分子系统学分析平台的建立和应用

分子系统学建立在实验和计算的基础之上。DNA快速测序技术的普及为分子系统学家提供了大量数据，而序列分析技术则是探索数据发现知识的重要工具。在基因组时代，随着大量模式生物完整基因组序列的获得，分子系统学正面临着前所未有的机遇和挑战。一方面，生命之树计划有助于确定新的模式生物和开展相应的基因组计划;另一方面，模式生物的基因组计划有助于阐明它们之间的进化关系和基因组的进化模式。更为重要的是，分子系统学序列分析技术已经发展成为探索与整合基因组数据的强有力工具，从而在生命科学中发挥重要作用。事实上，分子系统学和基因组学的相互渗透正在形成一门崭新的交叉学科——系统发育基因组学。 为了奠定分子系统学研究中信息管理和数据分析工作的坚实基础，我们建立了分子系统发育分析平台。该平台为研究人员提供专业数据库服务和数据分析技术支持，以及相关的网络资源。 分子系统发育分析平台包括了3个专业数据库。第一个是DNA凭证标本数据库。该数据库中的记录包括了7项字段：英文科名、中文科名、物种拉丁名、采集人、采集号、采集地和采集时间。用户可以通过设定单个或多个字段的取值进行检索。截止2004年6月1日，该数据库共包括3491条标本记录。第二个是引物数据库。PCR引物是分子系统学实验的重要条件之一。该数据库中的记录包括3项字段：引物名称、序列内容和退火温度。用户可以通过设定单个或多个字段的取值进行检索。截止2004年6月1日，该数据库共包括170条用于扩增植物细胞核、叶绿体和线粒体基因组DNA序列的引物记录。第三个是生物计算数据库。该数据库为研究人员提供传输和保存序列分析数据和结果文件的服务。 为了确保数据库的安全性和使用性，我们开发了数据库的接口和检索工具，以及系统管理员和用户资格认证程序。通过前者，使用者可以进行数据的上传、下载、管理和检索等操作。而后者则是对不同使用者身份和权限进行设定。管理员的权限高于用户，主要负责本系统的日常维护和管理工作，以及对新增管理员和用户进行资格认证。 分析技术支持旨在帮助用户快速掌握常用的系统发育分析方法，进行有效的数据分析，从复杂的统计学算法和计算机程序中解放出来，将精力集中于计算结果的生物学解释。在该部分中，我们首先简要介绍了常用的分析方法，并且针对分子系统学中的不同问题提供了相应的解决方案。这些问题包括：系统发育重建、替代速率和分歧时间的估计、祖先分布区的重建、性状进化假说的检验、以及密码子水平适应性进化的检测。我们特别强调了似然比检验和贝叶斯推测作为方法论上的重要进展在分子系统学中所发挥的关键作用。本部分还包括大量常用的分子系统学程序或软件包及其快速使用说明和命令模块。下载安装之后，用户即可按照说明使用命令模块进行数据分析。 此外，该平台还提供了一些常用的网络资源地址，如生物信息中心、分子进化和系统发育实验室、专业期刊和相关数据库等。 最后还给出了4个应用实例，即针对特定分子系统学问题的解决方案和初步的分析结果。 第一个例子说明系统发育重建方法的应用。为了确定杨梅科的系统学位置，对6种DNA序列和叶绿体trnL-F区内的间隔性状进行了分析。单个分析表明这6种序列之间在系统学信息上存在显著差异。叶绿体基因组序列的合并分析强烈支持杨梅科和（木麻黄科，（桦木科，核果桦科））的姐妹群关系，而间隔性状的存在能够充分提高其分辨率和支持率。 第二个例子说明如何推测历史生物地理学过程。我们对壳斗目8科25属植物叶绿体基因组的trnL-F、matK、rbcL和atpB的合并序列进行了最大简约分析，得到唯一的最大简约树。基于该系统树和25属植物的地理分布数据，采用扩散－替代分析方法重建了系统树每个节点上的祖先分布区，推测了壳斗目的分布历史。结果表明，壳斗目的历史生物地理学过程由3次替代事件和20次扩散事件组成。其中最重要的替代事件是由于冈瓦纳大陆和劳亚大陆分离所导致的南青冈科及其姐妹群之间的分化。另外，在壳斗科和核心高等金缕梅类中多次发生从欧亚大陆到北美洲、甚至南美洲的平行扩散事件。 第三个例子说明如何估计分歧时间。我们仍然使用扩散－替代分析中所用的最大简约树作为分析的依据，并根据等级制似然比检验确定的最优替代模型对该系统树的支长进行了最大似然优化。似然比检验表明，该系统树不服从分子钟假说。我们以冈瓦纳大陆和劳亚大陆分离的地质事件和5个属的最早化石记录作为标定点，采用罚分似然法在没有分子钟的条件下估计了壳斗目的科间分歧时间。结果表明，绝大多数科间分歧事件都发生在白垩纪。 第四个例子说明如何检测密码子水平的适应性进化。分支间可变选择压力模型的似然比检验表明SARS冠状病毒的S基因在跨种传播过程中发生了正选择。

