62,757 research outputs found
Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices
Integrative biological simulations have a varied and controversial history in
the biological sciences. From computational models of organelles, cells, and
simple organisms, to physiological models of tissues, organ systems, and
ecosystems, a diverse array of biological systems have been the target of
large-scale computational modeling efforts. Nonetheless, these research agendas
have yet to prove decisively their value among the broader community of
theoretical and experimental biologists. In this commentary, we examine a range
of philosophical and practical issues relevant to understanding the potential
of integrative simulations. We discuss the role of theory and modeling in
different areas of physics and suggest that certain sub-disciplines of physics
provide useful cultural analogies for imagining the future role of simulations
in biological research. We examine philosophical issues related to modeling
which consistently arise in discussions about integrative simulations and
suggest a pragmatic viewpoint that balances a belief in philosophy with the
recognition of the relative infancy of our state of philosophical
understanding. Finally, we discuss community workflow and publication practices
to allow research to be readily discoverable and amenable to incorporation into
simulations. We argue that there are aligned incentives in widespread adoption
of practices which will both advance the needs of integrative simulation
efforts as well as other contemporary trends in the biological sciences,
ranging from open science and data sharing to improving reproducibility.Comment: 10 page
Nanoinformatics: developing new computing applications for nanomedicine
Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others
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Innovating Pedagogy 2015: Open University Innovation Report 4
This series of reports explores new forms of teaching, learning and assessment for an interactive world, to guide teachers and policy makers in productive innovation. This fourth report proposes ten innovations that are already in currency but have not yet had a profound influence on education. To produce it, a group of academics at the Institute of Educational Technology in The Open University collaborated with researchers from the Center for Technology in Learning at SRI International. We proposed a long list of new educational terms, theories, and practices. We then pared these down to ten that have the potential to provoke major shifts in educational practice, particularly in post-school education. Lastly, we drew on published and unpublished writings to compile the ten sketches of new pedagogies that might transform education. These are summarised below in an approximate order of immediacy and timescale to widespread implementation
Report of the user requirements and web based access for eResearch workshops
The User Requirements and Web Based Access for eResearch Workshop, organized jointly by NeSC and NCeSS, was held on 19 May 2006. The aim was to identify lessons learned from e-Science projects that would contribute to our capacity to make Grid infrastructures and tools usable and accessible for diverse user communities. Its focus was on providing an opportunity for a pragmatic discussion between e-Science end users
and tool builders in order to understand usability challenges, technological options, community-specific content and needs, and methodologies for design and development. We invited members of six UK e-Science projects and one US project, trying as far as
possible to pair a user and developer from each project in order to discuss their contrasting perspectives and experiences. Three breakout group sessions covered the
topics of user-developer relations, commodification, and functionality. There was also extensive post-meeting discussion, summarized here.
Additional information on the workshop, including the agenda, participant list, and talk slides, can be found online at http://www.nesc.ac.uk/esi/events/685/
Reference: NeSC report UKeS-2006-07 available from http://www.nesc.ac.uk/technical_papers/UKeS-2006-07.pd
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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
Simplifying the Development, Use and Sustainability of HPC Software
Developing software to undertake complex, compute-intensive scientific
processes requires a challenging combination of both specialist domain
knowledge and software development skills to convert this knowledge into
efficient code. As computational platforms become increasingly heterogeneous
and newer types of platform such as Infrastructure-as-a-Service (IaaS) cloud
computing become more widely accepted for HPC computations, scientists require
more support from computer scientists and resource providers to develop
efficient code and make optimal use of the resources available to them. As part
of the libhpc stage 1 and 2 projects we are developing a framework to provide a
richer means of job specification and efficient execution of complex scientific
software on heterogeneous infrastructure. The use of such frameworks has
implications for the sustainability of scientific software. In this paper we
set out our developing understanding of these challenges based on work carried
out in the libhpc project.Comment: 4 page position paper, submission to WSSSPE13 worksho
An Introduction to Programming for Bioscientists: A Python-based Primer
Computing has revolutionized the biological sciences over the past several
decades, such that virtually all contemporary research in the biosciences
utilizes computer programs. The computational advances have come on many
fronts, spurred by fundamental developments in hardware, software, and
algorithms. These advances have influenced, and even engendered, a phenomenal
array of bioscience fields, including molecular evolution and bioinformatics;
genome-, proteome-, transcriptome- and metabolome-wide experimental studies;
structural genomics; and atomistic simulations of cellular-scale molecular
assemblies as large as ribosomes and intact viruses. In short, much of
post-genomic biology is increasingly becoming a form of computational biology.
The ability to design and write computer programs is among the most
indispensable skills that a modern researcher can cultivate. Python has become
a popular programming language in the biosciences, largely because (i) its
straightforward semantics and clean syntax make it a readily accessible first
language; (ii) it is expressive and well-suited to object-oriented programming,
as well as other modern paradigms; and (iii) the many available libraries and
third-party toolkits extend the functionality of the core language into
virtually every biological domain (sequence and structure analyses,
phylogenomics, workflow management systems, etc.). This primer offers a basic
introduction to coding, via Python, and it includes concrete examples and
exercises to illustrate the language's usage and capabilities; the main text
culminates with a final project in structural bioinformatics. A suite of
Supplemental Chapters is also provided. Starting with basic concepts, such as
that of a 'variable', the Chapters methodically advance the reader to the point
of writing a graphical user interface to compute the Hamming distance between
two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables,
numerous exercises, and 19 pages of Supporting Information; currently in
press at PLOS Computational Biolog
Global Computing II. Terms of reference for the FP6-EU-FET call.
The European Commission has decided to continue and develop its FET “Global Computing,” and will shortly announce the opening of “Global Computing II.” The call is expected in May 2004, with application deadlines in September, and expected start date for selected projects in March 2005
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