Groups Partitioning Over CORBA for Cooperative Work

Many examples illustrate the usefulness of group partitioning in distributed systems. The process group abstraction is a powerful tool for the development of fault-tolerant distributed applications. This solution is also particularly relevant to group entities sharing similar properties or stakes when applied to the field of cooperative work. When dealing with distributed applications, communication standards have evolved from socket-based interfaces to Remote Procedure Calls and nowadays, towards distributed object platforms like CORBA. This standard from the Object Management Group masks distribution and heterogeneity and provides a good basis for distributed application development. This paper presents a review of group mechanisms found in the literature then focuses on the implementation of groups over CORBA. An implementation of such a service over CORBA illustrates the impact of group auto-organization. Performance we obtain show that our service is efficient and provides good mechanisms to manage operations in a group.     

Developing and evaluating abstractions for distributed supercomputing

To fully realize its potential, distributed supercomputing requires abstractions and environments facilitating development of efficient applications. In this paper we present PARDIS, a system which addresses this demand by providing support for interoperability of PARallel DIStributed applications. The design of PARDIS is based on the Common Object Request Broker Architecture (CORBA). Like CORBA, it provides interoperability between heterogeneous components by specifying their interfaces in a meta-language, the CORBA IDL, which can be translated into the language of interacting components. However, PARDIS extends the CORBA object model by introducing SPMD objects representing data-parallel computations. This extension allows us to build interactions involving data-parallel components, which exchange distributed data structures whose definitions are captured by distributed sequences. We present microbenchmark results which evaluate the performance potential of SPMD objects for data structures of diverse complexity and different network configurations. Based on these results, we conclude that while encapsulating the existence of multiple interactions SPMD objects also allow their efficient utilization, and therefore constitute a useful abstraction. This revised version was published online in July 2006 with corrections to the Cover Date.     

Assessing natural resource use by forest-reliant communities in Madagascar using functional diversity and functional redundancy metrics

Biodiversity plays an integral role in the livelihoods of subsistence-based forest-dwelling communities and as a consequence it is increasingly important to develop quantitative approaches that capture not only changes in taxonomic diversity, but also variation in natural resources and provisioning services. We apply a functional diversity metric originally developed for addressing questions in community ecology to assess utilitarian diversity of 56 forest plots in Madagascar. The use categories for utilitarian plants were determined using expert knowledge and household questionnaires. We used a null model approach to examine the utilitarian (functional) diversity and utilitarian redundancy present within ecological communities. Additionally, variables that might influence fluctuations in utilitarian diversity and redundancy--specifically number of felled trees, number of trails, basal area, canopy height, elevation, distance from village--were analyzed using Generalized Linear Models (GLMs). Eighteen of the 56 plots showed utilitarian diversity values significantly higher than expected. This result indicates that these habitats exhibited a low degree of utilitarian redundancy and were therefore comprised of plants with relatively distinct utilitarian properties. One implication of this finding is that minor losses in species richness may result in reductions in utilitarian diversity and redundancy, which may limit local residents' ability to switch between alternative choices. The GLM analysis showed that the most predictive model included basal area, canopy height and distance from village, which suggests that variation in utilitarian redundancy may be a result of local residents harvesting resources from the protected area. Our approach permits an assessment of the diversity of provisioning services available to local communities, offering unique insights that would not be possible using traditional taxonomic diversity measures. These analyses introduce another tool available to conservation biologists for assessing how future losses in biodiversity will lead to a reduction in natural resources and provisioning services from forests.     

