A Molecular Biology Database Digest

Computational Biology or Bioinformatics has been defined as the application of mathematical and Computer Science methods to solving problems in Molecular Biology that require large scale data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential role in Computational Biology research and development. This paper introduces into current Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the integration of Molecular Biology data from different sources. This paper is primarily intended for an audience of computer scientists with a limited background in Biology

Why biologists should read Aristotle (or why philosophy matters for the life sciences and why the life sciences matter for philosophy)

This note discusses the importance of Natural History (biology) in the development of Aristotle philosophy and scientific outlook, and so the importance of considering Aristotle's philosophy as a necessary and useful background for contemporary biology

Regional development: contribution of evolutionary biology

This paper tries to set out a potential of application of some evolutionary biology concepts to the issue of regional development. The objective is to show that employment of these concepts or at least inspiration by them may enrich some theories of regional development and enhance the explanatory framework of regional evolution.First, the views of institutional economics and geography on evolutionary biology contribution are summarised, then some evolutionary concepts are applied to the path dependence concept e. g., in effort to find a possible way of classification of this phenomenon. However, we discuss some other evolutionary concepts, as coevolution, adaptation, preadaption, general approach to comprehension of evolution, etc. in connexion with some chosen theories and problems of regional development.Regional development ; evolutionary biology ; path dependence ; theories of regional development

Stem cells and the origin of gliomas: A historical reappraisal with molecular advancements.

The biology of both normal and tumor development clearly possesses overlapping and parallel features. Oncogenes and tumor suppressors are relevant not only in tumor biology, but also in physiological developmental regulators of growth and differentiation. Conversely, genes identified as regulators of developmental biology are relevant to tumor biology. This is particularly relevant in the context of brain tumors, where recent evidence is mounting that the origin of brain tumors, specifically gliomas, may represent dysfunctional developmental neurobiology. Neural stem cells are increasingly being investigated as the cell type that originally undergoes malignant transformation - the cell of origin - and the evidence for this is discussed

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

Issues of shaping the students’ professional and terminological competence in science area of expertise in the sustainable development era

The paper deals with the problem of future biology teachers’ vocational preparation process and shaping in them of those capacities that contribute to the conservation and enhancement of our planet’s biodiversity as a reflection of the leading sustainable development goals of society. Such personality traits are viewed through the prism of forming the future biology teachers’ professional and terminological competence. The main aspects and categories that characterize the professional and terminological competence of future biology teachers, including terminology, nomenclature, term, nomen and term element, have been explained. The criteria and stages of shaping the future biology teachers’ professional and terminological competence during the vocational training process have been fixed. Methods, techniques, technologies, guiding principles and forms of staged work on the forming of an active terminological dictionary of students have been described and specified. The content of the distant special course “Latin. Botanical Terminology”, which provides training for future teachers to study the professional subjects and to understand of international scientific terminology, has been presented. It is concluded that the proper level of formation of the future biology teachers’ professional and terminological competence will eventually ensure the qualitative preparation of pupils for life in a sustainable development era

The Development of Biology Material Resources by Metacognitive Strategy

The Development of Biology Material Resources by Metacognitive Strategy The study was aimed at finding out the suitability of Biology Materials using the metacognitive strategy. The materials were textbooks, self-understanding Evaluation Sheet and the key, lesson plan, and tests including the answer key. The criteria of appropriateness included the relevance of the resources with the content validity, face va­lidity and the language. This research and development study was carried out employing a 3D model, namely define, design and develop. At the define stage, three topics were selected for analysis, they were virus, Endocrine System, and Genetic material. During the design phase, the physical appearance of the materials was suited with the Metacognitive Strategy. At the develop phase, the material resources were examined and validated by two Biology experts and senior teachers of Biology. The results showed that the Biology material Resources using Metacognitive Strategy developed in the study has fell into the category of very good ( score > 3.31) and was therefore considered suitable

Interactive learning in biology with PhotoCD and associated software

This paper describes the pioneering development of flexible‐learning courseware in the teaching and learning of cell biology using a novel optical disk‐based technology — PhotoCD — and its associated computer software. The use of this format in an educational context for the manipulation of, and interaction with, photographic images in electronic form is presented for the first time. Examples of courseware which use PhotoCD, image‐enhancement and image‐management software in biology education are given, and an evaluation by undergraduates in biology education (student teachers) of these teaching and learning strategies is presente

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

Erwin Schroedinger, Francis Crick and epigenetic stability

Schroedinger's book 'What is Life?' is widely credited for having played a crucial role in development of molecular and cellular biology. My essay revisits the issues raised by this book from the modern perspective of epigenetics and systems biology. I contrast two classes of potential mechanisms of epigenetic stability: 'epigenetic templating' and 'systems biology' approaches, and consider them from the point of view expressed by Schroedinger. I also discuss how quantum entanglement, a nonclassical feature of quantum mechanics, can help to address the 'problem of small numbers' that lead Schroedinger to promote the idea of molecular code-script for explanation of stability of biological order.Comment: New and improved version of the essay, now published in the online journal 'Biology Direct'. Contains more expanded discussion on entanglement. 18 pages, 2 figures. The file includes open reviews by E.Koonin, V.Vedral and E.Karsent