23,057 research outputs found
Overcoming the Newtonian Paradigm: The Unfinished Project of Theoretical Biology from a Schellingian Perspective
Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that
has always had to give ground, it is shown that many of the most important advances in mathematics
and physics over the last two centuries have followed from Schelling’s demand for a new physics that
could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many
biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but
progressive tradition of anti-reductionist biomathematics. It is shown that the mathematicoephysico
echemical morphology research program, the biosemiotics movement, and the relational biology of
Rosen, although they have developed independently of each other, are built on and advance this antireductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics
Developing Predictive Molecular Maps of Human Disease through Community-based Modeling
The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics
Why it is important to build robots capable of doing science
Science, like any other cognitive activity, is grounded in the sensorimotor interaction of our bodies with the environment. Human embodiment thus constrains the class of scientific concepts and theories which are accessible to us. The paper explores the possibility of doing science with artificial cognitive agents, in the framework of an interactivist-constructivist cognitive model of science. Intelligent robots, by virtue of having different sensorimotor capabilities, may overcome the fundamental limitations of human science and provide important technological innovations. Mathematics and nanophysics are prime candidates for being studied by artificial scientists
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
Hypotheses, evidence and relationships: The HypER approach for representing scientific knowledge claims
Biological knowledge is increasingly represented as a collection of (entity-relationship-entity) triplets. These are queried, mined, appended to papers, and published. However, this representation ignores the argumentation contained within a paper and the relationships between hypotheses, claims and evidence put forth in the article. In this paper, we propose an alternate view of the research article as a network of 'hypotheses and evidence'. Our knowledge representation focuses on scientific discourse as a rhetorical activity, which leads to a different direction in the development of tools and processes for modeling this discourse. We propose to extract knowledge from the article to allow the construction of a system where a specific scientific claim is connected, through trails of meaningful relationships, to experimental evidence. We discuss some current efforts and future plans in this area
A framework for deriving semantic web services
Web service-based development represents an emerging approach for the development of distributed information systems. Web services have been mainly applied by software practitioners as a means to modularize system functionality that can be offered across a network (e.g., intranet and/or the Internet). Although web services have been
predominantly developed as a technical solution for integrating software systems, there is a more business-oriented aspect that developers and enterprises need to deal with in order to benefit from the full potential of web services in an electronic market. This ‘ignored’ aspect is the representation of the semantics underlying the services themselves as well as the ‘things’ that the services manage. Currently languages like the Web Services Description Language (WSDL) provide the syntactic means to describe web services, but
lack in providing a semantic underpinning. In order to harvest all the benefits of web services technology, a framework has been developed for deriving business semantics from syntactic descriptions of web services. The benefits of such a framework are two-fold. Firstly, the framework provides a way to gradually construct domain ontologies from previously defined technical services. Secondly, the framework enables the
migration of syntactically defined web services toward semantic web services. The study follows a design research approach which (1) identifies the problem area and its relevance from an industrial case study and previous research, (2) develops the
framework as a design artifact and (3) evaluates the application of the framework through a relevant scenario
Ontology of core data mining entities
In this article, we present OntoDM-core, an ontology of core data mining
entities. OntoDM-core defines themost essential datamining entities in a three-layered
ontological structure comprising of a specification, an implementation and an application
layer. It provides a representational framework for the description of mining
structured data, and in addition provides taxonomies of datasets, data mining tasks,
generalizations, data mining algorithms and constraints, based on the type of data.
OntoDM-core is designed to support a wide range of applications/use cases, such as
semantic annotation of data mining algorithms, datasets and results; annotation of
QSAR studies in the context of drug discovery investigations; and disambiguation of
terms in text mining. The ontology has been thoroughly assessed following the practices
in ontology engineering, is fully interoperable with many domain resources and
is easy to extend
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Skills and Knowledge for Data-Intensive Environmental Research.
The scale and magnitude of complex and pressing environmental issues lend urgency to the need for integrative and reproducible analysis and synthesis, facilitated by data-intensive research approaches. However, the recent pace of technological change has been such that appropriate skills to accomplish data-intensive research are lacking among environmental scientists, who more than ever need greater access to training and mentorship in computational skills. Here, we provide a roadmap for raising data competencies of current and next-generation environmental researchers by describing the concepts and skills needed for effectively engaging with the heterogeneous, distributed, and rapidly growing volumes of available data. We articulate five key skills: (1) data management and processing, (2) analysis, (3) software skills for science, (4) visualization, and (5) communication methods for collaboration and dissemination. We provide an overview of the current suite of training initiatives available to environmental scientists and models for closing the skill-transfer gap
Context Aware Computing for The Internet of Things: A Survey
As we are moving towards the Internet of Things (IoT), the number of sensors
deployed around the world is growing at a rapid pace. Market research has shown
a significant growth of sensor deployments over the past decade and has
predicted a significant increment of the growth rate in the future. These
sensors continuously generate enormous amounts of data. However, in order to
add value to raw sensor data we need to understand it. Collection, modelling,
reasoning, and distribution of context in relation to sensor data plays
critical role in this challenge. Context-aware computing has proven to be
successful in understanding sensor data. In this paper, we survey context
awareness from an IoT perspective. We present the necessary background by
introducing the IoT paradigm and context-aware fundamentals at the beginning.
Then we provide an in-depth analysis of context life cycle. We evaluate a
subset of projects (50) which represent the majority of research and commercial
solutions proposed in the field of context-aware computing conducted over the
last decade (2001-2011) based on our own taxonomy. Finally, based on our
evaluation, we highlight the lessons to be learnt from the past and some
possible directions for future research. The survey addresses a broad range of
techniques, methods, models, functionalities, systems, applications, and
middleware solutions related to context awareness and IoT. Our goal is not only
to analyse, compare and consolidate past research work but also to appreciate
their findings and discuss their applicability towards the IoT.Comment: IEEE Communications Surveys & Tutorials Journal, 201
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