42,029 research outputs found
Evolution and development of complex computational systems using the paradigm of metabolic computing in Epigenetic Tracking
Epigenetic Tracking (ET) is an Artificial Embryology system which allows for
the evolution and development of large complex structures built from artificial
cells. In terms of the number of cells, the complexity of the bodies generated
with ET is comparable with the complexity of biological organisms. We have
previously used ET to simulate the growth of multicellular bodies with
arbitrary 3-dimensional shapes which perform computation using the paradigm of
"metabolic computing". In this paper we investigate the memory capacity of such
computational structures and analyse the trade-off between shape and
computation. We now plan to build on these foundations to create a
biologically-inspired model in which the encoding of the phenotype is efficient
(in terms of the compactness of the genome) and evolvable in tasks involving
non-trivial computation, robust to damage and capable of self-maintenance and
self-repair.Comment: In Proceedings Wivace 2013, arXiv:1309.712
PocketCare: Tracking the Flu with Mobile Phones using Partial Observations of Proximity and Symptoms
Mobile phones provide a powerful sensing platform that researchers may adopt
to understand proximity interactions among people and the diffusion, through
these interactions, of diseases, behaviors, and opinions. However, it remains a
challenge to track the proximity-based interactions of a whole community and
then model the social diffusion of diseases and behaviors starting from the
observations of a small fraction of the volunteer population. In this paper, we
propose a novel approach that tries to connect together these sparse
observations using a model of how individuals interact with each other and how
social interactions happen in terms of a sequence of proximity interactions. We
apply our approach to track the spreading of flu in the spatial-proximity
network of a 3000-people university campus by mobilizing 300 volunteers from
this population to monitor nearby mobile phones through Bluetooth scanning and
to daily report flu symptoms about and around them. Our aim is to predict the
likelihood for an individual to get flu based on how often her/his daily
routine intersects with those of the volunteers. Thus, we use the daily
routines of the volunteers to build a model of the volunteers as well as of the
non-volunteers. Our results show that we can predict flu infection two weeks
ahead of time with an average precision from 0.24 to 0.35 depending on the
amount of information. This precision is six to nine times higher than with a
random guess model. At the population level, we can predict infectious
population in a two-week window with an r-squared value of 0.95 (a random-guess
model obtains an r-squared value of 0.2). These results point to an innovative
approach for tracking individuals who have interacted with people showing
symptoms, allowing us to warn those in danger of infection and to inform health
researchers about the progression of contact-induced diseases
Global parameter identification of stochastic reaction networks from single trajectories
We consider the problem of inferring the unknown parameters of a stochastic
biochemical network model from a single measured time-course of the
concentration of some of the involved species. Such measurements are available,
e.g., from live-cell fluorescence microscopy in image-based systems biology. In
addition, fluctuation time-courses from, e.g., fluorescence correlation
spectroscopy provide additional information about the system dynamics that can
be used to more robustly infer parameters than when considering only mean
concentrations. Estimating model parameters from a single experimental
trajectory enables single-cell measurements and quantification of cell--cell
variability. We propose a novel combination of an adaptive Monte Carlo sampler,
called Gaussian Adaptation, and efficient exact stochastic simulation
algorithms that allows parameter identification from single stochastic
trajectories. We benchmark the proposed method on a linear and a non-linear
reaction network at steady state and during transient phases. In addition, we
demonstrate that the present method also provides an ellipsoidal volume
estimate of the viable part of parameter space and is able to estimate the
physical volume of the compartment in which the observed reactions take place.Comment: Article in print as a book chapter in Springer's "Advances in Systems
Biology
Parallel implementation of stochastic simulation for large-scale cellular processes
Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes
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