Research projects always require a degree of data production and analysis, much of which is completed using ad hoc software, such as personal scripts. Ad hoc software poses two distinct problems in systems biology (i) The degree of domain expertise required to recreate the analysis, or reuse the script is high – problematic when data and models need to be exchanged between non-domain experts; (ii) encoding an analysis technique into a script can be time consuming and error prone – this leads to a redundancy in time spent “reinventing the wheel”, and means if errors are introduced by the mistakes in the script they are hard to trace.

Developing specialised software to support production and analysis of data and models allows us to overcome these issues. (i) analysis techniques coded in a reusable program allow experts and non-experts to run the analysis without the redundancy of recoding the analysis themselves; (ii) if errors are present in an analysis technique from the software it can be identified and rectified – allowing identification of affected data and models, and reducing the likelihood of untraceable errors; (iii) Much of the standardisation of data and models could be handled automatically by dedicated software.

Specialised software in systems and synthetic biology is a key aspect of facilitating the exchange of data and models between research experts in different domains. In many instances the ability to generate analysis scripts is less important than understanding why the analysis method is valid, and how to interpret the findings. There is software in systems biology to assist with model generation (COPASI, JWSOnline, OpenCell), simulation (COPASI, JWSOnlineOpenCell, and FAME), visualisation (COPASI, JWSOnline, Cytoscape, Cell Designer). There are also specialised software available for data and model management by FAIRDOM.

If there are any other specialised software that you think should be included on this page, please contact us with details.