Software · Built by Paul
Tools I built for the bench.
Calculators, analysis tools and workspaces for everyday lab work, plus desktop apps for the heavier imaging and instrument data in my own research.
Free tools that run in your browser
Nothing to install. Your data stays on your computer.
Bench Arcade
Nineteen free, browser-only tools for everyday bench work: plasmids, primers, buffers, dilutions, cell culture, qPCR, plate reader curves, gel and image analysis, mass spec peaks, CRISPR guides, statistics and more.
How it works →Gel Bench
Quantify SDS-PAGE and Western blot gels in your browser, with lane finding, band boxes, background subtraction, normalization and exports. Nothing is uploaded.
How it works →Clone Bench
Plasmid maps with annotation checks, diagnostic digests on a virtual gel, primer design and Sanger verification, running Biopython in your browser with your analyses saved.
How it works →Bench Mate
A personal lab workspace for protocols, notebook entries, freezer inventory, plasmid records and everyday bench calculations, stored locally in your browser.
How it works →RNAseq Bench Web
A private, browser-only single-cell RNA-seq workspace for QC, clustering, marker genes and interactive visualization. Your files never leave your device.
How it works →Desktop apps
For full-resolution images and raw instrument files too large for a web page.
Lamin Mesh Analyzer
Traces the nuclear lamin meshwork from full-resolution microscopy images and measures the area of every mesh opening.
How it works →MassSpec Bench
A workspace for targeted LC-MS: quantification, chromatogram review, calibration, QC and report generation.
How it works →Structure Bench
Brings AlphaFold models, experimental structures, variants, domains and confidence scores into one view.
How it works →IHCq
Chromogenic IHC quantification: finds every nucleus, scores DAB cell by cell in the nuclear, membrane or cytoplasmic compartment, and reports H-score, % positive with a confidence interval, Allred, IRS, HER2 (ASCO/CAP) and hotspots.
How it works →Paper Reader
A reading desk for scientific papers: a built-in guide pulls out the findings, every figure with its panels and statistics, the methods and abbreviations, and an optional Claude breakdown explains each figure in plain language.
How it works →Cell Surveillance
Follows every nucleus through a live-cell movie of a nuclear reporter and measures nuclear membrane ruptures, movement, divisions and deaths cell by cell, with a rupture threshold you set and export of any region you draw.
How it works →Recode Detector
Tests whether a proteomics run supports an alternative genetic code. It compares searches against a standard and an alternative protein database, shows which version of each protein the peptides support at every changed position, goes back to the raw Thermo or mzML data to check the actual fragmentation spectra against shuffled decoys, reports coverage and quality checks, saves every run, and writes a plain-English PDF report.
How it works →Codon Atlas
Predicts the genetic code from a genome sequence and searches it for alternative decoding. It aligns a six-frame translation to Pfam protein families and, for each of the 64 codons, works out which amino acid the conserved positions it lands on expect (the Codetta method), then flags reassigned codons, stop codons inside conserved domains, and the tRNAs that could read each codon, lists every affected site in the genes, and exports the protein databases needed to test a reassignment by proteomics.
How it works →PRIDE Packager
Prepares a proteomics dataset for deposition in PRIDE / ProteomeXchange, step by step. It recognises raw files from every vendor and the output of common search software, works out whether the dataset can be a COMPLETE submission, creates what is missing (mzTab and mzIdentML from a DIA-NN report with every identification pointing at its MS/MS spectrum, mzML peak lists from Thermo raw files, SHA-1 checksums, the submission summary and an SDRF sample sheet), checks everything PRIDE's validator checks, and builds one folder ready to upload with PRIDE's own Submission Tool.
How it works →Python Lab
An interactive course that teaches Python to biologists with no programming experience, from the first print() to writing their own lab software. Every lesson is short, ties a concept to bench work, and ends with an exercise that runs real Python on your computer and checks itself, building up to complete tools for sequences, qPCR, growth curves and sequencing reads.
How it works →BioCanvas
A scientific-figure studio on your Mac: journal-size artboards, 5,000+ free science icons with their licences tracked, science drawing tools, ready-made templates, and export to vector PDF and SVG.
How it works →