COEL: A Web-based Chemistry Simulation Framework

The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

Enriched biodiversity data as a resource and service

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts

Distributed aop middleware for large-scale scenarios

En aquesta tesi doctoral presentem una proposta de middleware distribuït pel desenvolupament d'aplicacions de gran escala. La nostra motivació principal és permetre que les responsabilitats distribuïdes d'aquestes aplicacions, com per exemple la replicació, puguin integrar-se de forma transparent i independent. El nostre enfoc es basa en la implementació d'aquestes responsabilitats mitjançant el paradigma d'aspectes distribuïts i es beneficia dels substrats de les xarxes peer-to-peer (P2P) i de la programació orientada a aspectes (AOP) per realitzar-ho de forma descentralitzada, desacoblada, eficient i transparent. La nostra arquitectura middleware es divideix en dues capes: un model de composició i una plataforma escalable de desplegament d'aspectes distribuïts. Per últim, es demostra la viabilitat i aplicabilitat del nostre model mitjançant la implementació i experimentació de prototipus en xarxes de gran escala reals.In this PhD dissertation we present a distributed middleware proposal for large-scale application development. Our main aim is to separate the distributed concerns of these applications, like replication, which can be integrated independently and transparently. Our approach is based on the implementation of these concerns using the paradigm of distributed aspects. In addition, our proposal benefits from the peer-to-peer (P2P) networks and aspect-oriented programming (AOP) substrates to provide these concerns in a decentralized, decoupled, efficient, and transparent way. Our middleware architecture is divided into two layers: a composition model and a scalable deployment platform for distributed aspects. Finally, we demonstrate the viability and applicability of our model via implementation and experimentation of prototypes in real large-scale networks

JISC Preservation of Web Resources (PoWR) Handbook

Handbook of Web Preservation produced by the JISC-PoWR project which ran from April to November 2008. The handbook specifically addresses digital preservation issues that are relevant to the UK HE/FE web management community”. The project was undertaken jointly by UKOLN at the University of Bath and ULCC Digital Archives department

Neuron Depot: keeping your colleagues in sync by combining modern cloud storage services, the local file system, and simple web applications

Neuroscience today deals with a "data deluge" derived from the availability of high-throughput sensors of brain structure and brain activity, and increased computational resources for detailed simulations with complex output. We report here (1) a novel approach to data sharing between collaborating scientists that brings together file system tools and cloud technologies, (2) a service implementing this approach, called NeuronDepot, and (3) an example application of the service to a complex use case in the neurosciences. The main drivers for our approach are to facilitate collaborations with a transparent, automated data flow that shields scientists from having to learn new tools or data structuring paradigms. Using NeuronDepot is simple: one-time data assignment from the originator and cloud based syncing thus making experimental and modeling data available across the collaboration with minimum overhead. Since data sharing is cloud based, our approach opens up the possibility of using new software developments and hardware scalabitliy which are associated with elastic cloud computing. We provide an implementation that relies on existing synchronization services and is usable from all devices via a reactive web interface. We are motivating our solution by solving the practical problems of the GinJang project, a collaboration of three universities across eight time zones with a complex workflow encompassing data from electrophysiological recordings, imaging, morphological reconstructions, and simulations

MAGDA: A Mobile Agent based Grid Architecture

Mobile agents mean both a technology and a programming paradigm. They allow for a flexible approach which can alleviate a number of issues present in distributed and Grid-based systems, by means of features such as migration, cloning, messaging and other provided mechanisms. In this paper we describe an architecture (MAGDA – Mobile Agent based Grid Architecture) we have designed and we are currently developing to support programming and execution of mobile agent based application upon Grid systems

Alternate Means of Digital Design Communication

This thesis reconceptualises communication in digital design as an integrated social and technical process. The friction in the communicative processes pertaining to digital design can be traced to the fact that current research and practice emphasise technical concerns at the expense of social aspects of design communication. With the advent of BIM (Building Information Modelling), a code model of communication (machine-to-machine) is inadequately applied to design communication. This imbalance is addressed in this thesis by using inferential models of communication to capture and frame the psychological and social aspects behind the communicative contracts between people. Three critical aspects of the communicative act have been analysed, namely (1) data representation, (2) data classification and (3) data transaction, with the help of a new digital design communication platform, Speckle, which was developed during this research project for this purpose. By virtue of an applied living laboratory context, Speckle facilitated both qualitative and quantitative comparisons against existing methodologies with data from real-world settings. Regarding data representation (1), this research finds that the communicative performance of a low-level composable object model is better than that of a complete and universal one as it enables a more dynamic process of ontological revision. This implies that current practice and research operates at an inappropriate level of abstraction. On data classification (2), this thesis shows that a curatorial object-based data sharing methodology, as opposed to the current file-based approaches, leads to increased relevancy and a reduction in noise (information without intent, or meaning). Finally, on data transaction (3), the analysis shows that an object-based data sharing methodology is technically better suited to enable communicative contracts between stakeholders. It allows for faster and more meaningful change-dependent transactions, as well as allow for the emergence of traceable communicative networks outside of the predefined exchanges of current practices