SemanticSBML: a tool for annotating, checking, and merging of biochemical models in SBML format

Semantic annotations in SBML (systems biology markup language) enable computer programs to check and process biochemical models based on their biochemical meaning. Annotations are an important prerequisite for model merging, which would be a major step towards the construction of large-scale cell models. The software tool semanticSBML allows users to check and edit MIRIAM annotations and SBO terms, the most common forms of annotation in SBML models. It uses a large collection of biochemical names and database identifiers to support modellers in finding the right annotations. Annotated SBML models can also be built from lists of chemical reactions. In model merging, semanticSBML suggests a preliminary merged model based on MIRIAM annotations in the original models. This model provides a starting point for manually aligning the elements of all input models. To resolve conflicting element properties, conflicts are highlighted and categorised. The user can navigate through the models, change the matching of model elements, check the conflicts between them and decide how they should be resolved. Alternatively, the software can resolve all conflicts automatically, selecting each time the attribute value from the input model with highest priority.
URL: "http://www.semanticsbml.org/":http://www.semanticsbml.org

An investigation of outdoor adventure leadership and programming preparation in physical education baccalaureate degree programs

The nature and scope of outdoor adventure leadership and programming preparation for physical education majors was investigated. A nationwide survey (Phase I) found that 184 (44.2%) institutions offered outdoor adventure leadership and programming courses to physical education majors. A mean of 6.7 semester hours, almost equally divided between theory/methods and activity, were offered. Phase II examined the development of 148 outdoor adventure leadership and programming competencies in 12 institutions with significant outdoor adventure components. Characteristics of the institutions, physical education programs, and outdoor adventure components were described. These institutions offered a mean of 23.6 semester hours in 13.2 predominantly elective activity-oriented courses. An average of 38 (21.2%) physical education majors were enrolled annually in outdoor adventure courses. A mean of 2.8 faculty members, specializing in two or more adventure areas, taught the courses. At least half the institutions offered backpacking, canoeing, climbing/rappelling, crosscountry skiing, cycling, SCUBA, orienteering, outdoor education, leadership, outdoor adventure education, and supervised leadership experiences

Changes in Myosin and Myosin Light Chain Kinase During Myogenesis

Myosins and myosin light chain kinases have been isolated from a cloned line of myoblasts (L5/A10) as this cell line undergoes differentiation toward adult muscle. At least three myosin isozymes were obtained during this developmental process. Initially a nonmuscle type of myosin was found in the myoblasts. The molecular weights of the myoblast light chains were 20 000 and 15 000. Myosin isolated from early myotubes had light chains with molecular weights of 20 000 and 19 500. Myosin isolated from myotubes which contained sarcomeres had light chains with molecular weights of 23 000, 18 500, and 16000. This last myosin was similar in light chain complement to adult rat thigh muscle. Two forms of the myosin light chain kinase activity were detected: a calciumindependent kinase in the myoblasts and a calcium-dependent kinase in the myotubes with sarcomeres. No myosin light chain kinase activity was detected in the early myotubes

Toward community standards and software for whole-cell modeling

Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells. Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in SBML. Results: Our analysis revealed several challenges to representing WC models using the current standards. Conclusion: We, therefore, propose several new WC modeling standards, software, and databases. Significance:We anticipate that these new standards and software will enable more comprehensive models

Distributing tasks via multiple input pathways increases cellular survival in stress

This is the author accepted manuscript. The final version is available from eLife Sciences Publications via the DOI in this record.Improving in one aspect of a task can undermine performance in another, but how such opposing demands play out in single cells and impact on fitness is mostly unknown. Here we study budding yeast in dynamic environments of hyperosmotic stress and show how the corresponding signalling network increases cellular survival both by assigning the requirements of high response speed and high response accuracy to two separate input pathways and by having these pathways interact to converge on Hog1, a p38 MAP kinase. Cells with only the less accurate, reflex-like pathway are fitter in sudden stress, whereas cells with only the slow, more accurate pathway are fitter in fluctuating but increasing stress. Our results demonstrate that cellular signalling is vulnerable to trade-offs in performance, but that these trade-offs can be mitigated by assigning the opposing tasks to different signalling subnetworks. Such division of labour could function broadly within cellular signal transduction.We thank Michael Elowitz, Robert Endres, Tanniemola Liverpool, FilippoMenolascina, Diego Oyarzun, Lynne Regan, the members of the Swain lab, and particularly Pascal Hersen for critical comments, Pascal Hersen for providing strains, and our funders: the Human Frontier Science Program, the Scottish Universities Life Sciences Alliance, and the UK’s BBSRC (MMC & PSS), the UK’s MRC (MV), the Wellcome Trust (LFM), the UK’s EPSRC (MV via grant EP/N014391/1, AAG, & RT), and Mexico’s CONACyT (AAG & LFM)

Richard Münch: Der bildungsindustrielle Komplex. Schule und Unterricht im Wettbewerbsstaat. Weinheim / Basel: Beltz Juventa 2018 (392 S.) [Rezension]

Rezension von: Richard Münch: Der bildungsindustrielle Komplex. Schule und Unterricht im Wettbewerbsstaat. Weinheim / Basel: Beltz Juventa 2018 (392 S.; ISBN 978-3-7799-3950-4; 27,95 EUR)