[Text] : статья / L. Calzone [et al.] // Molecular Systems Biology. - 2008. - Vol. 4. - p. 174-178DOI 10.1038/msb.2008.7
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Аннотация: We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB/RB1). Deregulations and/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway description format. In the current state the map contains 78 proteins, 176 genes, 99 protein complexes, 208 distinct chemical species and 165 chemical reactions. Overall, the map recapitulates biological facts from approximately 350 publications annotated in the diagram. The network contains more details about RB/E2F interaction network than existing large‐scale pathway databases. Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher‐level representation of RB/E2F network. The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Calzone, Laurence; Gelay, Amélie; Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Radvanyi, François; Barillot, Emmanuel
Труды сотрудников ИВМ СО РАН
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Найдено документов в текущей БД: 3
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
[Text] : статья / A. Zinovyev [et al.] // Bioinformatics. - 2008. - Vol. 24, Iss. 6. - p. 876-877DOI 10.1093/bioinformatics/btm553
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Аннотация: BiNoM (Biological Network Manager) is a new bioinformatics software that significantly facilitates the usage and the analysis of biological networks in standard systems biology formats (SBML, SBGN, BioPAX). BiNoM implements a full-featured BioPAX editor and a method of ‘interfaces’ for accessing BioPAX content. BiNoM is able to work with huge BioPAX files such as whole pathway databases. In addition, BiNoM allows the analysis of networks created with CellDesigner software and their conversion into BioPAX format. BiNoM comes as a library and as a Cytoscape plugin which adds a rich set of operations to Cytoscape such as path and cycle analysis, clustering sub-networks, decomposition of network into modules, clipboard operations and others.
Полный текст на сайте журнала
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel
Аннотация: BiNoM (Biological Network Manager) is a new bioinformatics software that significantly facilitates the usage and the analysis of biological networks in standard systems biology formats (SBML, SBGN, BioPAX). BiNoM implements a full-featured BioPAX editor and a method of ‘interfaces’ for accessing BioPAX content. BiNoM is able to work with huge BioPAX files such as whole pathway databases. In addition, BiNoM allows the analysis of networks created with CellDesigner software and their conversion into BioPAX format. BiNoM comes as a library and as a Cytoscape plugin which adds a rich set of operations to Cytoscape such as path and cycle analysis, clustering sub-networks, decomposition of network into modules, clipboard operations and others.
Полный текст на сайте журнала
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel
Extended Detailed Balance for Systems with Irreversible Reactions
[Text] : статья / A. N. Gorban, G. S. Yablonskii // Chemical Engineering Science. - 2011. - Vol. 66, Iss. 21. - p. 5388-5399DOI 10.1016/j.ces.2011.07.054
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Кл.слова (ненормированные):
Reaction network -- Detailed balance -- Microreversibility -- Pathway -- Irreversibility -- Kinetics
Аннотация: The principle of detailed balance states that in equilibrium each elementary process is equilibrated by its reverse process. For many real physico-chemical complex systems (e.g. homogeneous combustion, heterogeneous catalytic oxidation, most enzyme reactions, etc.), detailed mechanisms include both reversible and irreversible reactions. In this case, the principle of detailed balance cannot be applied directly. We represent irreversible reactions as limits of reversible steps and obtain the principle of detailed balance for complex mechanisms with some irreversible elementary processes. We prove two consequences of the detailed balance for these mechanisms: the structural condition and the algebraic condition that form together the extended form of detailed balance. The algebraic condition is the principle of detailed balance for the reversible part. The structural condition is the convex hull of the stoichiometric vectors of the irreversible reactions has empty intersection with the linear span of the stoichiometric vectors of the reversible reactions. Physically, this means that the irreversible reactions cannot be included in oriented cyclic pathways. The systems with the extended form of detailed balance are also the limits of the reversible systems with detailed balance when some of the equilibrium concentrations (or activities) tend to zero. Surprisingly, the structure of the limit reaction mechanism crucially depends on the relative speeds of this tendency to zero.
Полный текст на сайте правообладателя
Доп.точки доступа:
Yablonskii, G.S.; Горбань, Александр Николаевич
Кл.слова (ненормированные):
Reaction network -- Detailed balance -- Microreversibility -- Pathway -- Irreversibility -- Kinetics
Аннотация: The principle of detailed balance states that in equilibrium each elementary process is equilibrated by its reverse process. For many real physico-chemical complex systems (e.g. homogeneous combustion, heterogeneous catalytic oxidation, most enzyme reactions, etc.), detailed mechanisms include both reversible and irreversible reactions. In this case, the principle of detailed balance cannot be applied directly. We represent irreversible reactions as limits of reversible steps and obtain the principle of detailed balance for complex mechanisms with some irreversible elementary processes. We prove two consequences of the detailed balance for these mechanisms: the structural condition and the algebraic condition that form together the extended form of detailed balance. The algebraic condition is the principle of detailed balance for the reversible part. The structural condition is the convex hull of the stoichiometric vectors of the irreversible reactions has empty intersection with the linear span of the stoichiometric vectors of the reversible reactions. Physically, this means that the irreversible reactions cannot be included in oriented cyclic pathways. The systems with the extended form of detailed balance are also the limits of the reversible systems with detailed balance when some of the equilibrium concentrations (or activities) tend to zero. Surprisingly, the structure of the limit reaction mechanism crucially depends on the relative speeds of this tendency to zero.
Полный текст на сайте правообладателя
Доп.точки доступа:
Yablonskii, G.S.; Горбань, Александр Николаевич