MPI code encapsulating using parallel CORBA object

This paper describes a technique that allows an MPI code to be encapsulated into a component. Our technique is based on an extension to the Common Object Request Broker Architecture (CORBA) from the OMG (Object Management Group). The proposed extensions do not modify the CORBA core infrastructure (the Object Request Broker) so that it can fully coexist with existing CORBA applications. An MPI code is seen as a new kind of CORBA object that hides most of the cumbersome problems when dealing with parallelism. Such a technique can be used to connect MPI codes to existing CORBA software infrastructures which are now being developed in the framework of several research and development projects such as JACO3^*, JULIUS^** or TENT^*** from DLR. To illustrate the concept of parallel CORBA object, we present a virtual reality application that is made of the coupling of a light simulation application (radiosity) and a visualisation tool using VRML and Java.     

我国苹果属资源现代分布调查初报

种质资源是农业生物资源的重要组成部分。我国是苹果属植物的起源演化中心之一,加强我国苹果种质资源调查与收集,可以丰富我国苹果资源保存的多样性。国家果树种质苹果圃于2005-2016年开展了我国西北、华北、西南、东北和华东苹果属植物集中分布地区的调查和收集,旨在进一步摸清家底,扩展我国苹果属种质资源的保存类型和数量,为保护利用及科学研究提供基础资料。调查结果表明:我国苹果属种质资源类型多样,分布广泛,新收集资源621份,西北、西南和东北地区的苹果野生种资源丰富,地方品种少量分布;华北地区以地方品种为主,野生种类型较少。目前野生资源集中分布面积逐年减少,由先前的大范围散落分布逐渐转变为小面积集中分布;地方品种面临的问题较多,砍伐频发,流失严重。以连续11年的苹果属种质资源调查为依据,提出苹果资源收集保存面临的问题,并提出建议。     

Seahawk: moving beyond HTML in Web-based bioinformatics analysis

Background  

Traditional HTML interfaces for input to and output from Bioinformatics analysis on the Web are highly variable in style, content and data formats. Combining multiple analyses can therfore be an onerous task for biologists. Semantic Web Services allow automated discovery of conceptual links between remote data analysis servers. A shared data ontology and service discovery/execution framework is particularly attractive in Bioinformatics, where data and services are often both disparate and distributed. Instead of biologists copying, pasting and reformatting data between various Web sites, Semantic Web Service protocols such as MOBY-S hold out the promise of seamlessly integrating multi-step analysis.     

FLOSYS--a web-accessible workflow system for protocol-driven biomolecular sequence analysis.

FLOSYS is an interactive web-accessible bioinformatics workflow system designed to assist biologists in multi-step data analyses. FLOSYS allows the user to create complex analysis pathways (protocols) graphically, similar to drawing a flowchart: icons representing particular bioinformatics tools are dragged and dropped onto a canvas and lines connecting those icons are drawn to specify the relationships between the tools. In addition, FLOSYS permits to select input-data, execute the protocol and store the results in a personal workspace. The three-tier architecture of FLOSYS has been implemented in Java and uses a relational database system together with new technologies for distributed and web computing such as CORBA, RMI, JSP and JDBC. The prototype of FLOSYS, which is part of the bioinformatics workbench AnaBench, is accessible on-line at http://malawimonas.bcm.umontreal.ca: 8091/anabench. The entire package is available on request to academic groups who wish to have a customized local analysis environment for research or teaching.     

BioMOBY: an open source biological web services proposal

BioMOBY is an Open Source research project which aims to generate an architecture for the discovery and distribution of biological data through web services; data and services are decentralised, but the availability of these resources, and the instructions for interacting with them, are registered in a central location called MOBY Central. BioMOBY adds to the web services paradigm, as exemplified by Universal Data Discovery and Integration (UDDI), by having an object-driven registry query system with object and service ontologies. This allows users to traverse expansive and disparate data sets where each possible next step is presented based on the data object currently in-hand. Moreover, a path from the current data object to a desired final data object could be automatically discovered using the registry. Native BioMOBY objects are lightweight XML, and make up both the query and the response of a simple object access protocol (SOAP) transaction.     

