B语言-生物信息学可视化流程语言

可视化流程语言以流程控制为中心、以图形为描述方式,对数据进行处理,因而拥有广阔的应用空间。文章结合生物信息学实际需求,设计开发了一套可视化流程语言-B语言。具有模块化、并行化、可视化的特性,为实现生物信息领域应用程序的快速开发和大规模并行任务处理提供了有效的解决手段。     

B语言一生物信息学可视化流程语言

可视化流程语言以流程控制为中心、以图形为描述方式,对数据进行处理,因而拥有广阔的应用空间.文章结合生物信息学实际需求,设计开发了一套可视化流程语言-B语言.具有模块化、并行化、可视化的特性,为实现生物信息领域应用程序的快速开发和大规模并行任务处理提供了有效的解决手段.     

面向生物信息的网格工作流开发与运行环境

网格工作流系统通过组合网格计算结点上的资源为生物计算等领域的复杂计算任务提供了支持。为了解决已有系统中用户需要对流程语言细节有较深入了解以及操作和配置较为复杂等问题,设计和实现了面向生物信息领域的网格工作流开发与运行环境。生物信息领域的用户使用该系统,可以通过web的方式实现对生物计算模型较高抽象层次的在线流程设计、流程作业的提交、作业状态的管理以及计算结果的查看等操作。最后通过生物计算领域的基因计算任务说明了系统对生物信息学应用的支撑功能。     

基于领域专用语言的应用软件自动生成

在领域专用语言、领域专用库和应用产生器的基础上,提出一种自动生成应用软件的设计框架,详细论述了该设计框架的设计原理和具体的实现过程。该设计框架由三级组成:首先设计一种该应用领域的领域专用语言,它将该应用领域的应用系统作为领域分析的对象,语言上集数据、功能和界面于一体;其次实现该应用领域的一个领域专用库,它提供应用系统级的复用;在这两者的基础上,最后实现一个集工具、语言和库于一体的可视化应用产生器,用它可以快速地开发完整的应用软件。已成功地将该设计框架运用于GIS应用系统领域。用应用产生器开发应用软件,不仅加强了应用系统开发过程的集成,提高了软件的开发效率,实现了软件过程的复用,而且达到了系统级的软件复用。     

分子结构与基因序列数据综合可视化方法研究

随着系统生物学的兴起和迅速发展,为了探索不同生物层次信息之间的关联关系,对不同层次生物科学计算数据综合可视化的需求日益迫切。不同层次的生物数据的组织管理是实现综合可视化的基础和关键技术,因此文中面向生物信息可视化领域的需求,基于综合可视化集成框架,提出了一种分子结构与基因序列数据的元数据组织模型与关联数据自动生成方法。该方法通过定义包括分子结构、基因序列以及分子结构/基因序列关联信息三类数据的元数据模型,建立了该两个层次和领域数据的关联关系,确定了关联数据描述格式;利用先进的XML技术实现了分子领域和基因序列领域元数据的自动提取和转换。在此基础之上开发了一个分子结构数据与基因序列数据综合可视化原型系统,取得了良好的试用效果。     

SBV:基于SVG的生物信息可视化软件

生物信息可视化是从生物大数据中挖掘有效信息的重要手段。针对生物信息的海量性、可视化效果的精确性、各种可视化需求的多样性等挑战,设计并实现了一款基于SVG矢量图的生物信息可视化软件SBV (SVG for Bioinformatics Visualization)。SBV充分利用了SVG的可伸缩性、DOM和CSS表现形式的可定制性,实现了10余种常用的生物信息用图,可支持现有的大部分生物信息可视化,是一款易于操作的综合型生物信息画图软件。目前该软件已经在Github上开源,为后续开发 更多功能奠定了较好的基础。     

语义虚拟环境本体可视化模型的研究

当前信息可视化所面临的一个瓶颈就是,需要一种模型来把场景图形内容和特定领域的语义信息进行有效集成,使用户可以有效地解释个性化可视化信息。基于X3D标准以及本体用本体描述语言OWL描述X3D标准,构建了一个X3D标准本体和一个映射本体来实现X3D标准本体和其他具体领域本体之间类和属性的映射,以达到丰富虚拟场景语义的目的。基于X3D标准本体和映射本体设计了语义虚拟环境本体可视化模型,从而为具体领域本体实现可视化提供了一种方法。实验结果证明了该模型的可行性。     

可视化查询语言CQL的实现

为使得许多非计算机专业的用户，尤其是未接受过数据库编程语言训练的用户，能够独立操纵一个数据库系统，有效地解决工作、生活中的问题，我们研究并提供了一种空间数据库可视化查询语言CQL。借助该语言，用户可以直观、方便地操纵数据库系统或查询数据库信息。本文介绍了CQL语言的语素、语义、语法及语用的定义，同时给出了CQL编辑器、编译器和查询结果可视化的设计方法。     

