41,279 research outputs found
Open source bioimage informatics for cell biology
Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery
Modeling and Analysis of Scholar Mobility on Scientific Landscape
Scientific literature till date can be thought of as a partially revealed
landscape, where scholars continue to unveil hidden knowledge by exploring
novel research topics. How do scholars explore the scientific landscape , i.e.,
choose research topics to work on? We propose an agent-based model of topic
mobility behavior where scholars migrate across research topics on the space of
science following different strategies, seeking different utilities. We use
this model to study whether strategies widely used in current scientific
community can provide a balance between individual scientific success and the
efficiency and diversity of the whole academic society. Through extensive
simulations, we provide insights into the roles of different strategies, such
as choosing topics according to research potential or the popularity. Our model
provides a conceptual framework and a computational approach to analyze
scholars' behavior and its impact on scientific production. We also discuss how
such an agent-based modeling approach can be integrated with big real-world
scholarly data.Comment: To appear in BigScholar, WWW 201
Research and Education in Computational Science and Engineering
Over the past two decades the field of computational science and engineering
(CSE) has penetrated both basic and applied research in academia, industry, and
laboratories to advance discovery, optimize systems, support decision-makers,
and educate the scientific and engineering workforce. Informed by centuries of
theory and experiment, CSE performs computational experiments to answer
questions that neither theory nor experiment alone is equipped to answer. CSE
provides scientists and engineers of all persuasions with algorithmic
inventions and software systems that transcend disciplines and scales. Carried
on a wave of digital technology, CSE brings the power of parallelism to bear on
troves of data. Mathematics-based advanced computing has become a prevalent
means of discovery and innovation in essentially all areas of science,
engineering, technology, and society; and the CSE community is at the core of
this transformation. However, a combination of disruptive
developments---including the architectural complexity of extreme-scale
computing, the data revolution that engulfs the planet, and the specialization
required to follow the applications to new frontiers---is redefining the scope
and reach of the CSE endeavor. This report describes the rapid expansion of CSE
and the challenges to sustaining its bold advances. The report also presents
strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie
Exploring the Use of Virtual Worlds as a Scientific Research Platform: The Meta-Institute for Computational Astrophysics (MICA)
We describe the Meta-Institute for Computational Astrophysics (MICA), the
first professional scientific organization based exclusively in virtual worlds
(VWs). The goals of MICA are to explore the utility of the emerging VR and VWs
technologies for scientific and scholarly work in general, and to facilitate
and accelerate their adoption by the scientific research community. MICA itself
is an experiment in academic and scientific practices enabled by the immersive
VR technologies. We describe the current and planned activities and research
directions of MICA, and offer some thoughts as to what the future developments
in this arena may be.Comment: 15 pages, to appear in the refereed proceedings of "Facets of Virtual
Environments" (FaVE 2009), eds. F. Lehmann-Grube, J. Sablating, et al., ICST
Lecture Notes Ser., Berlin: Springer Verlag (2009); version with full
resolution color figures is available at
http://www.mica-vw.org/wiki/index.php/Publication
Unproceedings of the Fourth .Astronomy Conference (.Astronomy 4), Heidelberg, Germany, July 9-11 2012
The goal of the .Astronomy conference series is to bring together
astronomers, educators, developers and others interested in using the Internet
as a medium for astronomy. Attendance at the event is limited to approximately
50 participants, and days are split into mornings of scheduled talks, followed
by 'unconference' afternoons, where sessions are defined by participants during
the course of the event. Participants in unconference sessions are discouraged
from formal presentations, with discussion, workshop-style formats or informal
practical tutorials encouraged. The conference also designates one day as a
'hack day', in which attendees collaborate in groups on day-long projects for
presentation the following morning. These hacks are often a way of
concentrating effort, learning new skills, and exploring ideas in a practical
fashion. The emphasis on informal, focused interaction makes recording
proceedings more difficult than for a normal meeting. While the first
.Astronomy conference is preserved formally in a book, more recent iterations
are not documented. We therefore, in the spirit of .Astronomy, report
'unproceedings' from .Astronomy 4, which was held in Heidelberg in July 2012.Comment: 11 pages, 1 figure, .Astronomy 4, #dotastr
Discovery Is Never By Chance: Designing for (Un)Serendipity
Serendipity has a long tradition in the history of science as having played a key role in many significant discoveries. Computer scientists, valuing the role of serendipity in discovery, have attempted to design systems that encourage serendipity. However, that research has focused primarily on only one aspect of serendipity: that of chance encounters. In reality, for serendipity to be valuable chance encounters must be synthesized into insight. In this paper we show, through a formal consideration of serendipity and analysis of how various systems have seized on attributes of interpreting serendipity, that there is a richer space for design to support serendipitous creativity, innovation and discovery than has been tapped to date. We discuss how ideas might be encoded to be shared or discovered by ‘association-hunting’ agents. We propose considering not only the inventor’s role in perceiving serendipity, but also how that inventor’s perception may be enhanced to increase the opportunity for serendipity. We explore the role of environment and how we can better enable serendipitous discoveries to find a home more readily and immediately
Do you see what I mean?
Visualizers, like logicians, have long been concerned with meaning. Generalizing from MacEachren's overview of cartography, visualizers have to think about how people extract meaning from pictures (psychophysics), what people understand from a picture (cognition), how pictures are imbued with meaning (semiotics), and how in some cases that meaning arises within a social and/or cultural context. If we think of the communication acts carried out in the visualization process further levels of meaning are suggested. Visualization begins when someone has data that they wish to explore and interpret; the data are encoded as input to a visualization system, which may in its turn interact with other systems to produce a representation. This is communicated back to the user(s), who have to assess this against their goals and knowledge, possibly leading to further cycles of activity. Each phase of this process involves communication between two parties. For this to succeed, those parties must share a common language with an agreed meaning. We offer the following three steps, in increasing order of formality: terminology (jargon), taxonomy (vocabulary), and ontology. Our argument in this article is that it's time to begin synthesizing the fragments and views into a level 3 model, an ontology of visualization. We also address why this should happen, what is already in place, how such an ontology might be constructed, and why now
Towards a service-oriented e-infrastructure for multidisciplinary environmental research
Research e-infrastructures are considered to have generic and thematic parts. The generic part provids high-speed networks, grid (large-scale distributed computing) and database systems (digital repositories and data transfer systems) applicable to all research commnities irrespective of discipline. Thematic parts are specific deployments of e-infrastructures to support diverse virtual research communities. The needs of a virtual community of multidisciplinary envronmental researchers are yet to be investigated. We envisage and argue for an e-infrastructure that will enable environmental researchers to develop environmental models and software entirely out of existing components through loose coupling of diverse digital resources based on the service-oriented achitecture. We discuss four specific aspects for consideration for a future e-infrastructure: 1) provision of digital resources (data, models & tools) as web services, 2) dealing with stateless and non-transactional nature of web services using workflow management systems, 3) enabling web servce discovery, composition and orchestration through semantic registries, and 4) creating synergy with existing grid infrastructures
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