流域生态系统服务和水土资源匹配研究进展

生态系统服务精确评估和水土资源匹配状态,对统筹流域山水林田湖草一体化保护和修复,以及构建流域国土空间开发保护新格局具有深远影响。以生态系统服务与水土资源的响应关系为出发点,系统梳理了流域生态系统服务评估及水土资源匹配研究现状。主要贡献包括：(1)筛选大尺度生态系统服务评估精确性方法及其优势阐述;(2)提出将信息熵理论与多目标优化相结合的水土资源匹配模型算法;(3)指出基于系统耦合协调理论进行流域生态系统服务与水土资源响应机理研究的必要性。研究以期阐明流域生态系统服务与水土资源的关联性及其响应机制,为最终实现流域“土地利用经济-生态效益最大、缺水总量最小”的过程目标导向和“生态系统服务效益最大”的结果目标导向,提供理论支撑和技术指导。     

Design and implementation of a distributed multimedia collaborative environment

Multimedia applications are being developed and used for many aspects of our lives today. New high-speed, broadband networks have emerged and made the operation of these high-bandwidth requiring applications readily feasible. However, the development of distributed multimedia applications and efficient and reliable operation of these applications are still very difficult. This paper presents a flexible and reliable distributed multimedia collaborative environment called MAESTRO which provides a rich multimedia collaborative service API and which provides distributed multimedia services that can be used to develop a variety of multimedia applications easily. MAESTRO has been designed using CORBA. The system as well as applications running on it are managed and controlled in order to provide a reliable and efficient multimedia operations environment. We validate our claim by developing a number of multimedia applications using our distributed multimedia system and by using them for supporting distributed collaborative scientific and engineering research experiments. This revised version was published online in July 2006 with corrections to the Cover Date.     

Towards Real-Time Fault-Tolerant CORBA Middleware

An increasing number of applications are being developed using Distributed Object Computing (DOC) middleware, such as CORBA. Many of these applications require the underlying middleware, operating systems, and networks to provide dependable end-to-end Quality of Service (QoS) support to enhance their efficiency, predictability, scalability, and reliability. The Object Management Group (OMG), which standardizes CORBA, has addressed many of these application requirements individually in the Real-Time CORBA (RT-CORBA) and Fault-Tolerant CORBA (FT-CORBA) specifications. Though the implementations of RT-CORBA are suitable for mission-critical commercial or military distributed Real-Time and Embedded (DRE) systems, the usage of FT-CORBA with RT-CORBA implementations are not yet suitable for systems that have stringent simultaneous dependability and predictability requirements.This paper provides three contributions to the study and evaluation of dependable CORBA middleware for performance-sensitive DRE systems. First, we provide an overview of FT-CORBA and illustrate the sources of unpredictability associated with conventional FT-CORBA implementations. Second, we discuss the QoS requirements of an important class of mission-critical DRE systems to show how these requirements are not well served by FT-CORBA today. Finally, we empirically evaluate new dependability strategies for FT-CORBA that can help make the use of DOC middleware for mission-critical DRE systems a reality.     

Accessing and distributing EMBL data using CORBA (common object request broker architecture)

Background  

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data.     

The Distribution Characteristics and Application of Cyperaceae Plant Resources in Jiangsu Province

We used the combined method of general survey surveys, qua drat and transects method, investigated the Cyperaceae plant resources in Jiangsu Province by several field surveys and reviewing of literature, analysed the species diversity, distribution characteristics, distribution patterns and resource value. In order to establish the Cyperaceae plants germplasm bank, understand the distribution of resources application status, and then protect its species diversity and further exploitation. The results showed that specimen and germplasm collected include 116 species belonging to 16 genera, including seven variants. Cyperus rotundus Linn., Cyperus iria Linn., Carex brunnea Thunb. and other 10 species distributed widely, which distribution was widespread and species richness higher. The Cyperaceae plants were concentrated in Lianyungang, Yancheng area and Nanjing, Changzhou area, and low altitude section. The distribution types of genera and species were dominated by the world distribution, pan tropic distribution and temperate Asia distribution, have the transition from pan tropic distribution to Temperate zone. The research may collect scientific resources, effective protection, use and provide scientific basis for the evaluation.     