水库群智能云服务平台可视化系统设计与实现

为加强水利信息化建设,解决海量异构数据管理分散、水利信息化展示平台落后等问题,实现水利信息数字化、规范化、模块化管理的目标,本文设计并实现了一套水库群智能云服务平台大屏可视化系统。该系统基于Vue前端可视化开源框架和SpringCloud微服务后端开发框架,采用WebSocket数据传输协议作为核心驱动全屏信息通讯与交互,以WebGIS地理开发库Cesium.js为依托,结合ECharts、DataV等应用组件库,设计了一套大屏可视化集成方案,为水利成果展示提供了一个多端协同与信息共享的可视化平台,有利于促进流域水资源高效利用及科学化管理。通过在金沙江下游与三峡梯级的应用实例表明,该可视化系统集成技术能够实现流域水利信息形象、生动的全方位展示,具有较高的应用前景和参考价值,能够为水资源高效开发与利用提供技术支撑。     

一种模型驱动的交互式信息可视化开发方法

设计与实现面向领域应用的交互式信息可视化软件十分困难.缺乏统一的开发方法与支撑工具箱,为非专家用户提供对层次、网络、多维等数据类型的统一支持,对各种可视化技术与交互技术的统一支持,以及对信息可视化任务的统一支持针对此问题,提出了一种模型驱动的交互式信息可视化开发方法Daisy.首先,提出了交互式信息可视化界面模型IIVM(interactive information visualization interface model);然后,提出了基于IIVM的交互式信息可视化开发方法Daisy,讨论了该方法的两个核心技术:IIVM建模与描述文件生成方法、系统自动生成方法.同时。给出了Daisy工具箱,包括Daisy建模工具、Daisy系统自动生成工具以及运行时框架与组件库.最后,给出了该开发方法与工具箱的应用实例.实例表明,该方法能够为交互式信息可视化开发的统一支撑方法问题提供一种有效的解决方案.     

Using Verified Data-Flow Analysis-based Optimizations in Attribute Grammars

Building verified compilers is difficult, especially when complex analyses such as type checking or data-flow analysis must be performed. Both the type checking and program optimization communities have developed methods for proving the correctness of these processes and developed tools for using, respectively, verified type systems and verified optimizations. However, it is difficult to use both of these analyses in a single declarative framework since these processes work on different program representations: type checking on abstract syntax trees and data-flow analysis-based optimization on control flow or program dependency graphs.We present an attribute grammar specification language that has been extended with constructs for specifying attribute-labelled control flow graphs and both CTL and LTL-FV formulas that specify data-flow analyses. These formulas are model-checked on these graphs to perform the specified analyses. Thus, verified type rules and verified data-flow analyses (verified either by hand or with automated proof tools) can both be transcribed into a single declarative framework based on attribute grammars to build a high-confidence language implementations. Also, the attribute grammar specification language is extensible so that it is relatively straight-forward to add new constructs for different temporal logics so that alternative logics and model checkers can be used to specify data-flow analyses in this framework.     

A history of data-flow languages

Data-flow refers both to a language-level paradigm of computation and to a family of processor architectures based on this paradigm. This article elaborates data-flow language issues and the evolution of data-flow languages. In considering limits to the expressive power of these languages, underlying architectural issues are discussed. Although the article attempts to present a complete history of data-flow languages, it concentrates on those languages that specifically belong to this class and have been implemented for a data-flow machine. In many cases, the distinctions between issues of language semantics and machine architecture are unclear. Usually we have found that this reflects the evolution of data-flow, and the close association between language and architecture development. In some sections of the article, it may appear that there is an imbalance in the amount of detail presented when compared with other sections. This imbalance is proportional to the publications and the amount of information readily available for the topics     

Grafcet revisited with a synchronous data-flow language

The Grafcet (or sequential function charts) language is a graphic language often offered in programmable logic control systems (PLC) used for industrial control-command applications. Modeling of Grafcet by the synchronous data-flow language Signal gives both explicit semantics, and the corresponding simulator. The translation into a graph of tasks makes it possible to execute the Grafcet program on any hardware architecture. Moreover, the use of Signal's proof tools allows verification of Grafcet properties, opening the field of critical applications to this very expressive language     

A framework for data-flow distributed processing

A framework for data-flow distributed processing is established through the definition of a data-flow model and a set of language constructs for concurrent programming. The proposed approach is based on the following characteristics: i) the exploitation of parallelism at the operation level leads to the efficient and natural exploitation of parallelism at the program level, and ii) parallelism, communication, nondeterminism and history sensitivity are primitive concepts. The aim of the defined data-flow constructs is to enhance modularity and parallelism of programs. Two structuring levels are introduced, called «modules» and «frames», to permit both symmetric and asymmetric communication. Single assignment and guarded commands are employed inside modules. Examples of tipical programming problems, including shared resources management, are given together with a short account of a distributed data-flow architecture able to support data-flow distributed processing efficiently.     

