Summary EUBrazilOpenBio is a collaborative initiative addressing strategic barriers in biodiversity research by integrating open access data and user‐friendly tools widely available in Brazil and Europe. The project deploys the EU‐Brazil Hybrid Data Infrastructure that allows the sharing of hardware, software and data on‐demand. This infrastructure provides access to several integrated services and resources to seamlessly aggregate taxonomic, biodiversity and climate data, used by processing services implementing checklist cross‐mapping and ecological niche modelling. A Virtual Research Environment was created to provide users with a single entry point to processing and data resources. This article describes the architecture, demonstration use cases and some experimental results and validation. Copyright © 2014 John Wiley & Sons, Ltd.

Evolutionary computation (EC) paradigms are inspired by the optimization strategies utilized by biological systems. While these strategies can be found in every level of biological organization, almost all of the EC techniques which comprise techniques from evolutionary algorithm (EA) to swarm intelligence (SI) have been inspired by organism level optimization strategies. While EA is based on trans-generational genetic adaptation of organisms (biologically inspired), SI is mainly based on intra-generational collective behavioral adaptation of organisms (socially inspired). This paper describes the optimization strategies that bio-molecules utilize both for intra-generational and trans-generational adaptation of biological cells. These adaptive strategies which are known as epigenetic mechanisms emerged long before any other biological strategy and form the basis for Epigenetic algorithms (EGA). Further, the paper proposes an intra-generational EGA based on bio-molecular degradation and autocatalysis which are ubiquitous cellular processes and are pivotal for the adaptive dynamics and evolution of intelligent cellular organization.

The paper presents a virtual organization (VO) framework which incorporates wireless technology support at the point of care in a clinical environment It reflects a move to patient centric healthcare provided by multi-disciplinary care teams working in an integrated way for patient care. The work highlights the importance of wireless technologies for addressing point of care issues faced by care team members. It describes VO and Computer Supported Cooperative Work (CSCW) aspects in the clinical environment and analyzes existing virtual and collaborative infrastructures in the healthcare literature. In the light of current problem analysis, it proposes the approach of patient centric virtual organizations (PCVOs) development in the clinical environment PCVOs provide improved provision and sharing of patient information at the point of care which leads to enhanced collaborative working patterns for the care team members. In a comprehensive way, it discusses the study results and focuses on the development, implementation and evaluation strategy for the pilot prototype of case study conducted at a local NHS Cancer Centre for possible improvements in patient care infrastructure.

OGSA-DAI is an open-source middleware designed to facilitate the access and integration of distributed heterogeneous data resources. It provides a ready-made framework that promotes locality and product transparency to connect data resources to the grid environment. This paper reports on the evaluation of OGSA-DAI for bioinformatics grid applications by the BioDA project. We based our study on dialogue with OGSA-DAI and grid project developers as well as through practical case studies involving current projects. We also reveal the challenges and strategies in developing an OGSA-DAI exemplar for one of these projects, BiodiversityWorld - a grid-based problem solving environment that specializes in the exploration and analysis of patterns in global biodiversity. Finally, we summarize the key issues for projects considering adopting OGSA-DAI.

In the Biodiversity World (BDW) project we have created a flexible and extensible Web services-based grid environment for biodiversity researchers to solve problems in biodiversity and analyse biodiversity patterns. In this environment, heterogeneous and globally distributed biodiversity-related resources such as data sets and analytical tools are made available to be accessed and assembled by users into workflows to perform complex scientific experiments. One such experiment is bioclimatic modelling of the geographical distribution of individual species using climate variables in order to predict past and future climate-related changes in species distribution. Data sources and analytical tools required for such analysis of species distribution are widely dispersed, available on heterogeneous platforms, present data in different formats and lack interoperability. The BDW system brings all these disparate units together so that the user can combine tools with little thought as to their availability, data formats and interoperability. We describe the architecture of the BDW problem solving environment (PSE) consisting of a number of components providing uniform access to heterogeneous resources and analytical tools. Architectural components of the BDW system include a workflow management tool, resource wrappers, a communications layer, BDW datatypes and a metadata repository.

In the GRAB (Grid and Biodiversity) project we are developing a prototype to illustrate some aspects of the GRID's potential for collaborative biodiversity research. A catalogue of life, two species information systems (SISs) and a climate database are made available in a problem solving environment that demonstrates how bioclimatic modelling can be performed by bringing together such resources. We use Globus to provide access to these resources, in a secure environment. We also discuss more generally the GRID's potential for biodiversity research, and identify the main areas of development within the GRID that are needed to support such research.

