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Carole Goble - One of the best experts on this subject based on the ideXlab platform.

  • using provenance to manage knowledge of in Silico Experiments
    Briefings in Bioinformatics, 2007
    Co-Authors: Robert Stevens, Jun Zhao, Carole Goble
    Abstract:

    This article offers a briefing in one of the knowledge management issues of in Silico Experimentation in bioinformatics. Recording of the provenance of an Experiment-what was done; where, how and why, etc. is an important aspect of scientific best practice that should be extended to in Silico Experimentation. We will do this in the context of eScience which has been part of the move of bioinformatics towards an industrial setting. Despite the computational nature of bioinformatics, these analyses are scientific and thus necessitate their own versions of typical scientific rigour. Just as recording who, what, why, when, where and how of an Experiment is central to the scientific process in laboratory science, so it should be in Silico science. The generation and recording of these aspects, or provenance, of an Experiment are necessary knowledge management goals if we are to introduce scientific rigour into routine bioinformatics. In Silico Experimental protocols should themselves be a form of managing the knowledge of how to perform bioinformatics analyses. Several systems now exist that offer support for the generation and collection of provenance information about how a particular in Silico Experiment was run, what results were generated, how they were generated, etc. In reviewing provenance support, we will review one of the important knowledge management issues in bioinformatics.

  • The Origin and History of in Silico Experiments
    2004
    Co-Authors: Jun Zhao, Robert Stevens, Chris Wroe, Mark A. Greenwood, Carole Goble
    Abstract:

    It is not enough to be able to just run an e-Science in Silico Experiment; it is also vital to be able to understand and interpret the outputs of those Experiments. The results have little value if other scientists, or even the same scientist at a later date, are unable to identify their origin, or provenance. In myGrid, in Silico Experiments are run as workflows; these produce three kinds of results: data outcomes, knowledge outcomes and provenance about the Experiment. These results have a complex interlinking relationship between each other, within the context of the workflow that gave rise to them, as well as across workflows executed in the same or a different study. This poster describes the kind of provenance data recorded in myGrid during a workflow. It introduces myGrid's provenance data model and the Semantic Web-based technology used to support provenance-based tasks. These tasks include the verification and validation of results; the sharing and annotation of results; and the management of resources. For e-Science to succeed it must have provenance data support as its cornerstone.

Robert Stevens - One of the best experts on this subject based on the ideXlab platform.

  • using provenance to manage knowledge of in Silico Experiments
    Briefings in Bioinformatics, 2007
    Co-Authors: Robert Stevens, Jun Zhao, Carole Goble
    Abstract:

    This article offers a briefing in one of the knowledge management issues of in Silico Experimentation in bioinformatics. Recording of the provenance of an Experiment-what was done; where, how and why, etc. is an important aspect of scientific best practice that should be extended to in Silico Experimentation. We will do this in the context of eScience which has been part of the move of bioinformatics towards an industrial setting. Despite the computational nature of bioinformatics, these analyses are scientific and thus necessitate their own versions of typical scientific rigour. Just as recording who, what, why, when, where and how of an Experiment is central to the scientific process in laboratory science, so it should be in Silico science. The generation and recording of these aspects, or provenance, of an Experiment are necessary knowledge management goals if we are to introduce scientific rigour into routine bioinformatics. In Silico Experimental protocols should themselves be a form of managing the knowledge of how to perform bioinformatics analyses. Several systems now exist that offer support for the generation and collection of provenance information about how a particular in Silico Experiment was run, what results were generated, how they were generated, etc. In reviewing provenance support, we will review one of the important knowledge management issues in bioinformatics.

  • The Origin and History of in Silico Experiments
    2004
    Co-Authors: Jun Zhao, Robert Stevens, Chris Wroe, Mark A. Greenwood, Carole Goble
    Abstract:

    It is not enough to be able to just run an e-Science in Silico Experiment; it is also vital to be able to understand and interpret the outputs of those Experiments. The results have little value if other scientists, or even the same scientist at a later date, are unable to identify their origin, or provenance. In myGrid, in Silico Experiments are run as workflows; these produce three kinds of results: data outcomes, knowledge outcomes and provenance about the Experiment. These results have a complex interlinking relationship between each other, within the context of the workflow that gave rise to them, as well as across workflows executed in the same or a different study. This poster describes the kind of provenance data recorded in myGrid during a workflow. It introduces myGrid's provenance data model and the Semantic Web-based technology used to support provenance-based tasks. These tasks include the verification and validation of results; the sharing and annotation of results; and the management of resources. For e-Science to succeed it must have provenance data support as its cornerstone.

  • Performing \emph{In Silico} Experiments on the Grid: A Users' Perspective
    2003
    Co-Authors: Robert Stevens, Kevin Glover, Chris Greenhalgh, C Jennings, S Pearce, Milena Radenkovic, Anil Wipat
    Abstract:

    e-Science and the Grid are not the same; the large-scale movement of data and the exploitation of computation is not the same as the creation, performance and management of an in Silico Experiment. The notion of the marshalling of resources and creation of virtual organisations begins to bring in a flavour of science, but something more is needed over and above the classic Grid to enable e-Science. This paper looks at the requirements of e-Science from the user’s perspective. The Grid project aims to provide a toolkit of services that comprise the Information Grid and the applications that sit there upon. The aim is to provide a set of services that have the facilities to enable bioinformaticians (in particular) to perform in Silico Experiments using applications built upon components from a Grid enabled middleware layer. This paper introduces the Grid project and explores the nature of an in Silico Experiment for the bioinformatics domain. The paper then reviews the general user requirements for an empirical e-Scientist. We then introduce a biological scenario, where bench Experiments are coupled to in Silico Experiments, which we have used to drive the user requirements capture in Grid. Then, the Grid workbench, an application that demonstrates the functionality of Grid is reviewed. Finally, we match the current status of Grid to our general requirements and explore how we can use the current implementation to drive the capture of further, more detailed user requirements.

