My general purpose bioinformatics toolbox

I spend most of my time writing code and using an range of bioinformatics analysis packages. Unlike in many other professions, sometimes  there are no best tools for accomplishing a bioinformatics task. The tools are continuously improved and the choice of tools is dependent on the research question and the biology of whatever you are investigating. However  I have come to rely on some general purpose resources that make me more productive. Let me introduce you to my general purpose spanner box.

Code Editing


I have finally found nirvana in MacVim, which is the preferred version of  Vim for Mac OS. It allows screen splitting, window resizing and integrates with the console, such that you can run system commands right in the editor. You have to install the necessary scripts or plugins to support what you want to do.

It has increased my productivity, although it has a slightly steep learning curve.  This is a tool I recommend to any bioinformatician, if you are not already using it!

Cost: Free

Source Control


Git Source control

I use git for source control. It is awesome and fits very well with my workflow. Git has powerful features and easy to use and work with. I like the idea of distributed source control and it makes it easier to work on different versions of the same project!

Cost: Free

Bibliography manager



I use Papers, which is a commercial tool but I would recommend it to anyone. It helps me sort,annotate and read research articles. I once used Mendeley, which is an awesome tool as well.

Cost: $42 (has academic discounts)




One of the best tools which we may forget is a tool is the terminal! Since I use Mac OS, I enjoy the best of both worlds, a powerful Unix command line support, excellent graphics and support for proprietary software if need arises.



Pilot V Ball RT Pen


I don’t keep an electronic notebook since I prefer jotting down my notes and having a Notebook. I use a liquid ink Pilot V ball RT pen. The pen has a retractable cone-tip liquid ink rollerball, rubber grip and metal pocket clip. It is airplane-safe and writes a 0.4mm line. 

Cost: $5



D66174 NoteBook

My preference for a notebook is an  A4  D66174 Notebook.  Each book has about 180 pages.  It comes with a protective handcover. This is an archive for my written thoughts, discussions and workflows.

Cost $90 for a pack of five books.

What is your general purpose  bioinformatics toolbox?


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