Synthetic biology which is inspired by “plug-and-play” concept is supported by standardized biobricks and also computational tools for analysis and optimization . Here are bio-apps collections for you. Personally Tinkercell and UNAFold are mostly used.
Suggested pages listing useful bio-apps maybe you will like in synthetic biology research:
- WikiGenes Toolbox ( http://www.wikigenes.org/e/art/e/187.html). As a free on-line tutorial edited by people all around the world, WikiGenes has spirits of Linux: open-source, sharing, interest, so is WikiGenes-Synthetic-Biology page. It enables you fast-learn what is synthetic life.
- OpenWetWare (http://openwetware.org/wiki/Computational_Tools).
- JCVI (http://www.jcvi.org/cms/research/software/#c614). This page is from J. Craig Venter Institute.
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 Marchisio, M. A., & Stelling, J. (2009). Computational design tools for synthetic biology. Current Opinion in Biotechnology, 20(4), 479-485. Retrieved from http://www.sciencedirect.com/science/article/pii/S0958166909001001