Python as a Federation Tool for GENESIS 3.0

The GENESIS simulation platform was one of the first broad-scale modeling systems in computational biology to encourage modelers to develop and share model features and components. Supported by a large developer community, it participated in innovative simulator technologies such as benchmarking, parallelization, and declarative model specification and was the first neural simulator to define bindings for the Python scripting language. An important feature of the latest version of GENESIS is that it decomposes into self-contained software components complying with the Computational Biology Initiative federated software architecture. This architecture allows separate scripting bindings to be defined for different necessary components of the simulator, e.g., the mathematical solvers and graphical user interface. Python is a scripting language that provides rich sets of freely available open source libraries. With clean dynamic object-oriented designs, they produce highly readable code and are widely employed in specialized areas of software component integration. We employ a simplified wrapper and interface generator to examine an application programming interface and make it available to a given scripting language. This allows independent software components to be ‘glued’ together and connected to external libraries and applications from user-defined Python or Perl scripts. We illustrate our approach with three examples of Python scripting. (1) Generate and run a simple single-compartment model neuron connected to a stand-alone mathematical solver. (2) Interface a mathematical solver with GENESIS 3.0 to explore a neuron morphology from either an interactive command-line or graphical user interface. (3) Apply scripting bindings to connect the GENESIS 3.0 simulator to external graphical libraries and an open source three dimensional content creation suite that supports visualization of models based on electron microscopy and their conversion to computational models. Employed in this way, the stand-alone software components of the GENESIS 3.0 simulator provide a framework for progressive federated software development in computational neuroscience

ProteinParser:a Community Based Tool for the Generation of a Detailed Protein Consensus and FASTA Output

Comparison of bioinformatic data is a common application in the life sciences and beyond. In this communication, a novel Java based software tool, ProteinParser, is outlined. This soft- ware tool calculates a detailed consensus, or most common, amino acid at a given position in an aligned protein set, whilst also generating a full consensus protein FASTA output. A second application of this software tool, computing a consensus amino acid given a toler- ance threshold, is also demonstrated. The phytase and the common bacterial �-lactamase proteins are analysed as ‘proof of concept’ examples. Consensus proteins, as generated by ProteinParser, are regularly utilised in the selection of residues for protein stabilisation muta- genesis; however, this widely applicable software tool will find many alternative applications in areas such as protein homology modelling

Web-based support for managing large collections of software artefacts

There has been a long history of CASE tool development, with an underlying software repository at the heart of most systems. Usually such tools, even the more recently web-based systems, are focused on supporting individual projects within an enterprise or across a number of distributed sites. Little support for maintaining large heterogeneous collections of software artefacts across a number of projects has been developed. Within the GENESIS project, this has been a key consideration in the development of the Open Source Component Artefact Repository (OSCAR). Its most recent extensions are explicitly addressing the provision of cross project global views of large software collections as well as historical views of individual artefacts within a collection. The long-term benefits of such support can only be realised if OSCAR is widely adopted and various steps to facilitate this are described

An artefact repository to support distributed software engineering

The Open Source Component Artefact Repository (OSCAR) system is a component of the GENESIS platform designed to non-invasively inter-operate with work-flow management systems, development tools and existing repository systems to support a distributed software engineering team working collaboratively. Every artefact possesses a collection of associated meta-data, both standard and domain-specific presented as an XML document. Within OSCAR, artefacts are made aware of changes to related artefacts using notifications, allowing them to modify their own meta-data actively in contrast to other software repositories where users must perform all and any modifications, however trivial. This recording of events, including user interactions provides a complete picture of an artefact's life from creation to (eventual) retirement with the intention of supporting collaboration both amongst the members of the software engineering team and agents acting on their behalf

Environments to support collaborative software engineering

With increasing globalisation of software production, widespread use of software components, and the need to maintain software systems over long periods of time, there has been a recognition that better support for collaborative working is needed by software engineers. In this paper, two approaches to developing improved system support for collaborative software engineering are described: GENESIS and OPHELIA. As both projects are moving towards industrial trials and eventual publicreleases of their systems, this exercise of comparing and contrasting our approaches has provided the basis for future collaboration between our projects particularly in carrying out comparative studies of our approaches in practical use

Support for collaborative component-based software engineering

Collaborative system composition during design has been poorly supported by traditional CASE tools (which have usually concentrated on supporting individual projects) and almost exclusively focused on static composition. Little support for maintaining large distributed collections of heterogeneous software components across a number of projects has been developed. The CoDEEDS project addresses the collaborative determination, elaboration, and evolution of design spaces that describe both static and dynamic compositions of software components from sources such as component libraries, software service directories, and reuse repositories. The GENESIS project has focussed, in the development of OSCAR, on the creation and maintenance of large software artefact repositories. The most recent extensions are explicitly addressing the provision of cross-project global views of large software collections and historical views of individual artefacts within a collection. The long-term benefits of such support can only be realised if OSCAR and CoDEEDS are widely adopted and steps to facilitate this are described. This book continues to provide a forum, which a recent book, Software Evolution with UML and XML, started, where expert insights are presented on the subject. In that book, initial efforts were made to link together three current phenomena: software evolution, UML, and XML. In this book, focus will be on the practical side of linking them, that is, how UML and XML and their related methods/tools can assist software evolution in practice. Considering that nowadays software starts evolving before it is delivered, an apparent feature for software evolution is that it happens over all stages and over all aspects. Therefore, all possible techniques should be explored. This book explores techniques based on UML/XML and a combination of them with other techniques (i.e., over all techniques from theory to tools). Software evolution happens at all stages. Chapters in this book describe that software evolution issues present at stages of software architecturing, modeling/specifying, assessing, coding, validating, design recovering, program understanding, and reusing. Software evolution happens in all aspects. Chapters in this book illustrate that software evolution issues are involved in Web application, embedded system, software repository, component-based development, object model, development environment, software metrics, UML use case diagram, system model, Legacy system, safety critical system, user interface, software reuse, evolution management, and variability modeling. Software evolution needs to be facilitated with all possible techniques. Chapters in this book demonstrate techniques, such as formal methods, program transformation, empirical study, tool development, standardisation, visualisation, to control system changes to meet organisational and business objectives in a cost-effective way. On the journey of the grand challenge posed by software evolution, the journey that we have to make, the contributory authors of this book have already made further advances

An evaluation framework to drive future evolution of a research prototype

The Open Source Component Artefact Repository (OSCAR) requires evaluation to confirm its suitability as a development environment for distributed software engineers. The evaluation will take note of several factors including usability of OSCAR as a stand-alone system, scalability and maintainability of the system and novel features not provided by existing artefact management systems. Additionally, the evaluation design attempts to address some of the omissions (due to time constraints) from the industrial partner evaluations. This evaluation is intended to be a prelude to the evaluation of the awareness support being added to OSCAR; thus establishing a baseline to which the effects of awareness support may be compared

Historical awareness support and its evaluation in collaborative software engineering

The types of awareness relevant to collaborative soft- ware engineering are identified and an additional type, "historical awareness" is proposed. This new type of awareness is the knowledge of how software artefacts re- sulting from collaboration have evolved in the course of their development. The types of awareness that different software engineer- ing environment architectures can support are discussed. A way to add awareness support to our existing OSCAR sys- tem, a component of the GENESIS software engineering platform, is proposed. Finally ways of instrumenting and evaluating the awareness support offered by the modified system are outlined