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Molecular Cloning Designer Simulator

By Zhenyu Shi, Please cite our publication if you use MCDS

Abstract: With the development of synthetic biology, DNA manipulation is becoming more and more complex. Although a number of software programs have been devoted to molecular cloning design,few of them are able to perform project level design, simulation, and management, and the vector map-based management lacks the overview of the whole project, flexibility in design and the ability to handling genetic recombineering or to guide wet bench work. Hereby, we developed a new powerful all-in-one software platform with every design, simulation and experiment procedure organized in flowchart. It can design, simulate, manage and record most of the cloning techniques in general molecular cloning, genetic engineering and synthetic biology including recombinant DNA technology, SLIC (Sequence and Ligation Independent Cloning), Golden Gate, Gateway Cloning, Gibson isothermal assembly, yeast recombinant, site-specific recombination and integration, PhiC31 assembly, Lambda Red knockout/knockin, CRISPR digestion, and consequently allows the tracking and management of those experiments.

MCDS is currently an open source software. You can find its source codes in GitHub

.Net Framework 4.6 must be installed before running MCDS.

  • Download .Net Framework 4.6 from this link
      • Windows 10 users should already have .NET Framework 4.6 included in the OS. Follow this link for more information.
  • Download MCDS from GitHub
  • Videos: How to use MCDS
    • MCDS aims to set up a standard way for designing, describing and simulating molecular cloning and genetic engineering.
    • MCDS can design primers, simulate restriction enzyme digestion, gel electrophoresis, Gateway cloning, BioBrick assembly, Gibson assembly, yeast assembly, φC31 (or other) site-specific recombination and assembly, lambda red knockout/knockin, homologous recombination, CRISPR digestion. MCDS allows users to customize restriction enzymes, site-specific recombination sites, gRNAs.
    • MCDS can manage and track every molecular cloning and genetic engineering operation in a unique flowchart, which can be printed or exported as emf vector image. The flowchart of MCDS includes all necessary information including PCR primers, product length restriction enzyme sites and even digestion buffers (users can customize support for digestion buffers).
    • MCDS supports GeneBank formats, AB1 formats (and can display sequencing data) and provides embedded access to NCBI and KEGG.

The following is an example of the printed flowchart. You can also see the print file here.