The construction of information management system prototypes in Ada

The use of a data-flow diagram and data dictionary for the requirements specification of an information management system is described together with the benefits to be gained from using prototypes. Construction of such prototypes in Ada is discussed in detail with a simple example being given. The use of a flexible user interface, generic data-flows, exception handlers for error conditions and a top-down design method that makes use of separate compilation indicates that Ada is an appropriate language for the development of such systems. Consideration is also given to the use of Ada in the construction of actual as well as prototype information systems.     

可信编译器L2C的核心翻译步骤及其设计与实现

同步数据流语言（如Lustre）近年来在航空、高铁、核电等安全攸关领域得到广泛应用.这些领域对相关开发工具本身的安全性有着相当高的要求.为尽力解决好”误编译”问题,近期人们借助reliable-by-construction辅助定理证明器实现常规命令式语言编译器的构造和验证取得了很大的成功,如CompCert C编译器.L2C是基于这种方法开发的可信编译器,它以扩展的Lustre语言为源语言,以Clight （CompCert中的C语言子集）为目标语言.就我们所知,L2C是同类工作中唯一面向实际工业应用的同步数据流语言编译器.本文重点介绍L2C编译器的核心翻译步骤及其设计与实现过程中考虑的主要问题和相关经验.     

Detecting Data-flow Errors Based on Petri Nets With Data Operations

In order to guarantee the correctness of business processes, not only control-flow errors but also data-flow errors should be considered. The control-flow errors mainly focus on deadlock, livelock, soundness, and so on. However, there are not too many methods for detecting data-flow errors. This paper defines Petri nets with data operations (PN-DO) that can model the operations on data such as read, write and delete. Based on PN-DO, we define some data-flow errors in this paper. We construct a reachability graph with data operations for each PN-DO, and then propose a method to reduce the reachability graph. Based on the reduced reachability graph, data-flow errors can be detected rapidly. A case study is given to illustrate the effectiveness of our methods.      

Formal verification of programs in the functional data-flow parallel language

The article is devoted to the methods of proving parallel programs correctness, that are based on the axiomatic approach. Formal system for functional data-flow parallel programming language Pifagor is described. On the basis of this system programs correctness could be proved.     

An approach and tool for measurement of state variable based data-flow test coverage for aspect-oriented programs

ContextData-flow testing approaches have been used for procedural and object-oriented programs, and shown to be effective in detecting faults. However, few such approaches have been evaluated for aspect-oriented programs. In such programs, data-flow interactions can occur between base classes and aspects, which can affect the behavior of both. Faults resulting from such interactions are hard to detect unless the interactions are specifically targeted during testing.ObjectiveThis paper presents an approach and tool implementation for measuring data-flow coverage based on state variables defined in base classes or aspects in AspectJ programs. The paper also reports on an empirical study that compares the cost and effectiveness of data-flow test criteria that are based on state variables with two control-flow criteria.MethodEffectiveness of the criteria was evaluated for various fault types. Cost-effectiveness of test suites that cover all state variable definition-use associations (DUAs) was evaluated for three coverage levels: 100%, 90%, and 80%.ResultsThe effort needed to obtain a test case that achieves data-flow coverage is higher than the effort needed to obtain a test case that covers a block or a branch in an advised class. Covering certain data flow associations requires more effort than for other types of data flow associations. The data-flow test criteria based on state variables of a base-class are in general more effective than control-flow criteria.ConclusionsOverall, it is cost-effective to obtain test suites at the 90% coverage level of data-flow criteria.     

Defining a test coverage criterion for model-level testing of FBD programs

ContextThe Programmable Logic Controller (PLC) is being integrated into the automation and control of computer systems in safety–critical domains at an increasing rate. Thoroughly testing such software to ensure safety is crucial. Function Block Diagram (FBD) is a popular data-flow programming language for PLC. Current practice often involves translating an FBD program into an equivalent C program for testing. Little research has been conducted on coverage of direct testing a data-flow program, such as an FBD program, at the model level. There are no commonly accepted structural test coverage criteria for data-flow programs. The objective of this study is to develop effective structural test coverage criterion for testing model-level FBD programs. The proposed testing scheme can be used to detect mutation errors at the logical function level.ObjectiveThe purpose of this study is to design a new test coverage criterion that can directly test FBD programs and effectively detect logical function mutation errors.MethodA complete test set for each function and function block in an FBD program are defined. Moreover, this method augments the data-flow path concept with a sensitivity check to avoid fault masking and effectively detect logical function mutation errors.ResultsPreliminary experiments show that this test coverage criterion is comprehensive and effective for error detection.ConclusionThe proposed coverage criterion is general and can be applied to real cases to improve the quality of data-flow program design.