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Primeur weekly 2016-12-12

Crowd computing

New TN-Grid platform is hosting gene@home ...

Quantum computing

Further improvement of qubit lifetime for quantum computers ...

Focus on Europe

Cray works with Microsoft and CSCS to reach new performance milestone for deep learning at scale ...

PHENOMEN project to lay the foundations for a new age of information processing ...

Research into the theoretical bases of future wireless communications ...

Mont-Blanc project Event ARM: On the road to HPC ...

Middleware

Allinea webinar targets I/O optimization ...

Hardware

Mellanox's EDR 100Gb/s InfiniBand accelerates the largest National Institute of Health supercomputer ...

Mellanox announces record breaking performance enabling stateful packet processing at 400Gb/s with the NPS-400 network processor ...

Atos achieves SAP HANA certification for its bullion server operating up to 16TB of data ...

NVIDIA delivers AI supercomputer to Berkeley ...

New tender for the SURFnet8 service layer published ...

High performance graphene photodetectors set speed record ...

Applications

Scientists take 'blue-action' to help society cope with the impacts of Arctic climate changes ...

Eight new eScience projects to start in 2017 ...

University of Wyoming Faculty supercomputer use deadline is December 23, 2016 ...

Collaborating on Big Data to unravel disease processes ...

Weather the storm: Improving Great Lakes modelling ...

What to do with the data? ...

Big Data approach to water quality applied at shale drilling sites ...

The Cloud

Amazon Web Services Cloud now available to customers from data centres in Canada ...

New TN-Grid platform is hosting gene@home


7 Dec 2016 Berkeley - TN-Grid is a platform that uses Internet-connected computers to do research in various scientific projects. TN-Grid is based at the Research Area of Trento of the National Research Council of Italy (CNR) and currently hosted by the University of Trento (UNITN). The first project they are hosting is gene@home, a collaboration with Fondazione Edmund Mach (FEM) & the Department of Information Engineering and Computer Science (DISI) of UNITN.

Gene@home is a scientific project belonging to the infrastructure TrentoGrid. It is aimed to expand networks of genes, and to perform this task it exploits the computational power of volunteers through the BOINC platform, which allows distributed computing. The experiment is done on the plant Arabidopsis Thaliana.

Every living being has a genetic code and a set of genes, needed to produce proteins starting from coded pieces of information. Genes are necessary for life and maintenance of organisms, and are expressed inside cells: the contained information is transcribed and translated into proteins.

This gene expression phenomenon, based on a complex chain of events in which some particular proteins act on genes regions, can be simplified through a causal relationship between two genes. Causality is a kind of cause-and-effect binding between two variables: it means that the occurrence of the one is cause of the appearance of the other.

The gene expression information is usually represented in Gene Regulatory Networks (GRN), which use edges to indicate the causal relationship between two genes. This representation is very useful to predict and manipulate the behavior of a system.

Every GRN can be expanded, in order to add or suggest new genes related to the ones already known; this allows to amplify the research and the analysis of a network. However, there are just few methods available to perform the expansion, which is still an open challenge in the Bioinformatics world.

To perform the GRN expansion, gene@home exploits an algorithm called PC-IM. It is an iterative implementation of the PC algorithm, which founds a gene network and studies its causal relationships, aimed to estimate if a list of new genes can have a causal relationship with an already known GRN.

In particular, the new genes are partitioned in blocks and merged with the GRN; afterwards the PC is applied on each block to look for new possible relationships. At the end of the process the algorithm self-evaluates its performance, and basing on this decides the final network to return as an output.

More information is available at the gene@home website.
Source: BOINC

Back to Table of contents

Primeur weekly 2016-12-12

Crowd computing

New TN-Grid platform is hosting gene@home ...

Quantum computing

Further improvement of qubit lifetime for quantum computers ...

Focus on Europe

Cray works with Microsoft and CSCS to reach new performance milestone for deep learning at scale ...

PHENOMEN project to lay the foundations for a new age of information processing ...

Research into the theoretical bases of future wireless communications ...

Mont-Blanc project Event ARM: On the road to HPC ...

Middleware

Allinea webinar targets I/O optimization ...

Hardware

Mellanox's EDR 100Gb/s InfiniBand accelerates the largest National Institute of Health supercomputer ...

Mellanox announces record breaking performance enabling stateful packet processing at 400Gb/s with the NPS-400 network processor ...

Atos achieves SAP HANA certification for its bullion server operating up to 16TB of data ...

NVIDIA delivers AI supercomputer to Berkeley ...

New tender for the SURFnet8 service layer published ...

High performance graphene photodetectors set speed record ...

Applications

Scientists take 'blue-action' to help society cope with the impacts of Arctic climate changes ...

Eight new eScience projects to start in 2017 ...

University of Wyoming Faculty supercomputer use deadline is December 23, 2016 ...

Collaborating on Big Data to unravel disease processes ...

Weather the storm: Improving Great Lakes modelling ...

What to do with the data? ...

Big Data approach to water quality applied at shale drilling sites ...

The Cloud

Amazon Web Services Cloud now available to customers from data centres in Canada ...