INTELLIGENT AUTOMATED RESTRICTION MAPPING TOOL

智能自动化限制图谱工具

• 批准号: 2209201
• 负责人: PETER C NELSON
• 金额: $ 13.87万
• 依托单位: UNIVERSITY OF ILLINOIS AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 1993
• 资助国家: 美国
• 起止时间: 1993-12-10 至 1996-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2209201
• 关键词: artificial intelligence; automated data processing; computer program /software; computer simulation; computer system design /evaluation; genetic mapping; genetic markers; restriction fragment length polymorphism; restriction mapping

DESCRIPTION (Adapted from the Investigator's Abstract): Numerous restriction mapping programs have been devised since 1978, but none of them is as precise as manual map construction using digest gel photos, pencil, and graph paper. Given realistic data, programs usually find hundreds or even thousands of solutions, only one of which can be correct. Because of this, slow and demanding manual techniques are still in common use. The researchers propose to develop public domain software implementing a complete restriction mapping environment which will be far more powerful and useful than current restriction mapping software. This system will: 1) find solutions more quickly than any existing software; 2) find far fewer false maps than any existing software; 3) allow the user to "steer" the entire mapping process (if desired); and 4) guide the user with detailed, expert advice on handling specific mapping problems as they arise. In addition, the system will have: 5) built-in extensibility, so that simple modifications will also allow other genetic marker mapping problems to be solved by the same program and 6) the ability to record all user activity transparently, providing quantitative data on successful mapping strategies. The system will be based on extant restriction mapping programs, but it will overcome their limitations by including the following additional capabilities: 1) All known heuristics will be implemented. (Heuristics are logical rules of thumb which guide the search towards a true solution.) Existing programs use only a small subset of the known heuristics. Every added heuristic will speed up the search and reduce the set of possible solutions to a problem. 2) Hand mapping will be simulated on-screen via a "what you see is what you get" graphical user interface, with users choosing fully automatic mapping (the default), fully manual mapping (with simulated pencils and log paper), or various in-between levels of semi-automatic assisted mapping. This will allow users to control or adjust any part of the mapping process if they so desire. 3) An expert system (a program which can answer queries and make decisions by consulting a knowledge database) will guide users through the mapping process. It will assist the process of data acquisition, help the user solve difficulties, and tutor inexperienced users. Considerable preliminary design work has already taken place, so implementation can begin almost at once. Software will be developed and tested iteratively ("rapid prototyping") to assure end-user satisfaction. To insure portability at the source code level, the two major modules of the system (fragment length derivation and mapping) will be coded in C++ using Boochs' object-oriented design methodology, and the user interface will be designed using a portable interface-building tool that works on a variety of computing platforms (including DOS machines, and the Macintosh). The expert system will be implemented using CLIPS, a portable C-based public domain expert system shell.

描述（改编自调查员的摘要）：许多 自1978年以来已经设计了限制映射程序，但没有一个 使用摘要凝胶照片，铅笔，与手动图构造一样精确 和图形纸。 给定实际数据，程序通常会找到数百或 即使是成千上万的解决方案，只有一种可以正确。 由于 这种缓慢且苛刻的手动技术仍然普遍使用。 这 研究人员建议开发实施公共领域软件 完整的限制映射环境将更加强大 比当前的限制映射软件有用。 该系统将： 1）比任何现有软件更快地找到解决方案； 2）找到远 虚假地图少于任何现有软件； 3）允许用户“转向” 整个映射过程（如果需要）； 4）引导用户使用 有关处理特定映射问题时的详细专家建议 出现。 此外，该系统将具有：5）内置可扩展性，因此 简单的修改还将允许其他遗传标记映射 同一程序和6）能够记录所有问题的问题 用户活动透明，提供成功的定量数据 映射策略。 该系统将基于现存的限制映射程序，但 通过包括以下额外 功能：1）将实施所有已知的启发式方法。 （启发式法 是指导搜索真正解决方案的逻辑规则。） 现有程序仅使用已知启发式方法的一小部分。 每一个 添加的启发式将加速搜索并减少可能的集合 解决问题的解决方案。 2）将在屏幕上模拟手工映射 用户的图形用户界面“您看到的是您得到的” 选择全自动映射（默认），完全手动映射（带有 模拟的铅笔和日志纸）或各种层次之间 半自动辅助映射。 这将允许用户控制或 如果需要，请调整映射过程的任何部分。 3）专家 系统（可以通过咨询来回答查询并做出决定的程序 知识数据库）将指导用户完成映射过程。 它 将协助数据获取过程，帮助用户解决 困难，导师没有经验的用户。 已经进行了大量的初步设计工作，所以 实施几乎可以立即开始。 软件将开发，并 迭代（“快速原型”）测试以确保最终用户满意度。 为了确保源代码级别的可移植性，两个主要模块 系统（片段长度推导和映射）将在C ++中进行编码 使用Boochs面向对象的设计方法和用户界面 将使用可在 各种计算平台（包括DOS机器和Macintosh）。 专家系统将使用剪辑，一种基于C的Clips实施 公共领域专家系统外壳。