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Extreme Neuromorphic Scientific Computing in the Cloud

Success depends on superior scientific and technological innovation and NeuroGen will define the future of insilico discovery.

NeuroGen is a science-focused technology platform that will advance the discovery of human therapeutics. It is the world’s first insilico discovery platform designed by biology to optimize the entire drug discovery process; from target identification and elimination to insilico forced degradation and dissolution modeling.

The NeuroGen Insilico Discovery Platform provides, among many other benefits, the following:

  • Unifying Platform: Consolidates and normalizes genomic and proteomic models from numerous public domain sources in order to improve accuracy and processing performance.
  • Genomic Reference Repository: Contains codified representations of various genomes for the purpose of comparing results and improving accuracy. The reference models are pre-loaded into cache to eliminate database calls in order to further improve processing performance.
  • Metabolic & Signaling Pathways: Improves the discovery process by including the complex networks of biochemical interactions within the NeuroGen architecture, which also improves overall performance and accuracy.
  • Genomic & Proteomic Model Optimization: Optimizes insilico representations of genomes and proteomes in order to improve performance and accuracy.
  • Process Optimization: An adaptive workflow engine that guides discovery activities and refines its own pattern repository for continual optimization of the discovery process workflow.
  • Global Regulatory Compliance Architecture: Contains codified guidance for regulatory requirements in order to ensure compliance at every step of the discovery process.
  • Insilico Forced Degradation Modeling: Simulates external stresses to screen compound stabilities for rapid selection and elimination.
  • Insilico Dissolution Modeling: Provides the ability to simulate dosage form performance in a highly compressed timeframe over traditional methods with a high degree of accuracy by drawing upon a comprehensive chemical and biological compound pattern repository.
  • Validation: Validation provides assurance that a computer system (hardware, software & communications) will function as designed and in the event of a failure, the system will react and recover in a predictable way. A sequence of operations provides comprehensive documentation of what is supposed to happen under normal conditions and a failure-mode & effects analysis determines what will happen during anomalous conditions.

The following describes in more detail, some of the key attributes of the NeuroGen insilico drug discovery optimization platform:

The entire NeuroGen architecture down to the smallest line of script is being comprehensively documented as well as the complex matrices of dependencies among each module and each line is being mapped back to the detailed requirements specification for each component. Each component will be put through a gauntlet of performance and measurement tests to ensure speed, consistency and accuracy during execution. Validation protocols are being written for each module and the platform in its entirety, and carefully linked to the sequence of operations specification and to a comprehensive failure-mode & effects analysis.

Global Regulatory Compliance
A key component of the NeuroGen Drug Discovery Platform is our Global Regulatory Architecture (GRA) which provides guidance to each process stream according applicable regulatory requirements. The guidance issued by every major regulatory body was comprehensively interpreted and codified within NeuroGen in order to ensure compliance at every step, including the contentious and infamously vague guidance issued in 21-CFR-11 by the FDA in the United States. The GRA also complies with cGLP and cGCP guidance, where applicable.

The GRA consists of a global compliance pattern repository and a quality framework library which includes guidance for Six Sigma, ISO 9000 and others. Specific regulatory and/or quality filters are applied to the compliance evaluation criteria selected for each research project and are dynamically overlaid on the base process models within NeuroGen to guide all discovery activities according to the criteria selected. Performance metrics are calculated and validated against test & evaluation criteria in order to optimize process streams and report potential compliance deviations.

Unifying Platform
A key design attribute of the NeuroGen architecture is the Unifying Platform which consolidates and normalizes biological and chemical data from multiple public and private sources. The Unifying Platform is the first stage of optimization in that it restructures the datasets to exploit the power of the Extreme Factory™ High-Performance Cloud computing platform and provide maximum throughput.

Much of what is contained within the Unifying Platform is pre-staged which virtually eliminates database calls and thus, provides a dramatic increase in overall performance. Models that once required 30 days or longer to process can now be evaluated in milliseconds with far more accuracy and consistency.

