174,686 research outputs found
MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME
Computational experiments using spatial stochastic simulations have led to
important new biological insights, but they require specialized tools, a
complex software stack, as well as large and scalable compute and data analysis
resources due to the large computational cost associated with Monte Carlo
computational workflows. The complexity of setting up and managing a
large-scale distributed computation environment to support productive and
reproducible modeling can be prohibitive for practitioners in systems biology.
This results in a barrier to the adoption of spatial stochastic simulation
tools, effectively limiting the type of biological questions addressed by
quantitative modeling. In this paper, we present PyURDME, a new, user-friendly
spatial modeling and simulation package, and MOLNs, a cloud computing appliance
for distributed simulation of stochastic reaction-diffusion models. MOLNs is
based on IPython and provides an interactive programming platform for
development of sharable and reproducible distributed parallel computational
experiments
A Molecular Biology Database Digest
Computational Biology or Bioinformatics has been defined as the application of mathematical
and Computer Science methods to solving problems in Molecular Biology that require large scale
data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential
role in Computational Biology research and development. This paper introduces into current
Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the
integration of Molecular Biology data from different sources. This paper is primarily intended
for an audience of computer scientists with a limited background in Biology
Negative Results in Computer Vision: A Perspective
A negative result is when the outcome of an experiment or a model is not what
is expected or when a hypothesis does not hold. Despite being often overlooked
in the scientific community, negative results are results and they carry value.
While this topic has been extensively discussed in other fields such as social
sciences and biosciences, less attention has been paid to it in the computer
vision community. The unique characteristics of computer vision, particularly
its experimental aspect, call for a special treatment of this matter. In this
paper, I will address what makes negative results important, how they should be
disseminated and incentivized, and what lessons can be learned from cognitive
vision research in this regard. Further, I will discuss issues such as computer
vision and human vision interaction, experimental design and statistical
hypothesis testing, explanatory versus predictive modeling, performance
evaluation, model comparison, as well as computer vision research culture
E-BioFlow: Different Perspectives on Scientific Workflows
We introduce a new type of workflow design system called\ud
e-BioFlow and illustrate it by means of a simple sequence alignment workflow. E-BioFlow, intended to model advanced scientific workflows, enables the user to model a workflow from three different but strongly coupled perspectives: the control flow perspective, the data flow perspective, and the resource perspective. All three perspectives are of\ud
equal importance, but workflow designers from different domains prefer different perspectives as entry points for their design, and a single workflow designer may prefer different perspectives in different stages of workflow design. Each perspective provides its own type of information, visualisation and support for validation. Combining these three perspectives in a single application provides a new and flexible way of modelling workflows
Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity.
A crisis continues to brew within the pharmaceutical research and development (R&D) enterprise: productivity continues declining as costs rise, despite ongoing, often dramatic scientific and technical advances. To reverse this trend, we offer various suggestions for both the expansion and broader adoption of modeling and simulation (M&S) methods. We suggest strategies and scenarios intended to enable new M&S use cases that directly engage R&D knowledge generation and build actionable mechanistic insight, thereby opening the door to enhanced productivity. What M&S requirements must be satisfied to access and open the door, and begin reversing the productivity decline? Can current methods and tools fulfill the requirements, or are new methods necessary? We draw on the relevant, recent literature to provide and explore answers. In so doing, we identify essential, key roles for agent-based and other methods. We assemble a list of requirements necessary for M&S to meet the diverse needs distilled from a collection of research, review, and opinion articles. We argue that to realize its full potential, M&S should be actualized within a larger information technology framework--a dynamic knowledge repository--wherein models of various types execute, evolve, and increase in accuracy over time. We offer some details of the issues that must be addressed for such a repository to accrue the capabilities needed to reverse the productivity decline
The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web
Research in life sciences is increasingly being conducted in a digital and
online environment. In particular, life scientists have been pioneers in
embracing new computational tools to conduct their investigations. To support
the sharing of digital objects produced during such research investigations, we
have witnessed in the last few years the emergence of specialized repositories,
e.g., DataVerse and FigShare. Such repositories provide users with the means to
share and publish datasets that were used or generated in research
investigations. While these repositories have proven their usefulness,
interpreting and reusing evidence for most research results is a challenging
task. Additional contextual descriptions are needed to understand how those
results were generated and/or the circumstances under which they were
concluded. Because of this, scientists are calling for models that go beyond
the publication of datasets to systematically capture the life cycle of
scientific investigations and provide a single entry point to access the
information about the hypothesis investigated, the datasets used, the
experiments carried out, the results of the experiments, the people involved in
the research, etc. In this paper we present the Research Object (RO) suite of
ontologies, which provide a structured container to encapsulate research data
and methods along with essential metadata descriptions. Research Objects are
portable units that enable the sharing, preservation, interpretation and reuse
of research investigation results. The ontologies we present have been designed
in the light of requirements that we gathered from life scientists. They have
been built upon existing popular vocabularies to facilitate interoperability.
Furthermore, we have developed tools to support the creation and sharing of
Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page
Agent-Based Models and Simulations in Economics and Social Sciences: from conceptual exploration to distinct ways of experimenting
Now that complex Agent-Based Models and computer simulations
spread over economics and social sciences - as in most sciences of complex
systems -, epistemological puzzles (re)emerge. We introduce new
epistemological tools so as to show to what precise extent each author is right
when he focuses on some empirical, instrumental or conceptual significance of
his model or simulation. By distinguishing between models and simulations,
between types of models, between types of computer simulations and between
types of empiricity, section 2 gives conceptual tools to explain the rationale of
the diverse epistemological positions presented in section 1. Finally, we claim
that a careful attention to the real multiplicity of denotational powers of
symbols at stake and then to the implicit routes of references operated by
models and computer simulations is necessary to determine, in each case, the
proper epistemic status and credibility of a given model and/or simulation
Introduction Of Clusterization Principles In The Solution Of Problems Of Energy Efficiency And Ecological Safety Of The Existent Building Fund
The aim of the work is to introduce clusterization principles in the solution of problems of energy efficiency and ecological safety of the existent building fund. The material of the research is the process of modeling of energetically effective architecture-building clusters. In this sense it is topical and expedient to elaborate technologies and schemes, able to support making decisions as to the formation of energetically effective architecture-building clusters. The main attention is paid to the solution of infrastructure problems of energy saving of the architecture-building branch, connected with the absence of universal models, distinct algorithms of the formation of energy efficiency clusters and reliable instruments of their activity optimization. But realization of advantages of energy efficiency clusters is possible only at introducing effective mechanisms of the formation of a structure, able to provide a result, optimal by an energy efficiency criterion. The work offers a scheme of the formation process of such structure. The synthesis of models of energetically effective architecture-building clusters is based on principles of the systemic construction of geometric models and provides the imitative modeling of different development scenarios of synthesized clusters. At this stage of the research a function of making decisions as to the real cluster formation is left for experts. But an algorithm of the synthesis of models provides the formation of a knowledge base that will be in further a base of an “internal model” of the intellectual system of supporting decisions making, elaborated for modeling cluster structures. The scientific novelty of the work is in the elaboration of theoretical bases of the technology of coordinating the structure with object properties
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