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HD Physiology Project-Japanese efforts to promote multilevel integrative systems biology and physiome research.
The HD Physiology Project is a Japanese research consortium that aimed to develop methods and a computational platform in which physiological and pathological information can be described in high-level definitions across multiple scales of time and size. During the 5 years of this project, an appropriate software platform for multilevel functional simulation was developed and a whole-heart model including pharmacokinetics for the assessment of the proarrhythmic risk of drugs was developed. In this article, we outline the description and scientific strategy of this project and present the achievements and influence on multilevel integrative systems biology and physiome research
Updates in metabolomics tools and resources: 2014-2015
Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources—in the form of tools, software, and databases—is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table
COEL: A Web-based Chemistry Simulation Framework
The chemical reaction network (CRN) is a widely used formalism to describe
macroscopic behavior of chemical systems. Available tools for CRN modelling and
simulation require local access, installation, and often involve local file
storage, which is susceptible to loss, lacks searchable structure, and does not
support concurrency. Furthermore, simulations are often single-threaded, and
user interfaces are non-trivial to use. Therefore there are significant hurdles
to conducting efficient and collaborative chemical research. In this paper, we
introduce a new enterprise chemistry simulation framework, COEL, which
addresses these issues. COEL is the first web-based framework of its kind. A
visually pleasing and intuitive user interface, simulations that run on a large
computational grid, reliable database storage, and transactional services make
COEL ideal for collaborative research and education. COEL's most prominent
features include ODE-based simulations of chemical reaction networks and
multicompartment reaction networks, with rich options for user interactions
with those networks. COEL provides DNA-strand displacement transformations and
visualization (and is to our knowledge the first CRN framework to do so), GA
optimization of rate constants, expression validation, an application-wide
plotting engine, and SBML/Octave/Matlab export. We also present an overview of
the underlying software and technologies employed and describe the main
architectural decisions driving our development. COEL is available at
http://coel-sim.org for selected research teams only. We plan to provide a part
of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl
A survey on subjecting electronic product code and non-ID objects to IP identification
Over the last decade, both research on the Internet of Things (IoT) and
real-world IoT applications have grown exponentially. The IoT provides us with
smarter cities, intelligent homes, and generally more comfortable lives.
However, the introduction of these devices has led to several new challenges
that must be addressed. One of the critical challenges facing interacting with
IoT devices is to address billions of devices (things) around the world,
including computers, tablets, smartphones, wearable devices, sensors, and
embedded computers, and so on. This article provides a survey on subjecting
Electronic Product Code and non-ID objects to IP identification for IoT
devices, including their advantages and disadvantages thereof. Different
metrics are here proposed and used for evaluating these methods. In particular,
the main methods are evaluated in terms of their: (i) computational overhead,
(ii) scalability, (iii) adaptability, (iv) implementation cost, and (v) whether
applicable to already ID-based objects and presented in tabular format.
Finally, the article proves that this field of research will still be ongoing,
but any new technique must favorably offer the mentioned five evaluative
parameters.Comment: 112 references, 8 figures, 6 tables, Journal of Engineering Reports,
Wiley, 2020 (Open Access
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