114,419 research outputs found
Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana
Regulation of gene expression is crucial for organism growth, and it is one of the challenges in Systems Biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyse two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants to infer their regulatory network. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale-free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation
Fat vs. thin threading approach on GPUs: application to stochastic simulation of chemical reactions
We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimise data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximises parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie (J. Phys. Chem, Vol. 81, p. 2340-2361, 1977). In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system’s size
Memory and information processing in neuromorphic systems
A striking difference between brain-inspired neuromorphic processors and
current von Neumann processors architectures is the way in which memory and
processing is organized. As Information and Communication Technologies continue
to address the need for increased computational power through the increase of
cores within a digital processor, neuromorphic engineers and scientists can
complement this need by building processor architectures where memory is
distributed with the processing. In this paper we present a survey of
brain-inspired processor architectures that support models of cortical networks
and deep neural networks. These architectures range from serial clocked
implementations of multi-neuron systems to massively parallel asynchronous ones
and from purely digital systems to mixed analog/digital systems which implement
more biological-like models of neurons and synapses together with a suite of
adaptation and learning mechanisms analogous to the ones found in biological
nervous systems. We describe the advantages of the different approaches being
pursued and present the challenges that need to be addressed for building
artificial neural processing systems that can display the richness of behaviors
seen in biological systems.Comment: Submitted to Proceedings of IEEE, review of recently proposed
neuromorphic computing platforms and system
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