Due to the evolutionary nature of the engineering design process it is necessary to provide support for version management. The version model should be provided with an integrity checking mechanism to assure the consistency of object versions with the design constraints. Managing integrity constraints is complex due to their evolving nature and raises a number of issues that need to be dealt with. We present a conceptual framework for providing an integrity mechanism for object versions. The framework is based on the concept of the Constraint Version Object (CVO).

Concurrent engineering (CE) is a product development approach which requires a collaborative multidisciplinary team environment with effective communication. Due to the evolutionary nature of the engineering design process, it is necessary to provide support for version management. The version model should be provided with an integrity checking mechanism to assure the consistency of object versions with the design constraints. Managing integrity constraints is complex due to their evolving nature and raises a number of issues that need to be dealt with. The authors present a conceptual framework for providing an integrity mechanism for object versions. The framework is based on the concept of the Constraint Version Object (CVO).

Knowledge fusion refers to the process of locating and extracting knowledge from multiple, heterogeneous on-line sources, and transforming it so that the union of the knowledge can be applied in problem-solving. The KRAFT project has defined a generic agent-based architecture to support fusion of knowledge in the form of constraints expressed against an object data model. KRAFT employs three kinds of agent: facilitators locate appropriate on-line sources of knowledge; wrappers transform heterogeneous knowledge to a homogeneous constraint interchange format; mediators fuse the constraints together with associated data to form a dynamically-composed constraint satisfaction problem, which is then passed to an existing constraint solver engine to compute solutions. The paper presents the KRAFT architecture and the three kinds of agent, and includes a description of a demonstration KRAFT application in the domain of telecommunications service provision.

A principal problem with integrity constraints' use for monitoring dynamically changing database integrity is evaluation cost. This cost associated with performance of checking mechanisms is the main quantitative measure which must be supervised carefully. Based on literature, evaluating an integrity constraint cost includes these main components: (i) data amount accessed; (ii) data amount transferred across network; and (iii) number of sites involved. In distributed databases, where many networked sites are involved, not only amount of data accessed must be minimized but also amount of data transferred across network and number of sites involved. In [Ibrahim H, Gray WA, Fiddian NJ. SICSDD: Techniques and implementation. In Proceedings of Constraint Databases and Applications, Second International Workshop on Constraint Database Systems (CDB'97), Delphi, Greece, January 1997, pp 187–207], we introduced an integrity constraint subsystem for a relational distributed database. The subsystem consists of several techniques necessary for efficient constraint checking, particularly in a distributed environment where data distribution is transparent to application domain. Here, we show how these techniques effectively reduce constraint checking cost in such a distributed environment. This is done by analyzing and comparing generated simplified forms to respective initial constraints respecting amount of data to be accessed, amount of data transferred across network, and number of sites involved during evaluation of constraints or simplified forms. Generally, our strategy reduces data amount needing to be accessed since only fragments of relations subject to update are evaluated. Data amount transferred across network and number of sites that are involved are minimized by evaluating simplified forms at target site, i.e., site where update is performed. © 2001 John Wiley & Sons, Inc.

We demonstrate a prototype toolkit that uses constraints and constraint violation repair techniques to enable the automated detection and, where possible, the automated resolution of conflicts in taxonomic databases.

The LITCHI project is concerned with the integration and maintenance of databases of biological knowledge organised by species. We use constraints pertaining to good taxonomic practice in order to identify taxonomix conflicts in individual species databases and in databases formed by merging species databases from distinct sources. The LITCHI system can be used to resolve such conflicts incrementally. As the project has progressed, we have identified a number of distinctive features of the problem domain, and needs of the intended users, which have had a significant impact on the techniques and modes of operation that we found to be appropriate, especially in contrast with applications that handle rapidly-accumulating 'raw' data. It is upon these aspects of LITCHI that we concentrate in the present paper viewing LITCHI as an example of the more general problem of merging scientific data sets in which conflicts between the terminology used can occur.

Over recent years, international initiatives such as the 1993 UN Convention on Biological Diversity have highlighted the need for information about species diversity on a global scale. However, attempts to build global information systems by integrating smaller, independently created biodiversity databases have been hampered by differences in the sets of species names used. Some databases use different names to refer to the same species, while in other cases the same name can be applied to differing definitions of a species, or even entirely different species. The LITCHI project aims to assist biologists in the integration of databases by searching for conflicts within taxonomic checklists (i.e. lists of the species names used in a database and the relationships between them). In order to detect such conflicts, we have created a formal model of taxonomic practice, which describes (amongst other things) what it means for a checklist to be consistent and well-specified. This model has been used as the basis for a prototype tool that uses Prolog to search for naming conflicts within a relational database of checklists. We describe the background to our formal model and show how it has been used to implement the LITCHI system. Our prototype tool is already proving its worth by detecting conflicts and errors within real taxonomic checklists.

