Insilico De Novo Reconstruction of Cellular Networks

If the organism of your choice is not yet in our model repository, Insilico offers you the de novo reconstruction of a model of the organism straight from your genomic data. This network reconstruction includes several independent data curation and model verification routines to ensure that individual reaction steps, metabolic pathways and the model as a whole are consistent and function efficiently.

Transcriptomic data, proteomic data and metabolomic data can all be integrated in the network model. These experimental data is used to validate the predictions made through the reconstructed networks e.g. on the effects of gene perturbation or on the stratified effects of a certain drug dosage. In all cases, Insilico’s deep understanding of cellular processes allows our customers to test their hypotheses not only from a quantitative point of view but also at early stages in the development process.

Service Workflow De Novo Reconstruction of Cellular Networks See what data is required and which results are obtained

To reconstruct a new predictive network models, Insilico follows a cost-efficient two-step workflow which addresses your needs in an optimum fashion.

I. De novo reconstruction

The entirety of intracellular reactions of a given cell type is incorporated into a whole-cell network model and tailored to the genetic background of the specific cell type which is of interest to our customer. For this task, Insilico combines information from public databases, primary literature, and proprietary information if desired. Every model is curated manually and undergoes a suite of tests ensuring model functionality.

Input: Annotated genome, specific cell line properties, typical media and growth conditions

Result: Genome-based network model

II. Model verification

The network model is verified by control simulations which prove that experimentally observed phenotypes can be well described. This includes potential substrates as well as products and by-products including their corresponding yield.

Input: Description of experimentally observed phenotypes

Result: Verified network model

The verified network model can subsequently be used for Cell Line Engineering and Process Optimisation.