HyperLoom: A platform for defining and executing scientific pipelines in distributed environments

Real-world scientific applications often encompass end-to-end data processing pipelines composed of a large number of interconnected computational tasks of various granularity. We introduce HyperLoom, an open source platform for defining and executing such pipelines in distributed environments and providing a Python interface for defining tasks. HyperLoom is a self-contained system that does not use an external scheduler for the actual execution of the task. We have successfully employed HyperLoom for executing chemogenomics pipelines used in pharmaceutic industry for novel drug discovery.6

Modelling of Multi-Agent Systems: Experiences with Membrane Computing and Future Challenges

Formal modelling of Multi-Agent Systems (MAS) is a challenging task due to high complexity, interaction, parallelism and continuous change of roles and organisation between agents. In this paper we record our research experience on formal modelling of MAS. We review our research throughout the last decade, by describing the problems we have encountered and the decisions we have made towards resolving them and providing solutions. Much of this work involved membrane computing and classes of P Systems, such as Tissue and Population P Systems, targeted to the modelling of MAS whose dynamic structure is a prominent characteristic. More particularly, social insects (such as colonies of ants, bees, etc.), biology inspired swarms and systems with emergent behaviour are indicative examples for which we developed formal MAS models. Here, we aim to review our work and disseminate our findings to fellow researchers who might face similar challenges and, furthermore, to discuss important issues for advancing research on the application of membrane computing in MAS modelling.Comment: In Proceedings AMCA-POP 2010, arXiv:1008.314

HPC Cloud for Scientific and Business Applications: Taxonomy, Vision, and Research Challenges

High Performance Computing (HPC) clouds are becoming an alternative to on-premise clusters for executing scientific applications and business analytics services. Most research efforts in HPC cloud aim to understand the cost-benefit of moving resource-intensive applications from on-premise environments to public cloud platforms. Industry trends show hybrid environments are the natural path to get the best of the on-premise and cloud resources---steady (and sensitive) workloads can run on on-premise resources and peak demand can leverage remote resources in a pay-as-you-go manner. Nevertheless, there are plenty of questions to be answered in HPC cloud, which range from how to extract the best performance of an unknown underlying platform to what services are essential to make its usage easier. Moreover, the discussion on the right pricing and contractual models to fit small and large users is relevant for the sustainability of HPC clouds. This paper brings a survey and taxonomy of efforts in HPC cloud and a vision on what we believe is ahead of us, including a set of research challenges that, once tackled, can help advance businesses and scientific discoveries. This becomes particularly relevant due to the fast increasing wave of new HPC applications coming from big data and artificial intelligence.Comment: 29 pages, 5 figures, Published in ACM Computing Surveys (CSUR

Active architecture for pervasive contextual services

International Workshop on Middleware for Pervasive and Ad-hoc Computing MPAC 2003), ACM/IFIP/USENIX International Middleware Conference (Middleware 2003), Rio de Janeiro, Brazil This work was supported by the FP5 Gloss project IST2000-26070, with partners at Trinity College Dublin and Université Joseph Fourier, and by EPSRC grants GR/M78403/GR/M76225, Supporting Internet Computation in Arbitrary Geographical Locations, and GR/R45154, Bulk Storage of XML Documents.Pervasive services may be defined as services that are available "to any client (anytime, anywhere)". Here we focus on the software and network infrastructure required to support pervasive contextual services operating over a wide area. One of the key requirements is a matching service capable of as-similating and filtering information from various sources and determining matches relevant to those services. We consider some of the challenges in engineering a globally distributed matching service that is scalable, manageable, and able to evolve incrementally as usage patterns, data formats, services, network topologies and deployment technologies change. We outline an approach based on the use of a peer-to-peer architecture to distribute user events and data, and to support the deployment and evolution of the infrastructure itself.Peer reviewe