Multiderivative methods for linear second order boundary value prob1ems

Second, fourth and sixth order methods are developed and analysed for the numerical solution of linear second order boundary value problems. The methods are developed by replacing the exponential terms in a three—point recurrence relation by Padé approximants. The methods are tested on a problem from the literatur

Implicit methods for the simple wave equation

A family of finite difference methods is developed for the numerical solution of the simple wave equation. Local truncation errors are cal- culated for each member of the family and each is analyzed for stability. The concepts of A0 -stability and L0 -stability, well-used in the literature on other types of partial differential equation, are discussed in relation to second order hyperbolic equations. The numerical methods are extended to cover two-dimensional wave equations and the methods developed in the paper are tested on three problems from the literature. w925948

Multiderivative methods for nonlinear second order boundary value problems

Second, fourth and sixth order methods are developed and analysed for the numerical solution of non-linear second order boundary value problems. The methods arise from a two-step recurrence relation involving exponential terms, these being replaced by Padé approximants . The methods are tested on two problems from the literature

Classificatory Theory in Data-Intensive Science: The Case of Open Biomedical Ontologies

publication-status: Publishedtypes: ArticleThis is the author's version of a paper that was subsequently published in International Studies in the Philosophy of Science. Please cite the published version by following the DOI link.Knowledge-making practices in biology are being strongly affected by the availability of data on an unprecedented scale, the insistence on systemic approaches and growing reliance on bioinformatics and digital infrastructures. What role does theory play within data-intensive science, and what does that tell us about scientific theories in general? To answer these questions, I focus on Open Biomedical Ontologies, digital classification tools that have become crucial to sharing results across research contexts in the biological and biomedical sciences, and argue that they constitute an example of classificatory theory. This form of theorizing emerges from classification practices in conjunction with experimental know-how and expresses the knowledge underpinning the analysis and interpretation of data disseminated online.Economic and Social Research Council (ESRC)The British AcademyLeverhulme Trus

Unintended consequences of existential quantifications in biomedical ontologies

<p>Abstract</p> <p>Background</p> <p>The Open Biomedical Ontologies (OBO) Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the semantic web format Web Ontology Language (OWL), which draws upon formal logic. Based on the interpretations underlying OWL description logics (OWL-DL) semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors.</p> <p>Results</p> <p>We analyzed ontologies and ontology cross products available via the OBO Foundry site <url>http://www.obofoundry.org</url> for existential restrictions (<it>someValuesFrom</it>), from which we examined a random sample of 2,836 clauses.</p> <p>According to a rating done by four experts, 23% of all existential restrictions in OBO Foundry candidate ontologies are suspicious (Cohens' <it>κ </it>= 0.78). We found a smaller proportion of existential restrictions in OBO Foundry cross products are suspicious, but in this case an accurate quantitative judgment is not possible due to a low inter-rater agreement (<it>κ </it>= 0.07). We identified several typical modeling problems, for which satisfactory ontology design patterns based on OWL-DL were proposed. We further describe several usability issues with OBO ontologies, including the lack of ontological commitment for several common terms, and the proliferation of domain-specific relations.</p> <p>Conclusions</p> <p>The current OWL releases of OBO Foundry (and Foundry candidate) ontologies contain numerous assertions which do not properly describe the underlying biological reality, or are ambiguous and difficult to interpret. The solution is a better anchoring in upper ontologies and a restriction to relatively few, well defined relation types with given domain and range constraints.</p

Current trend in synthesis, Post-Synthetic modifications and biological applications of Nanometal-Organic frameworks (NMOFs)

Since the early reports of MOFs and their interesting properties, research involving these materials has grown wide in scope and applications. Various synthetic approaches have ensued in view of obtaining materials with optimised properties, the extensive scope of application spanning from energy, gas sorption, catalysis biological applications has meant exponentially evolved over the years. The far‐reaching synthetic and PSM approaches and porosity control possibilities have continued to serve as a motivation for research on these materials. With respect to the biological applications, MOFs have shown promise as good candidates in applications involving drug delivery, BioMOFs, sensing, imaging amongst others. Despite being a while away from successful entry into the market, observed results in sensing, drug delivery, and imaging put these materials on the spot light as candidates poised to usher in a revolution in biology. In this regard, this review article focuses current approaches in synthesis, post functionalization and biological applications of these materials with particular attention on drug delivery, imaging, sensing and BioMOFs