Ultimately, a scientific experiment is performed because a scientist expects that experiment to provide some insight into the functioning of a real biological system. Achieving deep understanding requires experiment data from many different methodologies to be integrated and evaluated in the context of a biological pathway.
This form of pathway analytics has traditionally required programming in math languages and manual curation of data, which has made computational biology nearly impossible for most bench scientists.
TDS Biological Modeler is a visual application to import biological models and schematically specify biological pathways for analyzing experimental data.
TDS Biological Modeler uses the same underlying model-driven informatics platform as TDS Protocol Modeler to enable the direct linkage between experiment data collected in the lab and analysis of data in biological pathway models.
TDS Biological Modeler is designed to allow easy reuse of pathway models and data from many sources, including KEGG, SBML, Affymetrix, and MAGEML.
Figure 3 shows a model of the EGF signaling pathway in TDS Biological Modeler. Rate constants, references, and expression data can all be stored in the same model of the pathway, and easily exported into other analysis packages.
TDS Biological Modeler's chemical network simulation capabilities have also proved useful for modeling and refining experimental assays. By providing detailed kinetic simulations of expected assay behavior, an assay model can validate that an assay is performing as expected, and optimize assay design by simulating the response to different experimental conditions.
To specify a series of chemical reactions in Biological Modeler, a scientist needs only to drag and drop icons onto the canvas to represent the chemical species and reactions of interest, define the connections, and specify the rate constants and mechanism of each reaction.
TDS Biological Modeler can then automatically translate the graphical model into an ODE-based mathematical representation and perform a simulation of the system's kinetics. This feature makes kinetic modeling more accessible to the large fraction of bench scientists lacking a formal training in mathematical modeling.
Additionally, the package provides several advanced model-based analysis capabilities. For example, a scientist might explore a model's behavior by scripting a large number of different simulation runs, and then saving the parameters for the most interesting simulations for more detailed study.
Built-in optimization algorithms allow scientists to estimate parameters of assay or biological models using actual experimental data. Finally, the TDS allows computational biologists to add their own analysis algorithms to the TDS Biological Modeler.
Discovery is challenged by constantly changing data requirements and increasing analytics complexity. Teranode Design Suite provides XDA functionality to enable labs to flexibly design and automate experiments. TDS accomplishes this by providing data management and computational analytics in a visual environment without the need for programming.
The benefit is that scientists can use computational biology at the bench to enable higher-value physical experiments that match the pace of research.