以活动为中心的个人信息管理

通过分析用户执行多任务的交互场景，基于活动理论，将任务、任务相关的信息以及任务间的关系统一纳入活动研究的框架，提出了以活动为中心的个人信息管理方式；从活动的静态结构、动态演变过程以及活动间的关系3个方面对活动进行建模；针对多活动场景中的用户交互和活动对象的内容提出了计算活动相关性的方法；并在此基础上。实现了以活动为中心的个人信息管理工具一一ACPIM(activity．centered personal information management)．评估结果显示：以活动为中心的个人信息管理有助于用户减轻认知和记忆负担，降低交互努力，从而提高工作效率．

个人信息管理的关键技术研究

随着互联网和移动通信等技术的飞速发展，以及普适计算模式代替传统的计算模式，使得每个人任何时候都处在信息的包围之中，并且面临的信息丰富多样。它们在人们的生活中的作用越来越大，但个人信息量日益增长，超越了个人对其管理控制的能力，使得个人处理信息面临越来越多的问题，如无法用有效的方式及时地记录随时遇到的信息、遗忘重要的提醒信息、个人花费大量的时间对信息进行组织和再查找操作等，这些严重影响了个人生活质量和工作效率，因此一个新的研究领域—个人信息管理(Personal Information Management, PIM)应运而生，并且目前已经成为研究的热点。 PIM研究个人在个人信息空间中获取、组织、检索和处理信息的活动过程。它是人们日常生活最基本的一部分，譬如个人经常要查找文件、管理Email、安排预约以及制定任务列表等。针对于PIM的信息非结构化、自然交互和个性化三大特点，以提高个人查找信息的效率以及快速开发PIM为目的，本文从个人信息的组织模式、PIM的实物界面隐喻、信息标签以及PIM的开发框架等关键技术上进行了研究。 本文首先介绍了PIM的研究发展现状，引出了当前对PIM研究的必要性和重要性。从个人日常对信息的需求过程分析，结合活动理论，研究了以活动为中心的个人信息的组织模式，提出了基于活动的信息项之间的相关度计算方法；接着讨论了适合笔式PIM的实物界面隐喻RSFDPF；通过分析个人信息特有的个人主观性属性，研究了个人主观的标签技术，以提高个人同信息交互的自然性以及查找信息的效率；最后针对笔式PIM的开发方法上，提出了基于模型驱动的快速开发适合不同人群和应用环境下的笔式PIM开发框架。 在本文所开展的对PIM的一些关键技术的研究中，主要的创新点包括： 1 基于活动理论，提出了以活动为中心的个人信息组织 当前的桌面计算机仍然是存放个人信息主要的地方，但是对个人信息的管理还是以应用程序-文档方式，单一的树形层次化结构管理个人信息，造成信息“孤岛”，影响个人执行复杂活动的效率，并且增加了个人记忆的负担。 通过分析用户执行多任务的交互场景，基于活动理论，将任务、任务相关的信息以及任务间的关系统一纳入活动研究的框架，从活动的静态结构、动态演变过程以及活动间的关系三方面对活动进行建模。 在个人完成复杂交互活动过程中，需要涉及多个信息项，由于信息项的在逻辑空间的分布性，造成用户组织、查找信息非常困难。个人信息项之间的相关性对于记忆和查找信息起着重要的线索作用，能够降低个人查找信息的认知努力。信息项之间的相关性不仅体现在信息的内容相似性上，而且隐含在个人对信息的交互活动过程当中，从这两个方面提出了定量计算信息项之间相关性的算法，根据个人活动模型，将参与活动的个人信息进行统一组织管理。 2 提出了笔式PIM的实物界面隐喻RSFDPF和基于主观方法的信息标签 当前层次结构化目录仍然是个人信息管理的主要方式，但是对于在笔交互环境中，已经严重影响了交互的自然性。 为了提高笔式PIM交互的自然性，通过分析个人在物理信息空间的办公室场景中处理个人信息的过程，将实物引入到界面中，建立了笔式PIM的实物界面隐喻：室-架-夹-桌面-堆-件(RSFDPF)，并对其进行了描述；另外，通过分析物理信息空间中个人对个人信息的主观属性，包括：个人对信息的看法、重要性等，提出将用户主观属性通过自然的笔式交互方式添加到个人信息之上，以提高个人查找和分类信息的效率。 3 提出了一种基于模型驱动的PIM开发框架 随着无所不在计算的日益发展，PIM被应用在越来越多的交互设备之上，其中笔式交互设备以其自然交互的特征和便携轻巧的物理特性迅速成为了新一代主流应用，但是笔式PIM需求的多样性、突出的个性化、应用设备和平台的差异性等特征，增加了开发笔式PIM的复杂度，如何缩短系统的开发周期，保证需求和实现的一致性以及系统的可扩充性和可移植性成了笔式个人信息管理系统开发的关键问题。 提出了一种基于模型驱动的开发笔式PIM的开发框架，建立了笔式PIM的开发模型和开发流程。 4 构建了面向研究工作者的笔式PIM原型 针对于研究者们进行的研究活动的大部分过程具有创造性和随意性以及所需要的信息组织具有非结构化和结构化混合等特点，基于模型驱动的PIM开发框架，构建了面向研究工作者的笔式PIM原型。

