OReFiL: an online resource finder for life sciences.
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BACKGROUND: Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced in special journal issues or websites with a search function, but others remain scattered throughout the Internet and in the published literature. The searchable resources on these sites are collected and maintained manually and are therefore of higher quality than automatically updated sites, but also require more time and effort. DESCRIPTION: We developed an online resource search system called OReFiL to address these issues. We developed a crawler to gather all of the web pages whose URLs appear in MEDLINE abstracts and full-text papers on the BioMed Central open-access journals. The URLs were extracted using regular expressions and rules based on our heuristic knowledge. We then indexed the online resources to facilitate their retrieval and comparison by researchers. Because every online resource has at least one PubMed ID, we can easily acquire its summary with Medical Subject Headings (MeSH) terms and confirm its credibility through reference to the corresponding PubMed entry. In addition, because OReFiL automatically extracts URLs and updates the index, minimal time and effort is needed to maintain the system. CONCLUSION: We developed OReFiL, a search system for online life science resources, which is freely available. The system's distinctive features include the ability to return up-to-date query-relevant online resources introduced in peer-reviewed papers; the ability to search using free words, MeSH terms, or author names; easy verification of each hit following links to the corresponding PubMed entry or to papers citing the URL through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar; and quick confirmation of the existence of an online resource web page. (+info)
oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language.
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OneChannelGUI is an add-on Bioconductor package providing a new set of functions extending the capability of the affylmGUI package. This library provides a graphical interface (GUI) for Bioconductor libraries to be used for quality control, normalization, filtering, statistical validation and data mining for single channel microarrays. Affymetrix 3' expression (IVT) arrays as well as the new whole transcript expression arrays, i.e. gene/exon 1.0 ST, are actually implemented. oneChannelGUI is available for most platforms on which R runs, i.e. Windows and Unix-like machines. AVAILABILITY: http://www.bioconductor.org/packages/2.0/bioc/html/oneChannelGUI.html (+info)
Movement to curtail animal dissections in zoology curriculum: review of the Indian experience.
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Animal dissections have been dropped from the curriculum in several developed countries, and virtual laboratories are taking their place, or at least the concept of the "three R's" is becoming accepted. Yet, the scenario in the developing countries in this regard has been dismal. However, recently, a movement has started in India in this area, thanks to the aggressive approach of PfA, I-CARE and InterNICHE, supported by a few zoology educators and policy makers, who joined this movement as freelancers. The aggressive campaigners against animal dissections put up convincing arguments to the orthodox zoology educators and higher education planners with such veracity that the arguments cannot be ignored. The arguments, to be presented in detail at the conference, and the campaign have been rewarded with success such that a few universities and autonomous colleges have revamped their zoology curricula so as to dispense with or reduce animal dissections. The Bharathidasan University, Tiruchirappalli, Tamil Nadu, India, has been the trendsetter, evolving what is known as the "Bharathidasan University Model". A memorandum from I-CARE and PfA to the University Grants Commission, Government of India, New Delhi, was sent out by the UGC to the universities with a request to consider the points positively. However, there is still a need to bring about an attitudinal change in the zoology educators and higher education planners such that they participate willingly in this endeavour. The role-players at all levels are identified and approached with a language that is understandable to each and are adequately supported by hands-on training in the alternative methods. Ultimately, the responsibility in this regard lies with the educators themselves, since they are the ones who, working in the academic committees that design the curricula, can cut down on the requirement for dissections. (+info)
The integration seminar: a first-year dental course integrating concepts from the biomedical, professional, and clinical sciences.
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This study describes the planning, implementation, and evaluation of a seminar course designed to facilitate discussion and understanding of cross-disciplinary concepts by first-year dental students. Dental and medical schools are implementing integrated curricula in which clinical courses are taught early in the curriculum and the clinical and basic sciences are taught not only concurrently, but in an integrated manner. This first-year course, Integration Seminar, was developed to cross traditional subject and departmental boundaries with the intent of fostering dental care providers who understand the interdependence of the major concepts within these areas. This report describes the development and structure of the Integration Seminar. Furthermore, student perception of this course was determined by evaluating year-end course surveys, and student performance outcomes were measured by comparing student scores on the National Board Dental Examination Part I (NBDE-I) prior to and after the inception of this course. We determined that a substantial majority of students recognized the integrated nature of the course. In addition, NBDE-I scores were significantly higher for the cohorts of students who had participated in the course, although this observation is likely dependent upon many other factors. This report may thus provide a course model for other schools with a similar goal of achieving an integrated curriculum. (+info)
Development and perspectives of scientific services offered by genomic biological resource centres.
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A number of fundamental technical developments like the evolvement of oligonucleotide microarrays, new sequencing technologies and gene synthesis have considerably changed the character of genomic biological resource centres in recent years. While genomic biological resource centres traditionally served mainly as providers of sparsely characterized cDNA clones and clone sets, there is nowadays a clear tendency towards well-characterized, high-quality clones. In addition, major new service units like microarray services have developed, which are completely independent of clone collections, reflecting the co-evolution of data generation and technology development. The new technologies require an increasingly higher degree of specialization, data integration and quality standards. Altogether, these developments result in spin-offs of highly specialized biotech companies, some of which will take a prominent position in translational medicine. (+info)
Building capacity in the life sciences in the developing world.
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The fundamental challenge facing the scientific community is how to devise innovative strategies that will bring all developing countries into the "biological fold" and to do so in ways that will take full advantage of advances in the biological sciences to curb poverty, improve public health, and promote human development. (+info)
Building, using, and maximizing the impact of concept inventories in the biological sciences: report on a National Science Foundation sponsored conference on the construction of concept inventories in the biological sciences.
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The meeting "Conceptual Assessment in the Biological Sciences" was held March 3-4, 2007, in Boulder, Colorado. Sponsored by the National Science Foundation and hosted by University of Colorado, Boulder's Biology Concept Inventory Team, the meeting drew together 21 participants from 13 institutions, all of whom had received National Science Foundation funding for biology education. Topics of interest included Introductory Biology, Genetics, Evolution, Ecology, and the Nature of Science. The goal of the meeting was to organize and leverage current efforts to develop concept inventories for each of these topics. These diagnostic tools are inspired by the success of the Force Concept Inventory, developed by the community of physics educators to identify student misconceptions about Newtonian mechanics. By working together, participants hope to lessen the risk that groups might develop competing rather than complementary inventories. (+info)
Effective use of course management systems to enhance student learning: Experimental Biology 2007.
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Course management systems are software packages that support teaching and learning by providing web-based tools, services, and resources. Electronic course management can facilitate course organization, teaching delivery, communication, collaboration, and assessment. This article reports on a symposium on the use of course management systems, presented by the Teaching of Physiology Section of the American Physiological Society, at the Experimental Biology Meeting of 2007. (+info)