BRIDGING THE GAP BETWEEN TECHNOLOGY AND SCIENCE WITH EXAMPLES FROM ECOLOGY AND BIODIVERSITY

Early informatics focused primarily on the application of technology and computer science to a specific domain; modern informatics has broadened to encompass human and knowledge dimensions. Application of technology is but one aspect of informatics. Understanding domain members’ issues, priorities, knowledge, abilities, interactions, tasks and work environments is another aspect, and one that directly impacts application success. Involving domain members in the design and development of technology in their domain is a key factor in bridging the gap between technology and science. This user-centered design (UCD) approach in informatics is presented via an ecoinformatics case study in three areas: collaboration, usability, and education and training

E-BioFlow: Different Perspectives on Scientific Workflows

We introduce a new type of workflow design system called\ud e-BioFlow and illustrate it by means of a simple sequence alignment workflow. E-BioFlow, intended to model advanced scientific workflows, enables the user to model a workflow from three different but strongly coupled perspectives: the control flow perspective, the data flow perspective, and the resource perspective. All three perspectives are of\ud equal importance, but workflow designers from different domains prefer different perspectives as entry points for their design, and a single workflow designer may prefer different perspectives in different stages of workflow design. Each perspective provides its own type of information, visualisation and support for validation. Combining these three perspectives in a single application provides a new and flexible way of modelling workflows

Mining substructures in protein data

In this paper we consider the 'Prions' database that describes protein instances stored for Human Prion Proteins. The Prions database can be viewed as a database of rooted ordered labeled subtrees. Mining frequent substructures from tree databases is an important task and it has gained a considerable amount of interest in areas such as XML mining, Bioinformatics, Web mining etc. This has given rise to the development of many tree mining algorithms which can aid in structural comparisons, association rule discovery and in general mining of tree structured knowledge representations. Previously we have developed the MB3 tree mining algorithm, which given a minimum support threshold, efficiently discovers all frequent embedded subtrees from a database of rooted ordered labeled subtrees. In this work we apply the algorithm to the Prions database in order to extract the frequently occurring patterns, which in this case are of induced subtree type. Obtaining the set of frequent induced subtrees from the Prions database can potentially reveal some useful knowledge. This aspect will be demonstrated by providing an analysis of the extracted frequent subtrees with respect to discovering interesting protein information. Furthermore, the minimum support threshold can be used as the controlling factor for answering specific queries posed on the Prions dataset. This approach is shown to be a viable technique for mining protein data

All in one Graphical Tool for the management of DIET a GridRPC Middleware

Also available as LIP Research Report 2008-24Grid Middleware are the link between large scale (and distributed) platforms and applications. Managing such a software system and the Grid environment itself can be a hard task when no dedicated (and integrated) tool exist. Some can be used through nice graphical interfaces, but they are usually dedicated to one or some limited tasks. They do not fulfill all the needs of a Grid end-user who wants to deploy Grid applications easily and rapidly. The aim of this paper is to present the case study of an all-in-one software system, designed for the management of a Grid Middleware and gathering user-friendly graphical interfaces answering to the various needs of end-users. Moreover the software system eases the use of the Grid by avoiding the scripting layer under a nice GUI enabling the user a faster and more efficient use of the Grid environment. By this means we demonstrate how the DietDashboard fulfills all the needs of a unified tool for Grid management. This paper gives a comparison with existing and well-known tools dedicated to some specific tasks such as Grid resources management, Grid monitoring, or Middleware management

Advancing Geospatial Data Curation

Digital curation is a new term that encompasses ideas from established disciplines: it defines a set of activities to manage and improve the transfer of the increasing volume of data products from producers of digital scientific and academic data to consumers, both now and in the future. Research topics in this new area are in a formative stage, but a variety of work that can serve to advance the curation of digital geospatial data is reviewed and suggested. Active research regarding geospatial data sets investigates the problems of tracking and reporting the data quality and lineage (provenance) of derived data products in geographic information systems, and managing varied geoprocessing workflow. Improving the descriptive semantics of geospatial operations will assist some of these existing areas of research, in particular lineage retrieval for geoprocessing results. Emerging issues in geospatial curation include the long-term preservation of frequently updated streams of geospatial data, and establishing systematic annotation for spatial data collections

Understanding Mobile Banking Applications’ Security risks through Blog Mining and the Workflow Technology

This paper provides a review of the security aspect of mobile banking applications. We employed blog mining as a research method to analyze blog discussion on security of mobile banking applications. Furthermore, we used the workflow technology to simulate real-life scenarios related to attacks on mobile banking applications. Insights are summarized to help banks and consumers mitigate the security risks of mobile banking applications

