User guides for biologists to learn computational methods

Journal of Microbiology - System-wide studies of a given molecular type are referred to as “omics.” These include genomics, proteomics, and metabolomics, among others. Recent...     

BioSPICE: access to the most current computational tools for biologists

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface. The current Dashboard permits data sources, models, simulation engines, and output displays provided by different investigators and running on different machines to work together across a distributed, heterogeneous network. Among several other features, the Dashboard enables users to create graphical workflows by configuring and connecting available BioSPICE components. Anticipated future enhancements to BioSPICE include a notebook capability that will permit researchers to browse and compile data to support model building, a biological model repository, and tools to support the development, control, and data reduction of wet-lab experiments. In addition to the BioSPICE software products, a project website supports information exchange and community building.     

A glossary for biometeorology

Here we present, for the first time, a glossary of biometeorological terms. The glossary aims to address the need for a reliable source of biometeorological definitions, thereby facilitating communication and mutual understanding in this rapidly expanding field. A total of 171 terms are defined, with reference to 234 citations. It is anticipated that the glossary will be revisited in coming years, updating terms and adding new terms, as appropriate. The glossary is intended to provide a useful resource to the biometeorology community, and to this end, readers are encouraged to contact the lead author to suggest additional terms for inclusion in later versions of the glossary as a result of new and emerging developments in the field.     

State-transition diagrams for biologists

It is clearly in the tradition of biologists to conceptualize the dynamical evolution of biological systems in terms of state-transitions of biological objects. This paper is mainly concerned with (but obviously not limited too) the immunological branch of biology and shows how the adoption of UML (Unified Modeling Language) state-transition diagrams can ease the modeling, the understanding, the coding, the manipulation or the documentation of population-based immune software model generally defined as a set of ordinary differential equations (ODE), describing the evolution in time of populations of various biological objects. Moreover, that same UML adoption naturally entails a far from negligible representational economy since one graphical item of the diagram might have to be repeated in various places of the mathematical model. First, the main graphical elements of the UML state-transition diagram and how they can be mapped onto a corresponding ODE mathematical model are presented. Then, two already published immune models of thymocyte behavior and time evolution in the thymus, the first one originally conceived as an ODE population-based model whereas the second one as an agent-based one, are refactored and expressed in a state-transition form so as to make them much easier to understand and their respective code easier to access, to modify and run. As an illustrative proof, for any immunologist, it should be possible to understand faithfully enough what the two software models are supposed to reproduce and how they execute with no need to plunge into the Java or Fortran lines.     

A computational tool for quantitative analysis of vascular networks

Angiogenesis is the generation of mature vascular networks from pre-existing vessels. Angiogenesis is crucial during the organism' development, for wound healing and for the female reproductive cycle. Several murine experimental systems are well suited for studying developmental and pathological angiogenesis. They include the embryonic hindbrain, the post-natal retina and allantois explants. In these systems vascular networks are visualised by appropriate staining procedures followed by microscopical analysis. Nevertheless, quantitative assessment of angiogenesis is hampered by the lack of readily available, standardized metrics and software analysis tools. Non-automated protocols are being used widely and they are, in general, time--and labour intensive, prone to human error and do not permit computation of complex spatial metrics. We have developed a light-weight, user friendly software, AngioTool, which allows for quick, hands-off and reproducible quantification of vascular networks in microscopic images. AngioTool computes several morphological and spatial parameters including the area covered by a vascular network, the number of vessels, vessel length, vascular density and lacunarity. In addition, AngioTool calculates the so-called "branching index" (branch points/unit area), providing a measurement of the sprouting activity of a specimen of interest. We have validated AngioTool using images of embryonic murine hindbrains, post-natal retinas and allantois explants. AngioTool is open source and can be downloaded free of charge.     

OBO-Edit--an ontology editor for biologists

OBO-Edit is an open source, platform-independent ontology editor developed and maintained by the Gene Ontology Consortium. Implemented in Java, OBO-Edit uses a graph-oriented approach to display and edit ontologies. OBO-Edit is particularly valuable for viewing and editing biomedical ontologies. Availability: https://sourceforge.net/project/showfiles.php?group_id=36855.     

Natural insights for chemical biologists

Chemical biologists studying natural-product pathways encoded in genomes have unearthed new chemistry and insights into the evolution of biologically active metabolites.     

A glossary of plant hair terminology

This is a compilation of English terms having to do with hairs and hairy surfaces of plants. The glossary is divided into two sections. Part I includes terms for types and attributes of individual hair kinds and hair clusters. Part II deals with kinds and characteristics of induments.     

A course in communication and information retrieval for undergraduate biologists

Most librarians, and at least some lecturers in institutions of higher education, recognise the need for students to receive instruction in the use of information sources. In the life sciences, the continuing growth in the number of these sources creates problems for biologists. To help students cope with the situation, a compulsory course in Communication and Information Retrieval has been introduced into the BSc degree in biology at Paisley College of Technology. The course, taught by the College library staff, covers the structure of scientific literature, the language barrier, techniques of literature searching and scientific writing, and the information network in the life sciences.     

Structures and technology for biologists

Structural genomics efforts are already producing a quarter of all 'new' macromolecular structures (<30% sequence identity to previously solved structures) and are stimulating development of systematic and automated approaches to structure determination. The thousands of new structures likely to be determined and the technologies and infrastructure likely to be developed over the next decade will benefit all biologists.