Online social sharing of bookmarks & lists of literature in a collaborative way

DiscoveryPublishingFREE

Biocompare

An online review resource of lab equipment for the world's scientific community.

DiscoveryPublishingFREE
Bioconductor logo

Bioconductor

R Packages for Genomic Analysis

AnalysisBioinformaticsFREE, OPEN SOURCE

Bioicons

AnalysisVisualizationOPENS SOURCE
Biomni logo

Biomni

General-Purpose Biomedical AI Agent

AI Research AssistantAnalysisFREE
Biopython logo

Biopython

Python Tools for Computational Biology

AnalysisBioinformaticsFREE, OPEN SOURCE

BioRender

Visual Communication Tool for Modern Life Science

AnalysisVisualizationFREE, PAID SUBSCRIPTION

bioRxiv

bioRxiv is an open access preprint repository for the biological sciences

PublishingWritingFREE

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.