Discovery Process Stream Models
Thousands of man-hours were spent analyzing, documenting, optimizing and codifying base-level discovery process streams in order to create an adaptive workflow engine that guides discovery activities and refines its own pattern repository for continual optimization of the discovery process workflow. The process pattern repository is utilized by various components of NeuroGen to optimize process efficiency and eliminate redundancy in geographically dispersed research teams.

Resource and Process Optimization and Management
From our inception, it was a strategic goal to optimize the efficiency by which large-scale biological computational modeling was performed. Through a tedious structural analysis and decomposition of thousands of samples, we identified numerous areas where the structure of the models could be improved upon in order to optimize the complex multi-dimensional computation associated with insilico drug discovery.

Additionally, when we analyzed the discovery process workflows, numerous deficiencies were identified in the base-level process streams and more specifically, in the “informal” processes that occur among members in a research group, especially those that are geographically dispersed. Through a comprehensive analysis of affinity relationships we identified additional opportunities to optimize work streams through collaborative modeling capabilities and process segmentation.

The solution however, required the development of our own system management and optimization capabilities. NeuroGen contains an agent-based process monitor that continually feeds performance metrics back to the resource scheduler to anticipate computational requirements based upon the complexity of the models and the number of variants being requested by members of the research team.

The process analyzer agent monitors process performance against the base-process pattern repository in order to identify improvements and eliminate redundant process steps. It also provides guidance based upon the regulatory requirements defined by the Global Regulatory Architecture. The process analyzer then pre-schedules resources and terminates them when the analysis is complete.

Insilico Forced Degradation Modeling
NeuroGen's insilico forced degradation modeling capabilities simulates external stresses to screen compound stabilities for rapid selection and elimination. Longer term storage simulations can also be modeled for inclusion in filings and submissions to regulatory bodies. insilico degradation modeling can include various stresses, including:

  • pH (acid/base): Chemical processes are often catalyzed by the presence of acids and bases. The simulated exposure of materials to these can therefore accelerate insilico degradation reactions and provide early indications of possible instabilities with reasonable predictability.
  • Temperature: NeuroGen can simulate the temperature-variance of diffusion coefficients, population of crystal vacancies, creep rates, and many other thermally-induced processes/reactions.

NeuroGen will also simulate other stresses such as Light, Oxidation and Concentration. insilico forced degradation modeling can increase safety, minimize risk, provide early insights to the likely stability of a compound, save countless hours and conserve precious research dollars. The models provide predictive degradation capabilities of scientifically relevant probability using a sophisticated hybrid Markov process algorithm.

Insilico Dissolution Modeling
Dissolution is the only indicator of continuing dosage form performance batch-to-batch over time and there has been a dramatic increase in use to document bioequivalence execution of the dissolution procedure in accordance with cGMP's and with principles of sound metrologic science.

NeuroGen provides the ability to simulate dosage form performance in a highly compressed timeframe over traditional methods with a high degree of accuracy by drawing upon a comprehensive chemical and biological compound pattern repository.

Silicon Genomics strives to serve the scientific community and society by providing innovative technologies that aid researchers in transforming the promise of science and biotechnology into therapies that have the power to restore health or even save lives.

NeuroGen was designed to help our clients move scientific breakthroughs from insilico discovery to the lab through the clinic to the marketplace and to support other aspects of their business. Our clients success depends on superior scientific and technological innovation and NeuroGen is leading the practice of insilico discovery.

However, we compete against time and past performance to rapidly achieve high quality results and cannot be lulled into complacency by previous achievements. Silicon Genomics is committed to continuing the rapid evolution of NeuroGen and a mindset that "the best is never good enough" when it comes to developing the tools to facilitate the development of life-saving human therapeutics.

Download the NeuroGen Fact Sheet and read our latest Research entitled "Towards insilico Science".