The PlaNet Consortium: a network of European plant databases connecting plant genome data in an integrated biological knowledge resource

The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network. Objectives are the implementation of infrastructure and data sources to capture plant genomic information into a comprehensive, integrated platform. This will facilitate the systematic exploration of Arabidopsis and other plants. New methods for data exchange, database integration and access are being developed to create a highly integrated, federated data resource for research. The connection between the individual resources is realized with BioMOBY. BioMOBY provides an architecture for the discovery and distribution of biological data through web services. While knowledge is centralized, data is maintained at its primary source without a need for warehousing. To standardize nomenclature and data representation, ontologies and generic data models are defined in interaction with the relevant communities.Minimal data models should make it simple to allow broad integration, while inheritance allows detail and depth to be added to more complex data objects without losing integration. To allow expert annotation and keep databases curated, local and remote annotation interfaces are provided. Easy and direct access to all data is key to the project.     

云南省古茶树资源调查与分析

为更好地保护和开发利用古茶树资源,2010-2017年对云南省12个地区58个县/市的古茶树资源进行了全面普查,依据《Flora of China》英文修订版分类确立了古茶树资源物种名录,建立初步的古茶树资源数据信息库。以此为基础,利用地理信息系统和统计学分析了云南古茶树资源种类组成、地理分布特征、生境类型及形态多样性。结果表明:云南古茶树种类多,调查共获得古茶树资源分布点474个,记录样本植株2570份,隶属7种6变种;古茶树资源分布广而不均,主要分布于滇西、滇南、滇东南及滇中哀牢山山脉,滇东南是古茶树物种多样性的分布中心,滇西是特有种的分化中心,云南古茶树资源的地理分布可能存在滇西-大理茶(Camellia taliensis(W.W.Sm.)Melch.)、滇南-普洱茶(C.sinensis var.assamica(J.W.Mast.)Kitam.)和滇东南-厚轴茶(C.crassicolumna H.T.Chang)3个现有分布中心;古茶树资源生境复杂多样,可大致分为原生林、次生林和高山旱地等3类,不同生境分布的古茶树种类及其生长状况有差异;古茶树资源具有丰富的形态多样性,其描述型性状多样性指数为0.58~1.48,数值型性状变异系数为4.37%~51.03%,总体上营养器官的变异性高于花部器官。本工作为进一步探讨云南地区古茶树资源的系统演化、多样性保护及合理利用提供了重要的本底资料。此外,根据古茶树资源现状,初步提出了一些保护利用建议。     

A proposal for a standard CORBA interface for genome maps

MOTIVATION: The scientific community urgently needs to standardize the exchange of biological data. This is helped by the use of a common protocol and the definition of shared data structures. We have based our standardization work on CORBA, a technology that has become a standard in the past years and allows interoperability between distributed objects. RESULTS: We have defined an IDL specification for genome maps and present it to the scientific community. We have implemented CORBA servers based on this IDL to distribute RHdb and HuGeMap maps. The IDL will co-evolve with the needs of the mapping community. AVAILABILITY: The standard IDL for genome maps is available at http:// corba.ebi.ac.uk/RHdb/EUCORBA/MapIDL.htm l. The IORs to browse maps from Infobiogen and EBI are at http://www.infobiogen.fr/services/Hugemap/IOR and http://corba.ebi.ac.uk/RHdb/EUCORBA/IOR CONTACT: manu@infobiogen.fr, tome@ebi.ac.uk     

