Software

Hitman's fall

Dalzeil (Dark/Light): Single function to toggle between light and dark modes of the user interface. It can live in your dock, providing instant access to the interface switch. There are more sophisticated solutions available, but this is really simple and free. [Download]

The Coulson plot generator: An open source Java application for creating a multiple pie diagram and comparing subunit occupancy across a range of entities as shown at left. Numbers of pies, segments, labels and colors are customizable. CPG creates an editable PDF from a comma separated text file (.csv), and has zoom capability for larger datasets. The format is especially useful for visualizing patterns in big data. Originally developed for comparative genomics, the Coulson plot is also appropriate for display of other hierarchical data. The format was conceived by Richard M. Coulson and coded as an application by Helen Field. Icon designed by MCF. Available as binary or source code at GitHub.

RNAit2: Web-based tool for identification of primers for RNAi in kinetoplastids. The software uses Primer3 to predict suitable primers for PCR, and then checks that the predicted product has no off-target potential. Data are returned for the user to assess, settings are customizable. RNAit was originally developed by Seth Redmond and the present iteration has been recoded by James Abbott at the University of Dundee and runs with a python backend within a virtual machine; your data are therefore completely secure. RNAit2 source code available at GitHub.

If you use CPG or RNAit in a publication, please cite as follows:

Field, H.I., Coulson, R.M.R., and Field, M.C., (2013) ‘An automated graphics tool for comparative genomics: The Coulson plot generator.’ BMC Bioinformatics 14 141

Redmond, S., Vadivelu, J., and Field, M.C., (2003) ‘RNAit: An automated web-based tool for the selection of RNAi targets in Trypanosoma brucei.’ Molecular and Biochemical Parasitology 128 115 - 118