Case of GAMS software in the pharmaceutical industry - for high-throughput screening scheduling software
This article is translated by China Science Software Network
High-throughput screening is a scientific experimental method widely used in drug research, especially in the field of drug discovery. Because a large number of promising new drugs are difficult to analyze manually, the screening process is automated using robots. An automated screening system is used to treat microplates containing compounds. These automated screening systems can perform a series of tasks and experiments (called detection protocols) on a given set of microplates and generate experimental data.
CyBio was incorporated into Analytik Jena AG in 2009, and the Max Planck Institute Magdeburg developed an optimization method using GAMS to increase the throughput of robotic screening systems. Optimization of the GAMS-driven detection method greatly increases the production speed of high-throughput screening systems and improves the quality of experimental data.
problem
GAMS analysis optimization is an integral part of the CyBio scheduler, and until then, only experts were able to modify the time to increase throughput. This method only works for relatively small trials and is a task that takes hours to focus on. With the increasing complexity of inspection protocols, this task is now far beyond what humans can handle.
Another common problem is that an algebraic model describes the screening system to reduce idle time before focusing on the efficiency of the screening system to utilize key resources. Due to deposition, decay or temperature drift, the idle time of the compound can also cause systematic errors in the experimental data.
Setting
The central part of CyBio Scheduler is an algebraic model written in GAMS. It describes a screening system that minimizes idle time for all components to ensure the most efficient use of critical resources. Multiple resources can be used to accomplish different tasks, so the screening system can use other idle devices to process a large number of micro-boards at the same time. Short and direct micro-boards promote efficient use of resources, which increases productivity. The model avoids conflicts when coordinating resource access and ensures that the resulting schedule is unlocked.
Many constraints are inherent to the system, such as limited temporary storage or resources that cannot be used simultaneously and resources that must be accessed. Some constraints are specific to the analysis. Typically, the user defines the target time for the latency, including the upper and lower boundaries, or the maximum time interval between specific events. Thus, for example, the time between compound addition and measurement may be limited. Analysis definitions and these constraints create a system of separation inequalities.
Due to strict time requirements, the micro-board follows the same process every cycle. Fast and uniform microplate processing and CyBio scheduler reduce system errors due to deposition, attenuation or temperature drift, which is difficult to quantify. As a result, increased throughput not only reduces the investment per experiment, but also improves data quality.
User-friendliness
Users can free themselves from system layout decisions and focus on experimentation.
As the GAMS model runs in the background, CyBio Scheduler focuses on providing a simple and convenient user experience. It hides the complexity of mapping an analysis protocol to the current system design and finds a global optimal solution for the target to minimize cycle time.
Users can free themselves from system layout decisions and can focus on this experiment. CyBio Scheduler automatically inserts micro-board transfers where they need to resolve resource allocation conflicts, allowing for latent and easy assignment. Depending on the number of independent tasks, the components involved, and the constraints involved, the resulting model can be quite complex. The optimal solution is usually calculated fast enough for the user to verify that certain constraints can be relaxed in order to get better results.
For more information about GAMS software, please visit China Science Software Network
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