Many bioinformatics tools are written to be run on a Linux computer using the command line. Learning how to use Linux at the command line is an extremely worthwhile use of time, and a valuable skill for any scientist. While we offer training which is focused on command-line Linux, it is often desirable to make a tool more widely available to the broader scientific community.

We are able to develop both novel tools, and web-based interfaces to pre-existing tools to address bioinformatic requirements. Our preferred web development environment is the bootstrap framework which permits rapid development of interfaces which are compatible with all major browsers.

Relevant Examples

RNAit2: A re-implementation of the RNAit tool for RNAi design in Trypanosomes using HTML5 and python

Bioinformatics analysis typically does not require running a single program, but a series of different tools which need to be run in the correct order using appropriate parameters for the task in question. The tools involved can not necessarily read the data format produced by the preceding step in the process, consequently there may be intermediate file format conversions or indexing required. While such analysis is practical with small numbers of samples, larger scale projects require a degree of automation to make the process tractable.

Development of semi-automated pipelines permits the scaling-up of analysis, can improve the reproducibility of research and allows analysis process to be readily shared. While this can also simplify the process of running an analysis, it is important that the analyst has a solid understanding of the tasks being undertaken by a workflow, and can examine and interpret the results from the different stages of the pipeline to identify any problems with the data or the analysis. Such pipelines should not therefore be treated as black boxes, but more as convenience methods to aid in running analysis.

Many projects involving DAG staff utilise automated pipelines, and we can develop pipelines customised to specific analyses. We will be producing workflows for a range of standard bioinformatics analysis in the coming months, which will be freely available and integrated into our training program.

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