Molecular Cloning Designer Simulator

A novel all-in-one platform of Molecular Cloning Design, Simulation and Management with unique flowchart design.
Please refer to this publication if you used MCDS in your research:

With the development of synthetic biology, DNA manipulations are becoming more and more complex. Although a number of software programs are available for molecular cloning design, they all suffer from drawbacks in the context of managing the complex cloning and genetic modification processes that are now routine in modern molecular biology. To address the current limitations, we developed a powerful new all-in-one software platform that allows project level design, simulation, and management, with a novel interactive flowchart user interface. 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 an 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; and (4) it includes experimental information to conveniently guide wet lab work and can store results and comments to allow the tracking and management of the whole project in one platform. MCDS 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 homologous recombination for DNA assembly, site-specific recombination and chromosomal integration, PhiC31 assembly, Lambda Red knock-out/knock-in, and CRISPR digestion. The flowchart organization allows straightforward tracking and management of those complex experiments.

.Net Framework 4.6 must be installed before running MCDS (If you are using Windows 8 or below).

For Windows 10, .Net Framework 4.6 is a built-in part of the OS.
Download .Net Framework 4.6 from this link:
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.

Last edited May 12 at 7:39 PM by errisy, version 22