21,006 research outputs found
Abstract State Machines 1988-1998: Commented ASM Bibliography
An annotated bibliography of papers which deal with or use Abstract State
Machines (ASMs), as of January 1998.Comment: Also maintained as a BibTeX file at http://www.eecs.umich.edu/gasm
Open issues in semantic query optimization in relational DBMS
After two decades of research into Semantic Query Optimization (SQO) there is clear agreement as to the efficacy of SQO. However, although there are some experimental implementations there are still no commercial implementations. We
first present a thorough analysis of research into SQO. We identify three problems which inhibit the effective use of SQO in Relational Database Management Systems(RDBMS). We then propose solutions to these problems and describe first steps towards the implementation of an effective semantic query optimizer for relational databases
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
Background: Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the
biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in
the use of models as well as the development of improved software systems and the availability of better, cheaper
computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model
repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in
these repositories should be extensively tested and encoded in community-supported and standardised formats. In
addition, the models and their components should be cross-referenced with other resources in order to allow their
unambiguous identification.
Description: BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a
freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative
models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by
BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled
vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various
formats. Reaction network diagrams generated from the models are also available in several formats. BioModels
Database also provides features such as online simulation and the extraction of components from large scale models
into smaller submodels. Finally, the system provides a range of web services that external software systems can use to
access up-to-date data from the database.
Conclusions: BioModels Database has become a recognised reference resource for systems biology. It is being used by
the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the
clustering of models based upon their annotations. Model deposition to the database today is advised by several
publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying
software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU
General Public License
Designing Reusable Systems that Can Handle Change - Description-Driven Systems : Revisiting Object-Oriented Principles
In the age of the Cloud and so-called Big Data systems must be increasingly
flexible, reconfigurable and adaptable to change in addition to being developed
rapidly. As a consequence, designing systems to cater for evolution is becoming
critical to their success. To be able to cope with change, systems must have
the capability of reuse and the ability to adapt as and when necessary to
changes in requirements. Allowing systems to be self-describing is one way to
facilitate this. To address the issues of reuse in designing evolvable systems,
this paper proposes a so-called description-driven approach to systems design.
This approach enables new versions of data structures and processes to be
created alongside the old, thereby providing a history of changes to the
underlying data models and enabling the capture of provenance data. The
efficacy of the description-driven approach is exemplified by the CRISTAL
project. CRISTAL is based on description-driven design principles; it uses
versions of stored descriptions to define various versions of data which can be
stored in diverse forms. This paper discusses the need for capturing holistic
system description when modelling large-scale distributed systems.Comment: 8 pages, 1 figure and 1 table. Accepted by the 9th Int Conf on the
Evaluation of Novel Approaches to Software Engineering (ENASE'14). Lisbon,
Portugal. April 201
OPEN SOURCE HBIM FOR CULTURAL HERITAGE: A PROJECT PROPOSAL
Actual technologies are changing Cultural Heritage research, analysis, conservation and development ways, allowing new innovative
approaches. The possibility of integrating Cultural Heritage data, like archaeological information, inside a three-dimensional
environment system (like a Building Information Modelling) involve huge benefits for its management, monitoring and valorisation.
Nowadays there are many commercial BIM solutions. However, these tools are thought and developed mostly for architecture design
or technical installations. An example of better solution could be a dynamic and open platform that might consider Cultural Heritage
needs as priority. Suitable solution for better and complete data usability and accessibility could be guaranteed by open source
protocols. This choice would allow adapting software to Cultural Heritage needs and not the opposite, thus avoiding methodological
stretches.
This work will focus exactly on analysis and experimentations about specific characteristics of these kind of open source software
(DBMS, CAD, Servers) applied to a Cultural Heritage example, in order to verifying their flexibility, reliability and then creating a
dynamic HBIM open source prototype. Indeed, it might be a starting point for a future creation of a complete HBIM open source
solution that we could adapt to others Cultural Heritage researches and analysis
Designing Traceability into Big Data Systems
Providing an appropriate level of accessibility and traceability to data or
process elements (so-called Items) in large volumes of data, often
Cloud-resident, is an essential requirement in the Big Data era.
Enterprise-wide data systems need to be designed from the outset to support
usage of such Items across the spectrum of business use rather than from any
specific application view. The design philosophy advocated in this paper is to
drive the design process using a so-called description-driven approach which
enriches models with meta-data and description and focuses the design process
on Item re-use, thereby promoting traceability. Details are given of the
description-driven design of big data systems at CERN, in health informatics
and in business process management. Evidence is presented that the approach
leads to design simplicity and consequent ease of management thanks to loose
typing and the adoption of a unified approach to Item management and usage.Comment: 10 pages; 6 figures in Proceedings of the 5th Annual International
Conference on ICT: Big Data, Cloud and Security (ICT-BDCS 2015), Singapore
July 2015. arXiv admin note: text overlap with arXiv:1402.5764,
arXiv:1402.575
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