Generating eScience Workflows from Statistical Analysis of Prior Data

A number of workflow design tools have been developed specifically to enable easy graphical specification of workflows that ensure systematic scientific data capture and analysis and precise provenance information. We believe that an important component that is missing from these existing workflow specification and enactment systems is integration with tools that enable prior detailed analysis of the existing data - and in particular statistical analysis. By thoroughly analyzing the existing relevant datasets first, it is possible to determine precisely where the existing data is sparse or insufficient and what further experimentation is required. Introducing statistical analysis to experimental design will reduce duplication and costs associated with fruitless experimentation and maximize opportunities for scientific breakthroughs. In this paper we describe a workflow specification system that we have developed for a particular eScience application (fuel cell optimization). Experimental workflow instances are generated as a result of detailed statistical analysis and interactive exploration of the existing datasets. This is carried out through a graphical data exploration interface that integrates the widely-used open source statistical analysis software package, R, as a web service

Teaching Information Security with Workflow Technology – A Case Study Approach

In recent years, there has been a significant increase in the demand from professionals in different areas for improving the curricula regarding information security. The use of authentic case studies in teaching information security offers the potential to effectively engage students in active learning. In this paper, the authors introduce the approach of using workflow technology to compose case studies to enhance information security education. This approach allows students from different disciplines to collaborate in a distributed computing environment in order to learn important information security principles. Two case studies simulating real-life scenarios, including one for an online banking system and one for an online grading system, are recreated within a laboratory setting using workflow technology and are then presented in information security classes. Our educational practice shows that the benefits of using workflow technology in information security education have been well received by students

High-throughput bioinformatics with the Cyrille2 pipeline system

<p>Abstract</p> <p>Background</p> <p>Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses are often interdependent and chained together to form complex workflows or <it>pipelines</it>. Given the volume of the data used and the multitude of computational resources available, specialized pipeline software is required to make high-throughput analysis of large-scale omics datasets feasible.</p> <p>Results</p> <p>We have developed a generic pipeline system called Cyrille2. The system is modular in design and consists of three functionally distinct parts: 1) a web based, graphical user interface (<it>GUI</it>) that enables a pipeline operator to manage the system; 2) the <it>Scheduler</it>, which forms the functional core of the system and which tracks what data enters the system and determines what jobs must be scheduled for execution, and; 3) the <it>Executor</it>, which searches for scheduled jobs and executes these on a compute cluster.</p> <p>Conclusion</p> <p>The Cyrille2 system is an extensible, modular system, implementing the stated requirements. Cyrille2 enables easy creation and execution of high throughput, flexible bioinformatics pipelines.</p

Documenting models and workflows: the next challenge in the field of ecological data management

Los modelos ecológicos se han convertido en una pieza clave de esta ciencia. La generación de conocimiento se consigue en buena medida mediante procesos analíticos más o menos complejos aplicados sobre conjuntos de datos diversos. Pero buena parte del conocimiento necesario para diseñar e implementar esos modelos no está accesible a la comunidad científica. Proponemos la creación de herramientas informáticas para documentar, almacenar y ejecutar modelos ecológicos y flujos de trabajo. Estas herramientas (repositorios de modelos) están siendo desarrolladas por otras disciplinas como la biología molecular o las ciencias de la Tierra. Presentamos un repositorio de modelos (ModeleR) desarrollado en el contexto del Observatorio de seguimiento del cambio global de Sierra Nevada (Granada-Almería). Creemos que los repositorios de modelos fomentarán la cooperación entre científicos, mejorando la creación de conocimiento relevante que podría ser transferido a los tomadores de decisiones.Ecological models have become a key part of this scientific discipline. Most of the knowledge created by ecologists is obtained by applying analytical processes to primary data. But most of the information underlying how to create models or use analytic techniques already published in the scientific literature is not readily available to scientists. We are proposing the creation of computer tools that help to document, store and execute ecological models and scientific workflows. These tools (called model repositories) are being developed by other disciplines such as molecular biology and earth science. We are presenting a model repository (called ModeleR) that has been developed in the context of the Sierra Nevada Global Change Observatory (Granada-Almería. Spain). We believe that model repositories will foster cooperation among scientists, enhancing the creation of relevant knowledge that could be transferred to environmental managers.El desarrollo de ModeleR ha sido financiado por la Consejería de Medio Ambiente y Ordenación del Territorio de la Junta de Andalucía a través de la Red de Información Ambiental (REDIAM), gracias a un convenio llamado “Diseño y creación de un repositorio de modelos para la red de información ambiental de Andalucía”. A.J. Pérez-Luque agradece al MICINN por el contrato PTA 2011-6322-I