Lorenzo Scortichini - One of the best experts on this subject based on the ideXlab platform.

  • BioWMS: a web-based Workflow Management System for bioinformatics
    BMC Bioinformatics, 2007
    Co-Authors: Ezio Bartocci, Flavio Corradini, Emanuela Merelli, Lorenzo Scortichini
    Abstract:

    Background An in-Silico Experiment can be naturally specified as a workflow of activities implementing, in a standardized environment, the process of data and control analysis. A workflow has the advantage to be reproducible, traceable and compositional by reusing other workflows. In order to support the daily work of a bioscientist, several Workflow Management Systems (WMSs) have been proposed in bioinformatics. Generally, these systems centralize the workflow enactment and do not exploit standard process definition languages to describe, in order to be reusable, workflows. While almost all WMSs require heavy stand-alone applications to specify new workflows, only few of them provide a web-based process definition tool. Results We have developed BioWMS, a Workflow Management System that supports, through a web-based interface, the definition, the execution and the results management of an in-Silico Experiment. BioWMS has been implemented over an agent-based middleware. It dynamically generates, from a user workflow specification, a domain-specific, agent-based workflow engine. Our approach exploits the proactiveness and mobility of the agent-based technology to embed, inside agents behaviour, the application domain features. Agents are workflow executors and the resulting workflow engine is a multiagent system – a distributed, concurrent system – typically open, flexible, and adaptative. A demo is available at http://litbio.unicam.it:8080/biowms . Conclusion BioWMS, supported by Hermes mobile computing middleware, guarantees the flexibility, scalability and fault tolerance required to a workflow enactment over distributed and heterogeneous environment. BioWMS is funded by the FIRB project LITBIO (Laboratory for Interdisciplinary Technologies in Bioinformatics).

Basile F. E. Curchod - One of the best experts on this subject based on the ideXlab platform.

  • Steering the outcome of a photochemical reaction - an in Silico Experiment on the H2CSO sulfine using few - femtosecond dump pulses.
    The Journal of Chemical Physics, 2019
    Co-Authors: Benoît Mignolet, Basile F. E. Curchod
    Abstract:

    We propose a pump-dump control scheme using sub-10 fs pulses to enhance the photochemical formation of the three-membered C–S–O ring oxathiirane from the parent H2CSO sulfine molecule. The ultrashort nature of the pulses is essential to promptly alter the photoinduced dynamics, e.g., while a bond is elongating, which is key to selectively form the oxathiirane by radiative dumping. We carried out an in Silico pump-dump Experiment with excited-state dynamics simulations that include the interaction with electric field of the pump and dump pulses. By applying the dump pulse when the CS bond is elongating, the population transferred to the ground state will form the oxathiirane with a branching ratio of 4, much higher than the one solely due to nonradiative relaxation (0.66). The overall oxathiirane yield can be increased by up to 17% when the 6 fs IR dump pulse is applied at a delay time of 47 fs.We propose a pump-dump control scheme using sub-10 fs pulses to enhance the photochemical formation of the three-membered C–S–O ring oxathiirane from the parent H2CSO sulfine molecule. The ultrashort nature of the pulses is essential to promptly alter the photoinduced dynamics, e.g., while a bond is elongating, which is key to selectively form the oxathiirane by radiative dumping. We carried out an in Silico pump-dump Experiment with excited-state dynamics simulations that include the interaction with electric field of the pump and dump pulses. By applying the dump pulse when the CS bond is elongating, the population transferred to the ground state will form the oxathiirane with a branching ratio of 4, much higher than the one solely due to nonradiative relaxation (0.66). The overall oxathiirane yield can be increased by up to 17% when the 6 fs IR dump pulse is applied at a delay time of 47 fs.

Curchod, Basile F E - One of the best experts on this subject based on the ideXlab platform.

  • Steering the outcome of a photochemical reaction - an in Silico Experiment on the H2CSO sulfine using few - femtosecond dump pulses.
    'AIP Publishing', 2019
    Co-Authors: Mignolet Benoit, Curchod, Basile F E
    Abstract:

    We propose a pump-dump control scheme using sub-10 fs pulses to enhance the photochemical formation of the three-membered C–S–O ring oxathiirane from the parent H2CSO sulfine molecule. The ultrashort nature of the pulses is essential to promptly alter the photoinduced dynamics, e.g., while a bond is elongating, which is key to selectively form the oxathiirane by radiative dumping. We carried out an in Silico pump-dump Experiment with excited-state dynamics simulations that include the interaction with electric field of the pump and dump pulses. By applying the dump pulse when the CS bond is elongating, the population transferred to the ground state will form the oxathiirane with a branching ratio of 4, much higher than the one solely due to nonradiative relaxation (0.66). The overall oxathiirane yield can be increased by up to 17% when the 6 fs IR dump pulse is applied at a delay time of 47 fs