UltraScan Software Maintenance and Development

UltraScan软件维护和开发

• 批准号: 7405994
• 负责人: BORRIES DEMELER
• 金额: $ 28.65万
• 依托单位: UNIVERSITY OF TEXAS HLTH SCIENCE CENTER
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-04-15 至 2011-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7405994
• 关键词: Acceleration; Accounting; Address; Algorithms; Architecture; Biochemical; Biological; Biological Models; Biological Process; Calibration; Cells; Class; Classification; Collaborations; Collection; Commit; Communication; Communities; Compatible; Complex; Complex Mixtures; Computer software; Condition; DNA; Data; Data Analyses; Data Files; Data Set; Data Storage and Retrieval; Databases; Degenerative Disorder; Development; Diffusion; Dimerization; Disease; Dissociation; Documentation; Educational process of instructing; Educational workshop; Elements; Ensure; Environment; Equation; Equilibrium; Experimental Models; Extensible Markup Language; Facility Construction Funding Category; Feedback; Fluorescence; Funding; Genetic Programming; Goals; Grant; Heterogeneity; Individual; Information Systems; Internet; Isomerism; Italy; Kinetics; Label; Language; Learning; Least-Squares Analysis; Letters; Libraries; Licensing; Life; Linux; Maintenance; Malignant Neoplasms; Manuals; Maps; Methods; Modeling; Molecular; Molecular Conformation; Molecular Weight; Monitor; Monte Carlo Method; Names; Neurodegenerative Disorders; Noise; Nucleic Acids; Numbers; Operating System; Optics; Participant; Personal Satisfaction; Physiological; Pliability; Polymers; Positioning Attribute; Principal Investigator; Probability; Procedures; Process; Property; Proteins; Publishing; RNA; Range; Research; Research Personnel; Resolution; Roentgen Rays; Role; Running; Scanning; Scheme; Scotland; Sedimentation process; Shapes; Signal Transduction; Simulate; Software Tools; Solutions; Source; Source Code; Spectrum Analysis; Speed; Structure; System; Teaching Materials; Testing; Time; Training; Training and Education; Translating; Translations; United States National Institutes of Health; Universities; Update; Variant; Work; analytical ultracentrifugation; base; cluster computing; data acquisition; data modeling; detector; expiration; foreign language; graphical user interface; improved; innovation; insight; instrument; instrumentation; light scattering; macromolecule; new technology; novel; novel strategies; online tutorial; open source; parallel computing; polymerization; portability; programs; protein aggregation; research study; sedimentation coefficient; sedimentation equilibrium; sedimentation velocity; simulation; size; software development; solute; stoichiometry; success; tool; two-dimensional; user-friendly; web interface

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.

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流体动力学数据。这些实验的数据提供了对参与活细胞过程的大分子之间的动态相互作用的深入了解，并允许在最接近细胞生理条件的溶液状态下对其进行研究。目前涉及UltraScan的研究主要集中在疾病和癌症中涉及的大分子性质的作用，例如聚集，并侧重于对蛋白质，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，分布在全球范围内并不断增长。有了这笔赠款，我们寻求资金，以确保软件的持续维护和进一步开发。提出了以下新项目：开发接口，将最近商业化的荧光光学系统和新的AU-AOS数据采集系统集成到UltraScan中，用于分析超浓缩。我们还提出了新的分析算法解决可逆协会，实时分析，并在heteroassociating系统的动力学分析的发展。我们将提供一个接口的构象珠建模方法提出的SO MO，和先进的并行计算的Monte Carlo方法，遗传算法优化，和二维光谱分析。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。为了促进我们的UltraScan源代码GPL版本的协作，我们将增强源代码的文档并扩展用户手册。请求提供更多资金，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举措。这里提出的工作将提供软件工具，这将有利于高分辨率分析的生物物理和生物化学研究解决疾病的分子基础。例如，它可以提供线索，以确定参与神经退行性疾病的致病蛋白质，或在表征蛋白质和核酸之间的相互作用参与疾病，如癌症。