{"id":365,"date":"2019-04-19T10:53:15","date_gmt":"2019-04-19T07:53:15","guid":{"rendered":"http:\/\/conf.bionet.nsc.ru\/sbb2019\/?page_id=365"},"modified":"2023-09-01T12:43:01","modified_gmt":"2023-09-01T05:43:01","slug":"practice","status":"publish","type":"page","link":"https:\/\/conf.icgbio.ru\/sbb2019\/practice\/","title":{"rendered":"\u041f\u0440\u0430\u043a\u0442\u0438\u043a\u0430"},"content":{"rendered":"<p><span style=\"color: #800000;\"><strong>\u0410\u043a\u0431\u0435\u0440\u0434\u0438\u043d \u0418\u043b\u044c\u044f \u0420\u0438\u043d\u0430\u0442\u043e\u0432\u0438\u0447<\/strong>,<\/span><strong><br \/>\n<\/strong><span style=\"color: #000000;\">\u041e\u041e\u041e &#171;\u0411\u0418\u041e\u0421\u041e\u0424\u0422.\u0420\u0423&#187;, \u041d\u043e\u0432\u043e\u0441\u0438\u0431\u0438\u0440\u0441\u043a, \u0420\u043e\u0441\u0441\u0438\u044f<\/span><strong><br \/>\n<\/strong><a href=\"http:\/\/biomodelsgroup.ru\/people\/akberdin\/\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/biomodelsgroup.ru\/people\/akberdin\/<\/a>, <span style=\"color: #000000;\">email:<\/span> <a href=\"mailto:akberdinir@gmail.com\">akberdinir@gmail.com<\/a><br \/>\n<strong><span style=\"color: #000000;\">\u041f\u0440\u0430\u043a\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0435 \u0437\u0430\u043d\u044f\u0442\u0438\u0435:<\/span><br \/>\n<\/strong><span style=\"color: #0000ff;\">HANDS-ON TRAINING: Constraint-based modeling of metabolic systems<\/span><\/p>\n<p><span style=\"color: #000000;\"><strong>SHORT DESCRIPTION:<br \/>\n<\/strong>Cellular metabolism constitutes a complex dynamical system and gives rise to a wide variety of dynamical phenomena, including multiple steady states and temporal oscillations. The elucidation, understanding, and eventually prediction of the behavior of metabolic systems represent one of the primary challenges in the postgenomic era. Access to complete genome sequences of bacteria enables whole-genome metabolic reconstruction and flux-balance modeling. To this end, substantial effort has been dedicated in recent years to develop and investigate detailed models of cellular metabolic processes because a mathematical model can serve as a \u2018\u2018virtual laboratory\u2019\u2019 that allows the building up of a characteristic description of the system and gives insights into fundamental design principles of cellular functions, such as adaptability, robustness, and optimality.<\/span><br \/>\n<span style=\"color: #000000;\"> Trainees will study the complexity of cellular metabolism using constraint-based modeling approach. During this hands-on training, attendees will learn basic techniques for modeling of biochemical networks. The first part of the training introduces data access and storage via different databases for genome-scale modeling. The second part continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using Optflux. The hands on exercises throughout the training will ensure that trainees become familiar with the software tools (Optflux platform, Escher, Pathway tools, Kbase etc.) and with analyzing, creating, editing, importing, simulating and storing biochemical networks as well as genome-scale models (BIGG, BioModels database, ModelSeed, BioCyc etc.).<\/span><br \/>\n<span style=\"color: #000000;\"> <strong>KEY WORDS: <\/strong>systems biology, mathematical modeling, constraint-based approach, flux balance analysis, metabolic systems.<\/span><br \/>\n<span style=\"color: #000000;\"> <strong>LANGUAGE: <\/strong>English, Russian.