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SIAN: software for structural identifiability analysis of ODE models
Bioinformatics. 2019. Vol. 35. No. 16. P. 2873-2874.
Hong H., Ovchinnikov A., Pogudin G., Yap C.
Biological processes are often modeled by ordinary differential equations with unknown parameters. The unknown parameters are usually estimated from experimental data. In some cases, due to the structure of the model, this estimation problem does not have a unique solution even in the case of continuous noise-free data. It is therefore desirable to check the uniqueness a priori before carrying out actual experiments. We present a new software SIAN (Structural Identifiability ANalyser) that does this. Our software can tackle problems that could not be tackled by previously developed packages.
Priority areas:
IT and mathematics
Language:
English
Keywords: parameter identifiability
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Recent advances in single-cell genomics provide an alternative to largely gene-centric metagenomics studies, enabling whole-genome sequencing of uncultivated bacteria. However, single-cell assembly projects are challenging due to (i) the highly nonuniform read coverage and (ii) a greatly elevated number of chimeric reads and read pairs. While recently developed single-cell assemblers have addressed the former challenge, ...
Added: March 21, 2014
Zakhodiakin G., Успехи в химии и химической технологии 2014 Т. 28 № 10 (159) С. 97-100
This paper describes an approach to supply chain network optimization for a petrochemical enterprise. The state-task network is used for supply chain representation. A framework for comprehensive economic and environmental assessment based on life cycle assessment is proposed. The software implementation of proposed methodology is described. ...
Added: February 27, 2016
Рябенко Е.А., Математическая биология и биоинформатика 2012 Т. 7 № 2 С. 554-566
Рассматривается нелинейная модель данных ДНК-микрочипов, в которой интенсивность флуоресценции проб описывается функцией Лэнгмюра. Разработан метод настройки параметров модели на основе общедоступных данных нескольких тысяч экспериментов, основанный на минимизации функции потерь из класса AB-дивергенций; для выбора оптимальных значений гиперпараметров проведены численные эксперименты. Полученная модель описывает интенсивности флуоресценции проб микрочипа точнее стандартной линейной, а полученные на её ...
Added: October 14, 2016
Nolde D., Krylov N., Телегин П. Н. et al., Труды НИИСИ РАН 2018 Т. 7 № 4 С. 157-161
The performance of molecular dynamics software package Gromacs was measured on various
hardware: desktop computers, clusters based on x84_64 processors or many integrated core processors, and
heterogeneous system with gaming graphic cards or general purpose GPU systems. The optimal choice of hardware
for molecular dynamics simulations is discussed. ...
Added: February 10, 2020
Dubois J., Poupon C., Thirion B. et al., Cerebral Cortex 2015 Vol. 26 No. 5 P. 2283-2298
Linguistic processing is based on a close collaboration between temporal and frontal regions connected by two pathways: the “dorsal” and “ventral pathways” (assumed to support phonological and semantic processing, respectively, in adults). We investigated here the development of these pathways at the onset of language acquisition, during the first post-natal weeks, using cross-sectional diffusion imaging ...
Added: October 22, 2015
St. Petersburg : Федеральное государственное автономное образовательное учреждение высшего образования "Санкт-Петербургский политехнический университет Петра Великого", 2021
Bioinformatics Institute 2020/21. Project abstracts. Bioinformatics Summer School 2021. Abstracts. ...
Added: August 9, 2021
М. : Издательский дом "Типография" Россельхозакадемии, 2014
Vserossiyskaya nauchnaya konferentsiya 31 yanvarya 2014 g. "Matematika, informatika, estestvoznanie v ekonomike i v obshchestve". ...
Added: February 7, 2014
Nersisyan S., Galatenko A. V., Galatenko V. V. et al., Plos One 2021 Vol. 16 No. 4 Article e0249424
Analysis of regulatory networks is a powerful framework for identification and quantification of intracellular interactions. We introduce miRGTF-net, a novel tool for construction of miRNA-gene-TF networks. We consider multiple transcriptional and post-transcriptional interaction types, including regulation of gene and miRNA expression by transcription factors, gene silencing by miRNAs, and co-expression of host genes with their ...
Added: May 10, 2021
Sorokin K., Ayzenberg A., Анохин К. В. et al., / Cornell University. Series Computer Science "arxiv.org". 2022.
In present paper we test different approaches to reconstructing the topology of the physical space from neural activity data in A1 fields of mice brains, in particular, having a Cognitome-focused approach in mind. Animals were placed in different new environments and discovered them while their physical and neural activity was recorded. We discuss possible approaches ...
