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Updated: Feb 14, 2026

Improving Student Outcomes with an Adaptable Molecular Cloning Course-Based Undergraduate Research Experience
Published on: November 15, 2024
Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation
Zhenyu Shi1, Claudia E Vickers1
1Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia.
Abstract:
Molecular Cloning Designer Simulator (MCDS) is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2) it can perform a user-defined workflow of cloning steps in a single execution of the software; (3) it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and (5) it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com.
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