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January 15, 2009 (Vol. 29, No. 2)

Minimizing Challenges in Biological Modeling

SimBiology Software Provides a Platform for Model Creation, Stimulation, and Analysis

  • Modeling has long played a key role in the drug discovery process, from isolating drug targets to screening and pharmacokinetics. Many pharmaceutical companies are currently facing patent expirations without replacement candidates in the pipeline or are struggling with high candidate attrition. Leaner pipelines result in necessary cost decreases, which can often lead to staff reductions. These struggles underscore the need for successful modeling in pharmaceutical R&D.

    As a result of this elevated intensity, the needs of pharma modelers have also drastically increased. In general, pharma modelers face two main tasks: first, to complete their projects quickly and second, to communicate their results to their peers in the scientific community and to corporate managers.

    Modelers spend a great deal of time integrating various tools into their workflow to create a piecemeal solution that fits their needs. They use one tool to model data, another to perform simulation, and perhaps yet another tool for analysis. Once they have results, researchers will spend an even larger amount of time transferring the results into a format that scientists or executives will understand. This workflow is inefficient and an expensive waste of time.

    Creation of MathWorks'  SimBiology software was driven by customer demand to provide a modeling environment that minimizes this inefficiency. Modelers can perform their entire project workflow in a single environment, from creating a model to simulation and analysis. The interface is graphical so modelers have a pathway diagram to easily communicate with scientists and management, yet the underlying technology is mathematically strong to meet modelers’ needs.

  • Method of Operation

    SimBiology offers several different modes of interaction, all of which are fully integrated. The SimBiology desktop is a customizable graphical user interface (GUI) that offers a point-and-click environment for modeling. Modelers can move windows around the desktop using drag and drop or menu selections.

    Within the desktop, the block diagram editor allows users to work with the graphical view of their model in a drag-and-drop environment. This includes a library of predefined blocks users can use to create models. Lastly, for modelers who prefer to automate their modeling and analysis, all functionality can also be accessed from the command line.

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