Thursday 28 May 2015

How to Cite SLiMSuite programs

Most programs in the SLiMSuite package have citation instructions in their docstring. Either run with the help or help option (or if running through SLiMSuite or SeqSuite, use help=T) to bring up that information. Alternatively, the online documentation should show the papers to cite.

You can retrieve documentation for a given program by replacing slimsuite in the box below and clicking View Documentation.


If a program does not have its own citation, please cite SLiMSuite using: Edwards RJ & Palopoli N (2015): Computational Prediction of Short Linear Motifs from Protein Sequences. Methods Mol Biol. 1268:89-141.

For general use or reuse of code, please cite the Zenodo DOI for the GitHub release: DOI

External programs

See External Components of SLiMSuite for citing programs that SLiMSuite uses.

Wednesday 13 May 2015

Including the date in a log file name

It is often useful for data management purposes to include the run date in the name of a log file. One of the minor tweaks with the latest release of SeqSuite is the ability to do that automatically from the commandline (or ini file) without having to change the command. Simply include #DATE in the log=FILE command. e.g.:


If run today, for example, the log file generated would be mylog.2015-05-13.log. As well as helping record keeping, this is also a good way of having different log files for different runs whilst still using a single log=FILE command in an ini file.