Ruby:一个基于移动设备的个人信息管理系统

为满足移动环境对非结构化个人信息管理的自然性和高效性的需求,提出一个基于移动设备的个人信息管理系统Ruby.首先分析了移动环境对个人信息管理的需求,描述了系统框架,接着介绍了系统界面和交互过程,并阐述了支持该系统的2个主要技术:非结构化笔记编辑技术和基于笔迹标签的检索技术.对2个技术和整个系统的评估结果表明,该系统能够满足移动环境对自然交互、非结构化信息采集加工及个人信息自然检索的需求.

面向知识工作者的个人信息管理模型

为满足知识工作者对个人信息管理的灵活分类、时序管理和智能推荐的要求,提出一种个人信息管理系统模型。首先分析了知识工作者的个人信息管理特点,接着提出了模型的框架,描述了框架的层次结构。然后介绍了基于标签的个人信息推荐算法。最后对原型系统进行了评估。评估结果表明,该模型能够满足知识工作者对个人信息管理的要求。

中国东部上第三系硬粘土的工程地质特性及边坡开挖工程环境效应研究

The engineering geological properties of Neogene hard clays and related engineering problems are frontiers in the fields of Engineering Geology, Soil Mechanics and Rock Mechanics. Recently, it has been recognized that Neogene hard clay is the intermediate type of material between the soil and the rock. Many aspects of them, such as sampling, testing, calculating and engineering process, are special, which could not be researched by means of theories and methods of traditional Soil Mechanics of Rock Mechanics. In order to get real knowledge and instruct the engineering practice, intersect studying of multiple disciplines, including Engineering Geology, Soil Mechanics and Rock Mechanics, etc., is necessary. Neogene hard clay is one of the important study objects of regional problem rocks & soils in our country, which extensively distributed in China, especially in Eastern China. Taking the related areas along the middle line of the Project of Transferring Water from the South to the North (e.g. Nanyang basin, Fangcheng-Baofeng area and Handan-Yongnian area), South-west of Shandong, Xu-Huai area and Beijing area, etc. as main study areas, the paper divided Neogene hard clays into reduction environment dominated origin and oxidation environment dominated origin, which distributed on areas western and eastern to Mount Taihangshan respectively. Intermediate types are also existed in some areas, which mainly distribute near the edges of depositional basins; they are usually of transitions between diluvial and lacustrine deposits. As to Neogene hard clays from Eastern China, the clay particle content is high, and montmorillonite or illite/montmorillonite turbostratic mineral is the dominating clay mineral. The content of effective montmorillonite is very high in each area, which is the basis for the undesirable engineering properties of Neogene hard clays. For hard clays from the same area, the content of effective montmorillonite in gray-greenish hard clay is much higher than that in purple-brownish or brown-yellowish hard clay, which is the reason why the gray-greenish hard clay usually has outstanding expansive property. On the other hand, purple-brownish or brown-yellowish hard clay has relatively less montmorillonite, so its property is better. All of these prove that the composition (clay mineral) of Neogene hard clay is the control factor for the engineering properties. Neogene hard clays have obvious properties such as fissured, overconsolidated and expansive, which are the main reasons that many engineering problems and geological harzards usually occur in Neogene hard clays. The paper systematically elaborates the engineering properties of Neogene hard clays from Eastern China, analyses the relationships between engineering properties and basic indexes. The author introduces the ANN method into the prediction of engineering property indexes of hard clays, which provides a new way for quantitatively assessment and prediction of engineering property indexes. During investigation in the field, the author found that there exists obvious seam-sheared zone between different hard clays in Miocene Xiacaowan formation in Xu-Huai area. Similar phenomenon also exists near the borderline between Neogene hard clays and underlying coal measures in the Southwest of Shandong province, which could be observed in the cores. The discovery of seam-sheard zone has important theoretical and practical significance for engineering stability analysis and revealing the origin of fissures in Neogene hard clays. The macrostructure, medium structure and microstructure together control the engineering properties of hard clays. The author analyses and summarizes the structural effects on hard clays in detail. The complex of the strength property of hard clays is mostly related to the characteristics of fissures, which is one of the main factors that affect the choice of shear strength parameters. So structure-control theory must be inseparably combined with composition-control theory during the engineering geological and rock/soil mechanics research of hard clays. The engineering properties, such as fissured, overconsolidated and expansive, control the instability of engineering behaviors of Neogene hard clays under the condition of excavation, i.e. very sensitive to the change of existence environment. Based on test data analysis, the author elaborates the effects of engineering environment change on the engineering properties. Taking Nanyang basin as example, the author utilizes FEM to study the effects of various factors on stability of cutting canal slopes, than sets forth the characteristics, development laws and formation mechanism of the deformation and failure of hard clay canal slopes, summarizes the protection and reinforcement principles, as well as the protection and remedy steps. On the basis of comparison of engineering properties of domestic and foreign Neogene muddy deposits, in the view of whole globe and associated with the geological characteristics of China, the paper demonstrates that the intermediate type of the material between the soil and the rock, named "hard clay/soft rock", which can not be separated abruptly, really exists in China. The author has given a preliminary classification based on its geological origin and distribution law, which is very significant for promoting the mixture of Engineering Geology, Soil Mechanics and Rock Mechanics. In the course of large scales engineering construction in China, many engineering experiences and testing data are gained, summarizing these testing results and automatically managing them with computer technology are very necessary. The author develops a software named "Hard Clay-Soft Rock Engineering Geological Information Management and Analysis System (HRGIMS)", realizes the automatic and visual management of geo-engineering information, on the basis of information management, the functions of test data analysis and engineering property prediction are strengthened. This system has well merits for practice and popularization.