Added: November 17, 2022
M. : HSE, 2013
Human reasoning uses to distinguish things that do change and things do not. The latter are commonly expressed in the reasoning as objects, which may represent classes or instances, and classes being further divided into concept types and relation types. These became the main issue of knowledge engineering and have been well tractable by computer. ...
Added: October 27, 2013
Goncharov R., Сапанов П. М., Яшунский А. Д., Социология власти 2013 № 3 С. 57-72
В статье представлена технология, позволяющая собирать в полевых исследованиях пространственно локализованные данные об объектах городской среды. Технология основана на автоматической привязке фотографий к пространственным координатам. Приведен план полевых и камеральных мероприятий, предложены варианты ГИС-обработки собираемых таким образом данных. В качестве примера приведены данные об использовании белорусского языка в общественном пространстве городов Белоруссии. ...
Added: April 12, 2015
Usova E. V., Burakov A. V., Shpilman A.A., Biofizika 2010 Vol. 53 No. 6 P. 523-526
Added: October 15, 2018
Bukharov O., Bogolyubov D., Федоров В. М. et al., Криосфера Земли 2016 № 3 С. 43-50
The medium-term forecasting of the sea ice extent has been carried out by determining of the relationship between incoming solar radiation and the sea ice extent in the Northern Hemisphere. Different methods of the statistic and neural modeling have been used. Forecast shows that the main factor determining the variation of the maximum and minimum ...
Added: August 18, 2016
Kertesz-Farkas A., Noble W., Journal or Proteome Research 2015 Vol. 14 No. 8 P. 3027-3038
Added: September 25, 2015
Korotayev A., Вестник Института экономики Российской академии наук 2015 № 1 С. 149-162
The 19th century saw an explosive growth of the gap between the “First” and the “Third” World as regards per capita incomes and levels of life that has become to be known as the “Great Divergence”. In the 20th century the Great Divergence continued up to the early 1970s, and then – in the late ...
Added: December 3, 2015
Боброва Е. В., Решетникова В. В., Volkova K. et al., Журнал высшей нервной деятельности им. И.П. Павлова 2017 Т. 67 № 4 С. 485-492
Исследовали обучение управлению системой “Интерфейс мозг-компьютер” (ИМК) с помощью специально разработанного тренинга. Тренинг включал осуществление медленных циклических движений правой и левой рукой (длительность каждого движения соответствовала длительности представлений движений руки при работе с ИМК), представление этих движений, а также спокойное сидение до начала движений. До проведения тренинга и после него осуществлялось управление ИМК. По тесту ...
Added: October 20, 2017
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Added: January 30, 2013
[б.и.], 2019
. ...
Added: January 15, 2020
Rusinov I. S., Ershova A. S., Karyagina A. S. et al., BMC Genomics 2018 Vol. 19 No. 885 P. 1-11
Background. Restriction-modification (R-M) systems protect bacteria and archaea from attacks by bacteriophages and archaeal viruses. An R-M system specifically recognizes short sites in foreign DNA and cleaves it, while such sites in the host DNA are protected by methylation. Prokaryotic viruses have developed a number of strategies to overcome this host defense. The simplest anti-restriction ...
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Added: November 14, 2017
Verfaillie A., Svetlichnyy D., Imrichova H. et al., Genome Research 2016
Transcription factors regulate their target genes by binding to regulatory regions in the genome. Although the binding preferences of TP53 are known, it remains unclear what distinguishes functional enhancers from nonfunctional binding. In addition, the genome is scattered with recognition sequences that remain unoccupied. Using two complementary techniques of multiplex enhancer-reporter assays, we discovered that ...
Added: October 22, 2018
Красноярск : ИВМ СО РАН, 2013
Труды Пятой Международной конференции «Системный анализ и информационные технологии» САИТ-2013 (19–25 сентября 2013 г., г.Красноярск, Россия): ...
Added: November 18, 2013
Shchur V., Ziganurova L., Durbin R., / Cold Spring Harbor Laboratory. Series New Results "BioRxiv". 2018.
Estimation of the relationship between DNA sequences is one of the most important problems in genomics. Understanding these relationships is central to de- mographic inference, correction of population structure in GWAS, identifying signals of selection etc. The data structure containing the full information about sample genealogy is called the ancestral recombination graph (ARG). However, ARG ...
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