A Virtual Research Infrastructure for Genome and Lisa Research in Europe.
In VWCISC we propose a unique working and collaboration environment for international scientific communities. Science is increasingly collaborative at an international level, which enables projects to build teams of specialists best suited to the goals of the research effort, but which also puts heavy burdens on the scientists to communicate with one another. Email and international travel are primary collaboration tools, but increasingly specialist software is being developed to widen the collaboration channel. A number of software collaboration tools have been developed during the last 10 years, within the Grid and Cloud paradigms, that offer scientists easier and more functional ways to collaborate, and in Europe there has been very substantial funding for these efforts. But most scientific communities outside the field of computer science have not taken up these tools; they still rely on travel and email almost exclusively. A big reason is that there is no simple way to access the many different collaboration tools or to integrate them into the work of a project. Individually very useful, the tools still have high support overheads if they are to be employed in international projects. A simple example is the use of Grid-based tools: there is no universal Grid infrastructure software, and even within Europe tools will have to run on Globus in some nations, on gLite in others, and so on. The aim of our proposal, therefore, will be to offer EU scientific projects a general environment for international collaboration that solves the most difficult technical issues and leads to a system that looks identical to users in different countries, that can be installed on their local Grid protocols, that requires only a small amount of local support, that offers within this consistent environment a number of basic collaboration tools that many different projects will find useful, and that additionally offers a simple way of incorporating new tools specific to different projects. The vehicle for this environment will be a web Portal. Such an environment can be made universally accessible and will have a familiar interface. Collaborations that wish to use it will find that their members have a short learning curve and can discover resources intuitively. We will develop a pilot for this Portal that will serve two very different European scientific communities: the SysBio/Genome community and the LISA gravitational-wave research community. By showing how useful the Portal can be for these two projects we will demonstrate that it is a tool that should be useful for many others. In its final release, the Portal will offer an environment for collaboration that features easy infrastructure integration and infrastructure use. It should be also usable for other disciplines later on. The infrastructure will consist of data, software, and digital library repositories, and of compute resources connected into Grids. All the components of the infrastructure should be easily connectable by portlets within the portal. Our solution must allow users to connect new infrastructures easily. So it will be a framework, which contains an administration tool that permits connections to new Grids, digital libraries, software and data repositories, etc... However, the main collaboration tools as • access to digital Libraries, • access to a conference room, with the ability for video conferencing and a virtual white board, • access to an information exchange desk. Here we are not only thinking of different scientific discussion forums, • access to a “Groupware”. Which connects at least personal calendars and meeting scheduler, should be available as templates, where users themselves can supply necessary new configuration data (e.g. the connection data for video conferencing). We have selected the two research fields of the LISA and Gravitational Wave Research on the one hand, and System Biology and Genom research on the other, because both are real international communities, and importantly because they are currently the most successful grid users within Europe. Concerning the access to remote data, compute resources and repositories, these communities have different needs, but they are interested in a solution which can be used in production mode. Because we already use the Grid in production mode, we are aware of the problems of Grid computing, and we have solved them successfully. From our experience we know what is required, in order to have an easy and successful access to the Grid.
|Keywords||Genome, genomics, genome organization, genome architecture, structural sequencing, architectural sequencing, systems genomics, coevolution, holistic genetics, genome mechanics, genome statistical mechanics, genomic uncertainty principle, genome function, genetics, gene regulation, replication, transcription, repair, homologous recombination, simultaneous co-transfection, cell division, mitosis, metaphase, interphase, cell nucleus, nuclear structure, nuclear organization, chromatin density distribution, nuclear morphology, chromosome territories, subchromosomal domains, chromatin loop aggregates, chromatin rosettes, chromatin loops, chromatin fibre, chromatin density, persistence length, spatial distance measurement, histones, H1.0, H2A, H2B, H3, H4, mH2A1.2, DNA sequence, complete sequenced genomes, molecular transport, obstructed diffusion, anomalous diffusion, percolation, long-range correlations, fractal analysis, scaling analysis, exact yard-stick dimension, box-counting dimension, lacunarity dimension, local nuclear dimension, nuclear diffuseness, parallel super computing, grid computing, volunteer computing, Brownian Dynamics, Monte Carlo, fluorescence in situ hybridization, chromatin cross-linking, chromosome conformation capture (3C), selective high-resolution high-throughput chromosome interaction capture (T2C), confocal laser scanning microscopy, fluorescence correlation spectroscopy, super resolution microscopy, spatial precision distance microscopy, auto-fluorescent proteins, CFP, GFP, YFP, DsRed, fusion protein, in vivo labelling, information browser, visual data base access, holistic viewing system, integrative data management, extreme visualization, three-dimensional virtual environment, virtual paper tool.|
|Conference||Laboratoire Astro Particule et Cosmologie (APC), University Diderot-Paris VII, Paris, France, 24th September, 2010.|
Alexander Beck-Ratzka, & Knoch, T.A. (2010, September 24). A Virtual Research Infrastructure for Genome and Lisa Research in Europe. Presented at the Laboratoire Astro Particule et Cosmologie (APC), University Diderot-Paris VII, Paris, France, 24th September, 2010. Retrieved from http://hdl.handle.net/1765/93372