Математическая биология и биоинформатика: V Международная конференция, г. Пущино, 19-24 октября 2014 г.: Доклады
We present a database URS (the Universe of RNA Structures) of RNA structures and their elements (e.g. base-pairs, loops, stems, pseudoknots) and a search engine allowing one to search such elements and obtain statistics on them. The search engine is available on the web at http://server3.lpm.org.ru/urs/
Research on the modern level in such scientific fields as mathematical biology, bioinformatics and related closely connected with the latest achievements in the field of information technologies and is mainly based on processing of large volumes of digital information. The most promising direction is the use of cloud computing services as a methodological component and data centers, as the technology.
The paper formulates the problem of constructing a broadly applicable and flexible Conceptual Metagrammar (CM). It is to be a collection of the rules enabling us to construct step by step a semantic representation (or text meaning representation) of practically arbitrary sentence or discourse pertaining to mass spheres of human’s professional activity. The opinion is grounded that the first version of broadly applicable and flexible CM is already available in the scientific literature. It is conjectured that the definition of the class of SK-languages (standard knowledge languages) provided by the theory of K-representations (knowledge representations) can be interpreted as the first version of broadly applicable and flexible CM. The current version of the latter theory is stated in the author’s monograph published by Springer in 2010. The final part of the paper describes the connections with the related approaches, in particular, with the studies on developing a Multilingual Semantic Web.
The paper describes the structure and possible applications of the theory of K-representations (knowledge representations) in bioinformatics and in the development of a Semantic Web of a new generation. It is an original theory of designing semantic-syntactic analyzers of natural language (NL) texts with the broad use of formal means for representing input, intermediary, and output data. The current version of the theory is set forth in a monograph by V. Fomichov (Springer, 2010). The first part of the theory is a formal model describing a system consisting of ten operations on conceptual structures. This model defines a new class of formal languages – the class of SK-languages. The broad possibilities of constructing semantic representations of complex discourses pertaining to biology are shown. A new formal approach to developing multilingual algorithms of semantic-syntactic analysis of NL-texts is outlined. This approach is realized by means of a program in the language PYTHON.
This volume covers some of the topics that are related to the rapidly growing field of biomedical informatics. In June 11–12, 2010 a workshop entitled ‘Optimization and Data Analysis in Biomedical Informatics’ was organized at The Fields Institute. Following this event, invited contributions were gathered based on the talks presented at the workshop, and additional invited chapters were solicited from leading experts. In this publication, the authors share their expertise in the form of state-of-the-art research and review chapters, bringing together researchers from different disciplines and emphasizing the value of mathematical methods in the areas of clinical sciences.
The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.
The article highlights the reports of X International Symposium on Evolutionary Economics (Russia, Pushchino, Moscow Region, September 12-14, 2013).
We consider certain spaces of functions on the circle, which naturally appear in harmonic analysis, and superposition operators on these spaces. We study the following question: which functions have the property that each their superposition with a homeomorphism of the circle belongs to a given space? We also study the multidimensional case.
We consider the spaces of functions on the m-dimensional torus, whose Fourier transform is p -summable. We obtain estimates for the norms of the exponential functions deformed by a C1 -smooth phase. The results generalize to the multidimensional case the one-dimensional results obtained by the author earlier in “Quantitative estimates in the Beurling—Helson theorem”, Sbornik: Mathematics, 201:12 (2010), 1811 – 1836.
We consider the spaces of function on the circle whose Fourier transform is p-summable. We obtain estimates for the norms of exponential functions deformed by a C1 -smooth phase.