Computational Grids connect resources and users in a complex way in order to deliver nontrivial qualities of services. According to the current trend various communities build their own Grids and due to the lack of generally accepted standards these Grids are usually not interoperable. As a result, large scale sharing of resources is prevented by the isolation of Grid systems. Similarly, people are isolated, because the collaborative work of Grid users is not supported by current environments. Each user accesses Grids as an individual person without having the possibility of organizing teams that could overcome the difficulties of application development and execution more easily. The paper describes a new workflow-oriented portal concept that solves both problems. It enables the interoperability of various Grids during the execution of workflow applications, and supports users to develop and run their Grid workflows in a collaborative way. The paper also introduces a classification model that can be used to identify workflow-oriented Grid portals based on two general features: Ability to access multiple Grids, and support for collaborative problem solving. Using the approach the different potential portal types are introduced, their unique features are discussed and the portals and Problem Solving Environments (PSE) of our days are classified. The P-GRADE Portal as a Globus-based implementation for the classification model is also presented.
BackgroundMaking forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as “Web services”) and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust “in silico” science. However, use of this approach in biodiversity science and ecology has thus far been quite limited.ResultsBioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible ‘virtual laboratory’, free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity.ConclusionsOur work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12898-016-0103-y) contains supplementary material, which is available to authorized users.
Grid computing has gone through some generations and as a result only a few widely used middleware architectures remain. The Globus Toolkit is the most widespread middleware in most of the current production grid systems, but the LCG-2 middleware dominates in Europe. The paper describes a brokering solution that enables the interoperability of various Globus and LCG-2 based grids during the execution of workflow applications, and supports users to utilize computing and storage resources from multiple production grids by a single application. The development and execution of such applications can be managed by a Web-based Grid portal called P-GRADE Portal, and the brokering of the workflows is carried out by its integrated GTbroker and LCG-2 broker component.
With the increasingly rapid growth of data in life sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. Such approaches necessitate the use of large-scale computational resources and e-infrastructures, such as the European Grid Infrastructure (EGI). EGI, one of key the enablers of the digital European Research Area, is a federation of resource providers set up to deliver sustainable, integrated and secure computing services to European researchers and their international partners. Here we aim to provide the state of the art of Grid/Cloud computing in EU research as viewed from within the field of life sciences, focusing on key infrastructures and projects within the life sciences community. Rather than focusing purely on the technical aspects underlying the currently provided solutions, we outline the design aspects and key characteristics that can be identified across major research approaches. Overall, we aim to provide significant insights into the road ahead by establishing ever-strengthening connections between EGI as a whole and the life sciences community.
Real-time collaborative editing systems allow a group of users to view and edit the same item at the same time from geographically dispersed sites. Consistency maintenance in the face of concurrent accesses to shared entities is one of the core issues in the design of these systems. The paper introduces a locking based approach that grid application developer environments can apply to protect the consistency properties of workflows during collaborative editing scenarios. We developed two pessimistic locking algorithms to assure that under no circumstances can application developers break the acyclic criteria of workflow graphs or add invalid edges to them. We prove that the algorithms result consistent graphs, moreover, do not result the cancellation of any user's editing transaction. We see that the second, improved algorithm gives much better performance in terms of number of concurrent users that can work on a graph.
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