Summary form only given. The LITCHI project (Logic-based Integration of Taxonomic Conflicts in Heterogeneous Information Systems) aims to develop software to enable the automated detection and, where possible, resolution of conflicts in taxonomic checklists. A taxonomic checklist is a list of the names of species (and other taxa) used within a particular biological database. Since species names are typically used to gain access to data within biological databases, checklists provide a concise representation of the data values that can act as keys when querying such databases. More importantly, species names are also typically used as the join attribute when integrating several biological databases. However, naming of species is a subjective activity, and different scientific communities will have different ideas about the names that should be used for particular species. These conflicts of opinion arise as a result of the subjective nature of the classification process and geographical or historical differences in background knowledge. Some communities may use different names for the same species, while other groups of scientists may use the same name to refer to different species. Often, there is no one right naming scheme, but some consistent set of names must be used if biological databases are to be integrated. Therefore, there is a real need for a tool which will assist biologists in the integration of checklists, prior to the integration of species databases, so that these differences of opinion can be resolved.

The immense size of the distributed WWW knowledge-base and the dramatic rapid increase in the volume of data on the Internet, requires techniques and tools that reduce users' information overload and improve the effectiveness of on-line information access. Despite the potential benefits of existing indexing, retrieving and searching techniques in assisting users in the browsing process, little has been done to ensure that the information presented is as accurate and focused as individual or group of users would like it to be. In this paper we present a system that attempts to generate optimum results from this rich and ever flourishing knowledge-base. It makes use of the output produced from previously developed systems and generates a user profile to cater for the specific needs and interests of a particular group of users. This paper discusses the design issues involved, as well as practical issues such as interface agents, user profile generation, usability, and evolvability.

Resolving different levels of heterogeneity present in heterogeneous database environments is a subject that has been addressed in a number of research projects. Graphical user interfaces are becoming the de-facto form of user interface in many application areas, including database management systems. The use of a popular visualisation notation to present schemas at an abstract level and to permit direct user manipulation of this visualisation in formulating queries is one of the most widespread approaches to providing database graphical user interfaces. The existence of a variety of visualisation notations (which are in common use to visualise schemas) introduces additional heterogeneity to a distributed system, in visual representation at the end-user interface level. This paper describes the use of meta-programming techniques which are applied to resolve this visual model heterogeneity on existing databases, by allowing a user to select a preferred visualisation notation, both to view the schema and to query the database.

In the context of this paper a computing software system consists of a database, an associated user interface which allows users to analyse the data and the routines or programs which implement the analytic functions available through the user interface. It is assumed that the complete system - source code and data - already exists in a form which is as easily portable as possible between different computer environments. For such systems adaptability is the problem of adjusting the user interface and analytic capabilities to suit different user communities when such a system is transferred from one environment to another. This may include adaptation to specific hardware facilities as well as user requirements.In 1977/8 the International Planned Parenthood Federation (IPPF) funded a project at University College Cardiff to implement a portable computing software system originating from the Population Dynamics Group (PDG) at the University of Illinois. This system allowed users to perform population projections under different demographic conditions showing in a graphical presentation how the population of a country varies over selected time spans. The database consisted of population statistics for a number of countries. When implemented at Cardiff it was intended that this system should be used as a demographic training aid by the post graduate diploma students in the David Owen Centre for Population Growth Studies. These students are an international group who are specialists in the field of demography but have little or no computing background.This paper will discuss briefly how this portable system was implemented on a PDP 11 minicomputer at Cardiff and then give a fuller description of the adaptation of the user interface and analytic capabilities to the local community and its computer facilities. General conclusions will be drawn as to how such systems should be written so as to ease the problems of adaptability.

In most general purpose computer systems there is a wide variety of software available to users. Such software is usually provided in one of three organisational forms - routines in a library; collections of related functions grouped in a package with a common interface; independent programs called through operating system commands. This interdependent tripartite structure creates problems for non-sophisticated users as it involves different levels of user interface complexity.At the routine level a user must write programs in an appropriate host programming language to use the software. If he wishes to use a selection of routines written in incompatible languages then he may have to familiarise himself with more than one host language. In each language he must be aware of the calling conventions for routines, the possible representations of various types of data, the methods of passing parameters and the ways of inputting and outputting data to and from the external environment. This type of interface occurs with libraries like NAG and IMSL.