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PubMed2002

The Bioperl toolkit: Perl modules for the life sciences.

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.

Algorithms↗
PubMed2004

Uses and abuses of mathematics in biology.

In the physical sciences, mathematical theory and experimental investigation have always marched together. Mathematics has been less intrusive in the life sciences, possibly because they have until recently been largely descriptive, lacking the invariance principles and fundamental natural constants of physics. Increasingly in recent decades, however, mathematics has become pervasive in biology, taking many different forms: statistics in experimental design; pattern seeking in bioinformatics; models in evolution, ecology, and epidemiology; and much else. I offer an opinionated overview of such uses--and abuses.

Allergy and Immunology↗
PubMed2005

A life science Semantic Web: are we there yet?

More than ever, life science researchers depend on information from multiple sources. The Semantic Web offers a powerful new strategy for consolidating both text and structured data into a comprehensive collections and views. In addition, these aggregates are readable by both humans and machines and could be the basis of information management and knowledge exchange.

Biological Science Disciplines↗
PubMed2002

[Perspective on gravitational biology of amphibians].

We review here the scientific significance of the use of amphibians for research in gravitational biology. Since amphibian eggs are quite large, yet develop rapidly and externally, it is easy to observe their development. Consequently amphibians were the first vertebrates to have their early developmental processes investigated in space. Though several deviations from normal embryonic development occur when amphibians are raised in microgravity, their developmental program is robust enough to return the organisms to an ostensibly normal morphology by the time they hatch. Evolutionally, amphibians were the first vertebrate animal to come out of the water and onto land. Subsequently they diversified and have adaptively radiated to various habitats. They now inhabit aquatic, terrestrial, arboreal and fossorial niches. This diversity can be used to help study the biological effects of gravity at the organismal level, where macroscopic phenomena are associated with gravitational loading. By choosing different amphibian models and using a comparative approach one can effectively identify the action of gravity on biological systems, and the adaptation that vertebrates have made to this loading. Advances in cellular and molecular biology provide powerful tools for the study in many fields, including gravitational biology, and amphibians have proven to be good models for studies at those levels as well. The low metabolic rates of amphibians make them convenient organisms to work with (compared to birds and mammals) in the difficult and confined spaces on orbiting research platforms. We include here a review of what is known about and the potential for further behavioral and physiological researches in space using amphibians.

Amphibians↗
PubMed1992

The NASA Specialized Center of Research and Training (NSCORT) in Gravitational Biology.

The Life Sciences Division of NASA has initiated a NASA Specialized Centers of Research and Training (NSCORT) program. Three Centers were designated in late 1990, as the culmination of an in-depth peer review analysis of proposals from universities across the nation and around the world. Kansas State University was selected as the NSCORT in Gravitational Biology. This Center is headquartered in the KSU Division of Biology and has a research, training, and outreach function that focuses on cellular and developmental biology.

Biological Science Disciplines↗
PubMed2003

Computational integrative physiology: at the convergence of the life and computational sciences.

OBJECTIVE: In this paper we outline how Computational Integrative Physiology (CIP) can help unravel the mechanisms of normal and pathological biological processes. Our objective is to illustrate how CIP is firmly grounded on the life and computational sciences. METHOD: After describing a general theoretical frame-work for CIP, we will center our discussion on cardiac rhythmic disorders with a particular focus on the Long QT syndrome that will serve as a case example. Within this context, we will describe multi-scale processes in biological, medical and in general mathematical terms, starting from the control of gene expression to the electrical activity of the entire heart. We will therefore proceed from the smaller microscopic scales to the larger macroscopic ones. In doing so, we will illustrate, at least in a qualitative sense, how CIP can be accomplished by showing some of the relations that can exist between mathematical variables characterizing models of different space-scales. CONCLUSION: We will conclude by putting forth how CIP and the related fields of bioinformatics and medical informatics are necessary to derive meaningful knowledge from the huge and exponentially growing biological and medical data.

Biological Science Disciplines↗
PubMedDate not supplied

[Resolution taken at the conference of the Academy of Medicine of USSR and of the Section of Biological Sciences of the Academy of Science of USSR with participation of higher educational institutions and of scientific and investigational institutes of the Ministry of Public Health of USSR on the problems of development of cellular and acellular forms of living substance according to O. B. Lepeshinskaia's theory. 22-24 April, 1952..].

Explore the source record for details and available documents.

Academies and Institutes↗
PubMed2005

An OGSA-based integration of life-scientific resources for drug discovery.

OBJECTIVES: The rapid progress of life-scientific research has the potential to dramatically change the paradigm of drug discovery. Efficient utilization of life-scientific resources, i.e., databases and analytic software tools, poses a challenging issue with regard to the reduction of time and cost in the drug discovery process. In this paper, a variety of heterogeneous Web-based life-scientific resources are integrated toward the improvement of drug discovery performance. METHODS: For the integration of heterogeneous life-scientific resources, a database federation technique based on three-layer architecture has been utilized. With the federation technique, life-scientific resources are integrated step by step through database layers, database integration layers and analysis layers to encapsulate complexity and heterogeneity. In this study, we have taken advantage of the latest Grid technology based on OGSA (Open Grid Services Architecture) for the implementation of our approach. RESULTS: The actual case of life-scientific resources for drug discovery demonstrates that our prototype system developed with the proposed technique works well for the identification process of candidate compounds to a target protein. In other words, the prototype system allows a researcher to retrieve candidate compounds with less effort than before. CONCLUSIONS: The usefulness of the prototypic system represents the ability of our approach to integrate heterogeneous life-scientific resources, which have the potential to dramatically improve efficiency in drug discovery, resulting in the shortening of drug development. On the other hand, the system requires further consideration from the aspect of practical use. Dynamic aggregation of the resources is one example of such a consideration.

Biological Science Disciplines↗
PubMed2005

Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective.

Progress in the life sciences, including genome sequencing and high-throughput experimentation, offers an opportunity for understanding biology and medicine from a systems perspective. This 'new view', which complements the more traditional component-based approach, involves the integration of biological research with approaches from engineering disciplines and computer science. The result is more than a new set of technologies. Rather, it promises a fundamental reconceptualization of the life sciences based on the development of quantitative and predictive models to describe crucial processes. To achieve this change, learning communities are being formed at the interface of the life sciences, engineering and computer science. Through these communities, research and education will be integrated across disciplines and the challenges associated with multidisciplinary team-based science will be addressed.

Biological Science Disciplines↗
PubMed1994

A survey of the teaching and learning of biological sciences on undergraduate nursing courses.

Curriculum planners developing degree courses in nursing have to decide how much time to allocate to each of the academic disciplines including biological sciences. There is no research-based evidence to suggest what depth and detail of knowledge of biological sciences is required to support nursing practice. There is also some debate about the teaching methods used and who should teach the biological sciences. This paper reports the results of a small survey investigating the teaching of biological sciences on 16 nursing degree courses in the UK. The survey uncovered great variation in the number of hours spent on biological sciences in the different universities and in the science entry requirements of the different universities. Most teachers of biological sciences had a first degree in the subject but few were nurses. The possible implications of these findings are discussed. Problems associated with shared learning and didactic teaching methods are also highlighted. Although the biological sciences input will largely be a matter of institutional preferences, nursing needs to develop a research-based framework to aid curriculum planning.

Biological Science Disciplines↗