港西油田现代油藏管理研究与实践

Through years of practice, reservoir management has already become the basic mode of foreign oil companies to realize the high-efficient development of the oil field. From the view of reservoir development and technological economy, reservoir management regards the study of the reservoir engineering, designs of reservoir projects and the dynamic analysis of the reservoir's performance as a system. In the fields of reservoir description, the establishment of the geological models and development models, the dynamic simulations of reservoir exploitation and the design of the oil engineering, reservoir management emphasizes the cooperation of the geology and the engineering, the combination of the engineering technology and the economic evaluation. In order to provide the means and basis for the reservoir geology study, reservoir evaluation, reserves calculation, numerical simulation, development plan and risk analysis, it adopts the reservoir management activities(team work) to make and implement the optimized oil field development management strategies so that secientific and democratic decision making can be achieved. Under the planned economic system for a long time, the purpose of Chinese reservoir development has been to fulfill the" mandatory" production task. With the deepening of the reform, the management organization of Chinese petroleum enterprises has been gradually going through the transition and reforms to the operational entity and the establishment of the mode of oil companies under the socialist market economy system. This research aims at introducing the advanced reservoir management technique from foreign countries to further improve the reservoir development results and wholly raise the economic benefits of Chinese mature land facieses sandstone reservoirs in the later stage of the water flooding. We are going to set up a set of modern reservoir management modes according to the reservoir features, current situation and existing problems of GangXi oil field of DaGang oil company. Through the study and implementation of the reservoir description and numerical simulation technology effectively, we plan to work out integrated adjustment projects, to study the related technology of oil recovery; to set up the effective confirmable data procedure and data management system of the reservoir management, to establish the coordinated model and workbench related to geology, engineering and economy in order to realize the real time supervision and evaluation on the process of reservoir development. We hope to stipulate modernization management tools for GangXi oil fields to rationally utilize various kinds of existing technological methods and to realize the economic exploitation and achieve the maximum benefits from the reservoir. The project of the modem reservoir management will be carried out on the GangXi oil field of DaGang oil company for this oil field is typical and has integrated foundamental materials and perfect networks. Besides, it is located in the good geographical position enjoying very convenient traffic. Implementing modern reservoir management will raise the recovery ratio, reduce the production cost and improve the working efficiency. Moreover, the popularization of modern reservoir management will improve the comprehensive benefits of DaGang oil company and even the whole Petro China. Through the reserch of this project, the following technical indicators can be reached: Establishing the concept of modern reservoir management. Establishing a set of integrated data information management system adapt to the features of GangXi reservoir. 3. Forming technical research modes of modern reservoir management suitable for mature reservoirs in the later developing stage. 4. Advancing projects of GangXi reservoir which are maxium optimized in engineering technique and economic benefits of oil exploitation. Besides, this set of technology, research principle and method can guide the mature reservoir of DaGang oil field and even the whole PetroChina to develop the further research of reservoir adjustment and improve the reservoir recovery factor and developing level constantly.

