Snapshot of InSilicoKO for determining a set of gene knockouts to maximize the microaerobic synthesis of R-1,2-propanediol production in Escherichia coli.
InSilicoKO was released by In Silico Fermentation in May 2024. Please continue reading this page to learn more about the application and to download this free software.
A common application of genome-scale metabolic reconstructions is microbial strain design for metabolite overproduction. Powerful computational methods for reaction/gene knockout design have been developed and made freely available through software packages such as Constraint-Based Reconstruction and Analysis (COBRA). However, effective utilization of these strain design methods requires familiarity with high-level programming languages such as MATLAB. This requirement can be a serious obstruction for industrial practitioners involved in fast-paced metabolic engineering projects.
InSilicoKO is a MATLAB application that streamlines the computational development of knockout strain designs for metabolite production. The GUI tool generates reaction/gene knockouts that maximize the secretion of a target product given a genome-scale metabolic reconstruction of the wild-type strain and user-specified constraints on the strain design algorithm. The workflow allows the definition of the growth medium (compatible with MediumFBA), the secreted metabolite to be maximized, the reactions to be included as deletion candidates, the maximum number of deleted reactions, and the minimum allowable growth rate. Any optimized strain design can be altered manually, or the entire strain design can be performed manually. The final step of the workflow is to functionally delete the identified reactions through gene knockouts, thereby ensuring a feasible design.
The following PDF file provides an overview of how InSilicoKO can be used to design a gene knockout strain to maximize the microaerobic synthesis of R-1,2-propanediol production in glucose minimal medium using Escherichia coli. The genome-scale metabolic reconstruction iML1515 available in the BIGG repository was used for this example.
InSilicoKO has the following requirements:
- Version 2021a or newer version of MATLAB.
- Installed COBRA toolbox for MATLAB.
- A linear program (LP) solver compatible with COBRA. A list of compatible LP solvers is available here. To perform optimized strain design, the LP solver must have the capability of solving mixed-integer linear program (MILP) problems. In the absence of a compatible MILP solver, only manual strain design is possible.
- Genome-scale metabolic reconstructions compatible with COBRA. InSilicoKO has been tested with selected reconstructions from the Virtual Metabolic Human resource (i.e., AGORA1 models), the BIGG repository, and the KBase platform.
InSilicoKO can be freely downloaded using the link below. The software is distributed under The GNU General Public License v3.0.
The Zip file should be processed as follows:
- Download and unzip the file using Zip archive software.
- The unzipped file will contain the following files: (1) the main application, InSilicoKO_ver_2_0.mlappinstall; (2) saved App states for a R-1,2-propanediol production strain designed using the BIGG model iML1515 and for a propionate production strain designed using the AGORA1 model Bacteroides_thetaiotaomicron_VPI_5482; and (3) exported gene knockout models for the R-1,2-propanediol and propionate production strains.
- Save the files in the desired working directory.
- To install the InSilicoKO application, go to the Apps tab on the main Matlab page and click “Install App”. Select the saved InSilicoKO_ver_2_0.mlappinstall. The InSilicoKO application will appear as a new icon in the Apps tab.
- Launch the application by clicking on the icon.
Please contact me by email if you have any questions or feedback about InSilicoKO.
