PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Biological Science Disciplines”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4Linked to original sources
PubMed2005

KDE Bioscience: platform for bioinformatics analysis workflows.

Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nucleotide and protein sequences from local flat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research.

Biological Science Disciplines↗
PubMedDate not supplied

NanoSystems biology.

Systems biology is an approach in which the digital information of the genome, acted upon by environmental cues, generates the many molecular signatures of gene and protein expression, as well as other, more phenomenological experimental observations. These data may be integrated together to form a testable hypothesis of how a biological organism functions as a system. The central components of systems biology are genetically programmed networks (circuits) within cells and networks of cells. These components establish the organization and function of individual cells and tissues in response to environmental signals such as cell-to-cell communication within organ systems and whole organisms. Within this context, disease is considered as a genetic or environmental reprogramming of cells to gain or lose specific functions that are characteristics of disease. This paper is a combination of three tutorials with an outlined series of technologies, including microfluidics, nanotechnologies, and molecular imaging methods, and we describe how their development should be driven by the needs of systems biology. We also discuss how these technologies can enable a systems biology approach through a pathway from single cells to mouse models of disease and finally to patients. Within this technology base are approaches to develop, use and test molecules as probes that target proteins, DNA and mRNA to test systems biology models, as well as provide molecular diagnostics and molecular therapeutics within a systems biology framework.

Animals↗
PubMed2002

Text-based knowledge discovery: search and mining of life-sciences documents.

Text literature is playing an increasingly important role in biomedical discovery. The challenge is to manage the increasing volume, complexity and specialization of knowledge expressed in this literature. Although information retrieval or text searching is useful, it is not sufficient to find specific facts and relations. Information extraction methods are evolving to extract automatically specific, fine-grained terms corresponding to the names of entities referred to in the text, and the relationships that connect these terms. Information extraction is, in turn, a means to an end, and knowledge discovery methods are evolving for the discovery of still more-complex structures and connections among facts. These methods provide an interpretive context for understanding the meaning of biological data.

Biological Science Disciplines↗
PubMed2005

Web services in the life sciences.

Web services provide a standard way of publishing applications and data sources over the internet, enabling mass dissemination of knowledge. In the life sciences, the web-service approach is seen as being a road to standardizing the multitude of tools available from different providers. In this article, we present an overview of the technology (focusing on life-science applications), we list the currently available service providers and we discuss advanced issues raised by the concept.

Biological Science Disciplines↗
PubMed2003

A life scientist's gateway to distributed data management and computing: the PathPort/ToolBus framework.

The emergent needs of the bioinformatics community challenge current information systems. The pace of biological data generation far outstrips Moore's Law. Therefore, a gap continues to widen between the capabilities to produce biological (molecular and cell) data sets and the capability to manage and analyze these data sets. As a result, Federal investments in large data set generation produces diminishing returns in terms of the community's capabilities of understanding biology and leveraging that understanding to make scientific and technological advances that improve society. We are building an open framework to address various data management issues including data and tool interoperability, nomenclature and data communication standardization, and database integration. PathPort, short for Pathogen Portal, employs a generic, web-services based framework to deal with some of the problems identified by the bioinformatics community. The motivating research goal of a scalable system to provide data management and analysis for key pathosystems, especially relating to molecular data, has resulted in a generic framework using two major components. On the server-side, we employ web-services. On the client-side, a Java application called ToolBus acts as a client-side "bus" for contacting data and tools and viewing results through a single, consistent user interface.

Biological Science Disciplines↗