27,504 research outputs found
A Web-Based Distributed Virtual Educational Laboratory
Evolution and cost of measurement equipment, continuous training, and distance learning make it difficult to provide a complete set of updated workbenches to every student. For a preliminary familiarization and experimentation with instrumentation and measurement procedures, the use of virtual equipment is often considered more than sufficient from the didactic point of view, while the hands-on approach with real instrumentation and measurement systems still remains necessary to complete and refine the student's practical expertise. Creation and distribution of workbenches in networked computer laboratories therefore becomes attractive and convenient. This paper describes specification and design of a geographically distributed system based on commercially standard components
Grid Added Value to Address Malaria
Through this paper, we call for a distributed, internet-based collaboration
to address one of the worst plagues of our present world, malaria. The spirit
is a non-proprietary peer-production of information-embedding goods. And we
propose to use the grid technology to enable such a world wide "open source"
like collaboration. The first step towards this vision has been achieved during
the summer on the EGEE grid infrastructure where 46 million ligands were docked
for a total amount of 80 CPU years in 6 weeks in the quest for new drugs.Comment: 7 pages, 1 figure, 6th IEEE International Symposium on Cluster
Computing and the Grid, Singapore, 16-19 may 2006, to appear in the
proceeding
Innovative in silico approaches to address avian flu using grid technology
The recent years have seen the emergence of diseases which have spread very
quickly all around the world either through human travels like SARS or animal
migration like avian flu. Among the biggest challenges raised by infectious
emerging diseases, one is related to the constant mutation of the viruses which
turns them into continuously moving targets for drug and vaccine discovery.
Another challenge is related to the early detection and surveillance of the
diseases as new cases can appear just anywhere due to the globalization of
exchanges and the circulation of people and animals around the earth, as
recently demonstrated by the avian flu epidemics. For 3 years now, a
collaboration of teams in Europe and Asia has been exploring some innovative in
silico approaches to better tackle avian flu taking advantage of the very large
computing resources available on international grid infrastructures. Grids were
used to study the impact of mutations on the effectiveness of existing drugs
against H5N1 and to find potentially new leads active on mutated strains. Grids
allow also the integration of distributed data in a completely secured way. The
paper presents how we are currently exploring how to integrate the existing
data sources towards a global surveillance network for molecular epidemiology.Comment: 7 pages, submitted to Infectious Disorders - Drug Target
Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)
The Rosetta molecular modeling software package provides experimentally
tested and rapidly evolving tools for the 3D structure prediction and
high-resolution design of proteins, nucleic acids, and a growing number of
non-natural polymers. Despite its free availability to academic users and
improving documentation, use of Rosetta has largely remained confined to
developers and their immediate collaborators due to the code's difficulty of
use, the requirement for large computational resources, and the unavailability
of servers for most of the Rosetta applications. Here, we present a unified web
framework for Rosetta applications called ROSIE (Rosetta Online Server that
Includes Everyone). ROSIE provides (a) a common user interface for Rosetta
protocols, (b) a stable application programming interface for developers to add
additional protocols, (c) a flexible back-end to allow leveraging of computer
cluster resources shared by RosettaCommons member institutions, and (d)
centralized administration by the RosettaCommons to ensure continuous
maintenance. This paper describes the ROSIE server infrastructure, a
step-by-step 'serverification' protocol for use by Rosetta developers, and the
deployment of the first nine ROSIE applications by six separate developer
teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance,
Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated
by the number and diversity of these applications, ROSIE offers a general and
speedy paradigm for serverification of Rosetta applications that incurs
negligible cost to developers and lowers barriers to Rosetta use for the
broader biological community. ROSIE is available at
http://rosie.rosettacommons.org
The future of laboratory medicine - A 2014 perspective.
Predicting the future is a difficult task. Not surprisingly, there are many examples and assumptions that have proved to be wrong. This review surveys the many predictions, beginning in 1887, about the future of laboratory medicine and its sub-specialties such as clinical chemistry and molecular pathology. It provides a commentary on the accuracy of the predictions and offers opinions on emerging technologies, economic factors and social developments that may play a role in shaping the future of laboratory medicine
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
The organization and mining of malaria genomic and post-genomic data is
highly motivated by the necessity to predict and characterize new biological
targets and new drugs. Biological targets are sought in a biological space
designed from the genomic data from Plasmodium falciparum, but using also the
millions of genomic data from other species. Drug candidates are sought in a
chemical space containing the millions of small molecules stored in public and
private chemolibraries. Data management should therefore be as reliable and
versatile as possible. In this context, we examined five aspects of the
organization and mining of malaria genomic and post-genomic data: 1) the
comparison of protein sequences including compositionally atypical malaria
sequences, 2) the high throughput reconstruction of molecular phylogenies, 3)
the representation of biological processes particularly metabolic pathways, 4)
the versatile methods to integrate genomic data, biological representations and
functional profiling obtained from X-omic experiments after drug treatments and
5) the determination and prediction of protein structures and their molecular
docking with drug candidate structures. Progresses toward a grid-enabled
chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa
The complex interaction between Global Production Networks, Digital Information Systems and International Knowledge Transfers
Traditionally many studies of knowledge in economics have focused on localized networks and intra-regional collaborations. However, the rising frequency by which firms collaborate within the context of global networks of production and innovation, the increasingly intricate divisions of labor involved and the extensive use of the Internet to facilitate interaction are all relatively novel trends that underline the importance of knowledge creation and flows across different locations. Focusing on this topic, the present chapter examines the complex interactions between global production networks (GPN), digital information systems (DIS) and knowledge transfers in information technology industries. It seeks to disentangle the various conduits through which different kinds of knowledge are transferred within such networks, and investigate how recent generations of DIS are affecting those knowledge transfers. The paper concludes that the dual expansion of GPN and DIS is adding new complexity to the practice of innovation: To access knowledge necessary for sustained creativity firms often have to link up with remote partners in GPN, but to be able to absorb and utilize this knowledge, they also frequently have to engage in local interactive learning processes. These local- global linkages - and the various skills necessary to operate them - are strongly interdependent, mutually reinforcing and critical for the development and maintenance of innovation-based competitiveness.
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