Neurodata Without Borders: Creating a Common Data Format for Neurophysiology

The Neurodata Without Borders (NWB) initiative promotes data standardization in neuroscience to increase research reproducibility and opportunities. In the first NWB pilot project, neurophysiologists and software developers produced a common data format for recordings and metadata of cellular electrophysiology and optical imaging experiments. The format specification, application programming interfaces, and sample datasets have been released

The Diploid Genome Sequence of an Individual Human

Presented here is a genome sequence of an individual human. It was produced from ∼32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2–206 bp), 292,102 heterozygous insertion/deletion events (indels)(1–571 bp), 559,473 homozygous indels (1–82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

With a genome size of ∼580 kb and approximately 480 protein coding regions, Mycoplasma genitalium is one of the smallest known self-replicating organisms and, additionally, has extremely fastidious nutrient requirements. The reduced genomic content of M. genitalium has led researchers to suggest that the molecular assembly contained in this organism may be a close approximation to the minimal set of genes required for bacterial growth. Here, we introduce a systematic approach for the construction and curation of a genome-scale in silico metabolic model for M. genitalium. Key challenges included estimation of biomass composition, handling of enzymes with broad specificities, and the lack of a defined medium. Computational tools were subsequently employed to identify and resolve connectivity gaps in the model as well as growth prediction inconsistencies with gene essentiality experimental data. The curated model, M. genitalium iPS189 (262 reactions, 274 metabolites), is 87% accurate in recapitulating in vivo gene essentiality results for M. genitalium. Approaches and tools described herein provide a roadmap for the automated construction of in silico metabolic models of other organisms

DEVELOPMENT OF ORGANIZATION MANAGEMENT SYSTEM OF INNOVATION PROGRAMS

There the mechanisms which connect the organization management decisions with their use results, the tendencies of change of organization forms and programs have been brought out. The opportunity for use of study results and simulators in the development of organization forms and management techniques for large science-intensive programs in the civil engineering, in the resource supply of these programs has been showed. The period of realization of investment plan has been decreased up to 2,5 times. The application field is the small-storey house-building in towns and countryAvailable from VNTIC / VNTIC - Scientific & Technical Information Centre of RussiaSIGLERURussian Federatio

Assessment of the socio-economic development of the region (on the example of the Chuvash Republic)

The article proposes a methodology for an indicative assessment of the socio-economic development of the region in order to ensure the sustainability of development. The author’s methodology is based on the principles of indicative management; based on the use of a system of indicators of development indicators, intervals of threshold values; is a step-by-step process of assessing the social and economic development of the region; takes into account the contribution of each factor to ensuring sustainable development; allows you to identify “strong” and “problem” areas of social and economic development of the region. The analysis of the results obtained in dynamics makes it possible to assess the effectiveness of development indicators

Сomputer-based calculation of atmospheric pollutant emissions by automobile transport at controlled crossings

The paper uses pollutant emissions calculation methods in accordance with GOST (All-Union State Standard) in combination with the method of mathematical statistics, which makes it possible to determine the amount of emissions from automobile transport, which is in line at a red traffic light in the area of a controlled intersection. The methods allow calculating such environmental indicators as the mass of pollutant emissions, the concentration of pollutants and the Air Pollution Index. The authenticity of this technique is confirmed by testing the hypothesis on the Pearson Law of distribution of pollutants. Based on the combined methodology, the software has been developed with the purpose to monitor atmospheric air pollution. This approach will make it possible to qualitatively assess the level of atmospheric air pollution and take timely measures in the event of dangerous environmental conditions