UltraScan Software Maintenance and Development

描述（由申请人提供）：UltraScan是一个综合软件包，用于分析超离心和光散射实验的水动力数据。这些实验的数据提供了对参与活细胞过程的大分子之间动态相互作用的深入了解，并允许他们在最接近细胞生理条件的溶液状态下进行研究。目前涉及UltraScan的研究主要集中在疾病和癌症中大分子特性的作用，如聚集，以及对蛋白质、RNA和DNA等生物聚合物的结构和功能的基本理解。UltraScan软件在学术和工业环境中拥有超过1200名注册用户，在全球范围内不断增长。有了这笔拨款，我们寻求资金来确保软件的持续维护和进一步发展。提出以下新项目：开发接口，将最近商业化的荧光光学系统和新的AU-AOS分析超离心机数据采集系统集成到UltraScan中。我们还建议开发新的分析算法，以解决可逆关联，实时分析和异质关联系统动力学分析。我们将为在somo中提出的构象头建模方法提供接口，并推进蒙特卡罗方法、遗传算法优化和二维谱分析的并行计算。此外，我们建议开发新的方法来改进非线性最小二乘优化，将软件移植到新的平台，并使UltraScan适应第三方库和编译器的变化。为了促进UltraScan源代码的GPL发行版的协作，我们将增强源代码文档并扩展用户手册。要求提供额外资金，以支持通过讲习班和在线研讨会对UltraScan用户进行培训和教育的倡议。这里提出的工作将提供软件工具，以促进生物物理和生物化学研究的高分辨率分析，解决疾病的分子基础。例如，它可能为识别与神经退行性疾病有关的致病蛋白提供线索，或者为表征与癌症等疾病有关的蛋白质和核酸之间的相互作用提供线索。

DESCRIPTION (provided by applicant): UltraScan is a comprehensive software package for the analysis of hydrodynamic data from analytical ultracentrifugation and light scattering experiments. Data from such experiments provide insight into the dynamic interactions among macromolecules involved in the processes of the living cell, and allow their study in the solution state which most closely resemble the physiological conditions in the cell. Current studies involving UltraScan focus on the role of macromolecular properties involved in disease and cancer, such as aggregation, and focus on the basic understanding of structure and function of biological polymers like proteins, RNA and DNA. The UltraScan software enjoys a worldwide and growing distribution with over 1200 registered users in academic and industrial environments. With this grant we seek funding to ensure the continued maintenance and further development of the software. The following new projects are proposed: Development of interfaces to integrate the recently commercialized Fluorescence Optical System and the new AU-AOS data acquisition system for the analytical ultracentrifuge into UltraScan. We also propose the development of novel analysis algorithms addressing reversible association, real-time analysis, and the analysis of kinetics in heteroassociating systems. We will provide an interface for the conformational bead modeling approaches proposed in SO MO, and advance parallel computation of Monte Carlo approaches, genetic algorithm optimizations, and the 2-dimensional spectrum analysis. Further, we propose to develop novel approaches for improved nonlinear least squares optimization, to port the software to new platforms and to adapt UltraScan to changes in third-party libraries and compilers. To facilitate collaboration of our GPL release of the source code for UltraScan we will enhance the documentation of source code and expand the user manual. Additional funds are requested to support initiatives for training and education of UltraScan users through workshops and online seminars. The work proposed here will provide software tools that will facilitate high resolution analysis of biophysical and biochemical research addressing the molecular basis of diseases. For example, it may provide clues to identifying pathogenic proteins involved in neurodegenerative diseases, or in the characterization of interactions between proteins and nucleic acids involved in diseases such as cancer.