工程地质三维可视化技术及其工程应用研究

Study of 3D visualization technology of engineering geology and its application to engineering is a cross subject which includes geosciences, computer, software and information technology. Being an important part of the secondary theme of National Basic Research Program of China (973 Program) whose name is Study of Multi-Scale Structure and Occurrence Environment of Complicated Geological Engineering Mass(No.2002CB412701), the dissertation involves the studies of key problems of 3D geological modeling, integrated applications of multi-format geological data, effective modeling methods of complex approximately layered geological mass as well as applications of 3D virtual reality information management technology.The main research findings are listed below:Integrated application method of multi-format geological data is proposed,which has solved the integrated application of drill holes, engineering geology plandrawings, sectional drawings and cutting drawings as well as exploratory trenchsketch. Its application can provide as more as possible fundamental data for 3Dgeological modeling.A 3D surface construction method combined Laplace interpolation points withoriginal points is proposed, so the deformation of 3D model and the crossing error ofupper and lower surface of model resulted from lack of data when constructing alaminated stratum can be eliminated.3D modeling method of approximately layered geological mass is proposed,which has solved the problems of general modeling method based on the sections or points and faces when constructing terrain and concordant strata.The 3D geological model of VII dam site of Xiangjiaba hydropower stationhas been constructed. The applications of 3D geological model to the auto-plotting ofsectional drawing and the converting of numerical analysis model are also discussed.3D virtual reality information integrated platform is developed, whose mostimportant character is that it is a software platform having the functions of 3D virtualreality flying and multi-format data management simultaneously. Therefore, theplatform can load different 3D model so as to satisfy the different engineeringdemands.The relics of Aigong Cave of Longyou Stone Caves are recovered. Thereinforcement plans of 1# and 2# cave in phoenix hill also be expressed. The intuitiveexpression provided decision makers and designers a very good environment.The basic framework and specific functions of 3D geological informationsystem are proposed.The main research findings in the dissertation have been successfully applied to some important engineering such as Xiangjiaba hydropower station, a military airport and Longyou Stone Caves etc.

龙滩水电站左岸边坡监测信息系统研制及其监测资料分析

Guangxi Longtan Hydropower Station is not only a representative project of West Developing and Power Transmission from West to East in China, but also the second Hydropower Station to Three Gorges Project which is under construction in China. There are 770 X 104m3 creeping rock mass on the left bank slope in upper reaches, in which laid 9 water inlet tunnels and some underground plant buildings. Since the 435m high excavated slope threatens the security of the Dam, its deformation and stability is of great importance to the power station.Based on the Autodesk Map2004, Longtan Hydropower Station Monitoring Information System on Left Bank has been basically finished on the whole. Integrating the hydropower station monitoring information into Geographic Information System(GIS) environment, managers and engineers can dynamically gain the deformation information of the slop by query the symbols. By this means, designers can improve the correctness of analysis, and make a strategic and proper decision. Since the system is beneficial to effectively manage the monitoring-data, equitably save the cost of design and safe construction, and decrease the workload of the engineers, it is a successful application to the combination of hydropower station monitoring information management and computer information system technology.At the same time, on the basis of the geological analysis and rock mass toppling deformation and failure mechanism analysis of Longtan engineering left bank slope, the synthetic space-time analysis and influence factors analysis on the surface monitoring data and deep rock mass monitoring data of A-zone on left bank slope are carried on. It shows that the main intrinsic factor that effects the deformation of Zone A is the argillite limestone interbedding toppling structure, and its main external factors are rain and slope excavation. What's more, Degree of Reinforcement Demand(DRD) has been used to evaluate the slop reinforce effect of Zone A on left bank according to the Engineering Geomechanics-mate-Synthetics(EGMS). The result shows that the slop has been effective reinforced, and it is more stable after reinforce.At last, on the basis of contrasting with several forecast models, a synthetic forecast GRAV model has been presented and used to forecast the deformation of zone A on left bank in generating electricity period. The result indicates that GRAV model has good forecast precision, strong stability, and practical valuable reliability.