Walking the tightrope: trends in African freshwater systematic ichthyology

Africa is blessed with an abundance and rich diversity of freshwater fishes, reflecting its Gondwanan history and geographical position astride the equator. Africa is, however, relatively poorly serviced scientifically, in this respect presenting a challenge to the tension between conserving biodiversity and sustainable development. Biosystematics has experienced several paradigm shifts in the past half century, including the rise of cladistics and more recently the adoption of molecular DNA applications to taxonomy and phylogeny and the assembly and manipulation of large data sets in an era of major development of bioinformatics. The richness of African biodiversity is a magnet to the global systematic community that, to a degree, offsets the disadvantage of an impoverished indigenous scientific capacity. Conservation biology, however, is rooted more closely to the local situation and therefore requires indigenous taxonomic services that are inevitably scarce. Balancing this network of tensions between scientific knowledge generation and application is like walking a tightrope for existing African scientific resources, and to cope it is essential to embrace modern innovative approaches such as barcoding to identify organisms. This paper considers the historical development of African freshwater ichthyology, presents a suite of recent examples illustrating trends in systematic ichthyology in Africa and draws conclusions to suggest that both traditional and new-age approaches to taxonomy are necessary for a complete understanding and appreciation of African freshwater fish diversity and its conservation. The chosen examples also suggest that the tensions between the approaches can be effectively managed provided exponents work collaboratively. The emerging evidence indicates that the combined skills and insight of complex scientific teams including systematists, ecologists, molecular biologists and earth scientists are needed to resolve the deep complexity of evolution in terms of space, time and form.     

淡水鱼类功能多样性及其研究方法

目前,群落功能多样性备受生态学界关注,被认为是能解决生态问题的一种重要途径。我国对于群落功能多样性主要集中在植物群落和微生物群落,而在鱼类群落方面的研究几乎是空白。我国鱼类资源正面临着严重威胁,包括水坝建设导致的鱼类通道受阻、水库形成造成鱼类产卵场功能消失、过度捕捞、水质恶化和富营养化加重、外来种入侵等因素,导致渔业资源急剧衰退,水生生态系统功能下降。以淡水鱼类群落为例,对鱼类功能多样性的数据获取及处理分析与评价、测定指标及计算方法与研究难点等进行综述,以期为鱼类资源保护提供新的理论依据和切入点。     

Object mobility in large scale systems

Standards such as CORBA are spreading in the development of large scale projects. However, CORBA lacks a mobility mechanism which is an interesting feature to deal with system dynamics. In this paper, we propose a generic solution for object mobility in CORBA in the framework of its lifecycle service. Implementation at the object level handles the migration process using intermediary objects. A group mechanism is used to manage the object creation infrastructure so as to allow scalability. We have chosen a multi-agent auto-organizational group mechanism to reduce the administrative task for a large system. Performance tests show that reasonable performance can be achieved using a high level generic and portable implementation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Effects of habitat simplification on assemblages of cavity nesting bees and wasps in a semiarid neotropical conservation area

Habitat complexity is directly correlated to insect diversity in most natural environments. Structural complexity reflects an increase in vertical stratification and plant diversity and often leads to a greater availability of floral resources and nesting sites. Efficient conservation strategies require understanding of how changes in habitat structure affect insects that provide essential ecosystem services. We analyzed how the diversity and species composition of bees and wasps that nest in pre-existing cavities is affected by habitat complexity. Our study was developed in the semiarid region of northeastern Brazil, in the Ubajara National Park and surrounding area. Four types of habitats within two physiognomies were sampled for two consecutive years. We used 120 trap-nest (9000 cavities) distributed in 40 sample points. Overall, 657 cavities were occupied by 11 species of bees, nine of wasps, and six of cleptoparasitic/parasitoids. Bees and wasp diversity increases with habitat complexity. While species richness was higher in more complex physiognomies, abundance was higher in disturbed areas. Species composition also varied with habitat structure. Habitat simplification has adverse effects on the diversity and composition of assemblages. These effects are stronger in more complex habitats indicating that conservation of humid habitats within semiarid areas is essential to maintain bee and wasp regional diversity.