Biocurious is a weblog about biology, quantified.

Mac software for molecular biology

by PhilipJ on 10 May 2006

Warning, hardcore Apple nerdery to follow.

Not being a molecular biologists myself, I was painfully unaware of the kind of software molecular biologists use on Macs to do the kinds of things they have to do: plan out restriction digests for DNA, create oligos for PCR reactions, sequence DNA, etc. Well, having worked in a collaborator’s lab for a few months, it turns out they weren’t super sure either. At least on the DNA analysis front a lot of people were stuck using Classic (that is, OS 9) applications. These are slow and painful to use. The other software I was able to find was all written in Java, which as a rule is pretty slow and painful to use too. Then I stumbled across Mek & Tosj’s website.

Two grad students at the Netherlands Cancer Institute, they’ve been writing kickass software (for proof, Apple invited them to the World Wide Developer Conference in ‘04 where they won an Apple design award for the best student project!) for molecular biologists, and are giving it away for free! Finally, native-OS X applications that work like OS X applications should. It is wonderful. I’ve since gotten rid of all my old sequence analysis and restriction mapping software and replaced it with EnzymeX, which has also made all the various company catalogs obsolete. It can do full DNA sequence analysis for restriction digests, plan out reactions, and has (as far as I know) all the nucleases and associated info (which buffer to use, do I need to add BSA, can these two enzymes cut at the same time, or do I need to cut in sequence?). Goodbye NEB catalogue.

In addition to EnzymeX, there’s iRNAi, LabAssistant, 4Peaks, BioCocoa, and some Dashboard widgets that I highly recommend checking out. And people say there’s no software for macs!

  1. Sandra Porter    3943 days ago    #

    No software for Macs??

    You guys need to check out FinchTV. The URL is

    And yes, I am biased, but it’s a pretty nice tool for viewing chromats and editing.

    Cn3D from the NCBI is pretty nice, too.

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