<\/span><br \/>\n<span style=\"color: #000000;\"> <strong>Duration<\/strong><strong>: <\/strong>2\u20133 Hours.<\/span><br \/>\n<span style=\"color: #000000;\"> <strong>PREREQUISITES:<br \/>\n<\/strong>Some knowledge of mathematical modeling will be advantageous.<\/span><br \/>\n<span style=\"color: #000000;\"> The participants should bring their own laptop with Optflux platform installed<\/span> (<a href=\"https:\/\/sourceforge.net\/projects\/optflux\/files\/LatestRelease\/\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/sourceforge.net\/projects\/optflux\/files\/LatestRelease\/<\/a>).<br \/>\n<span style=\"color: #000000;\">Registration on KBase (<\/span><a href=\"https:\/\/kbase.us\/sign-up-for-a-kbase-account\/\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/kbase.us\/sign-up-for-a-kbase-account\/<\/a>)<span style=\"color: #000000;\"> and ModelSeed<\/span> (<a href=\"http:\/\/modelseed.org\/\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/modelseed.org\/<\/a>) <span style=\"color: #000000;\">web-sites is recommended but not mandatory.<\/span><br \/>\n<span style=\"color: #000000;\"> For more information please contact Dr Ilya Akberdin (akberdinir\/AT\/gmail.com).<br \/>\n<\/span><span style=\"color: #000000;\">It may also be helpful to visit the web-sources of software and tools we will use on the training:<\/span><br \/>\n<a href=\"http:\/\/www.optflux.org\/\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/www.optflux.org\/<\/a>,\u00a0 \u00a0\u00a0<a href=\"https:\/\/kbase.us\/\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/kbase.us\/<\/a>,\u00a0 \u00a0\u00a0<a href=\"http:\/\/modelseed.org\/\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/modelseed.org\/<\/a><br \/>\n<a href=\"https:\/\/escher.github.io\/#\/\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/escher.github.io\/#\/<\/a>,\u00a0 \u00a0\u00a0<a href=\"http:\/\/bigg.ucsd.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/bigg.ucsd.edu\/<\/a>,<br \/>\n<a href=\"https:\/\/www.ebi.ac.uk\/biomodels\/\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/www.ebi.ac.uk\/biomodels\/<\/a>,\u00a0 \u00a0https:\/\/memote.io\/<\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #800000;\"><strong>\u0411\u0430\u043a\u0443\u043b\u0438\u043d\u0430 \u0410\u043d\u0430\u0441\u0442\u0430\u0441\u0438\u044f \u042e\u0440\u044c\u0435\u0432\u043d\u0430<\/strong>,<\/span><br \/>\n\u041d\u043e\u0432\u043e\u0441\u0438\u0431\u0438\u0440\u0441\u043a\u0438\u0439 \u0433\u043e\u0441\u0443\u0434\u0430\u0440\u0441\u0442\u0432\u0435\u043d\u043d\u044b\u0439 \u0443\u043d\u0438\u0432\u0435\u0440\u0441\u0438\u0442\u0435\u0442, \u041d\u043e\u0432\u043e\u0441\u0438\u0431\u0438\u0440\u0441\u043a, \u0420\u043e\u0441\u0441\u0438\u044f<br \/>\n<strong>\u041f\u0440\u0430\u043a\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0435 \u0437\u0430\u043d\u044f\u0442\u0438\u0435<\/strong>:<br \/>\n<span style=\"color: #0000ff;\">\u0413\u043e\u043c\u043e\u043b\u043e\u0433\u0438\u0447\u0435\u0441\u043a\u043e\u0435 \u043c\u043e\u0434\u0435\u043b\u0438\u0440\u043e\u0432\u0430\u043d\u0438\u0435 \u0431\u0435\u043b\u043a\u043e\u0432.<\/span><\/p>\n<ol>\n<li>\u0417\u043d\u0430\u043a\u043e\u043c\u0441\u0442\u0432\u043e \u0441 \u0431\u0430\u0437\u043e\u0439 \u0431\u0435\u043b\u043a\u043e\u0432\u044b\u0445 \u0441\u0442\u0440\u0443\u043a\u0442\u0443\u0440 PDB \u0438 \u043a\u043b\u0430\u0441\u0441\u0438\u0444\u0438\u043a\u0430\u0446\u0438\u044f\u043c\u0438 \u0431\u0435\u043b\u043a\u043e\u0432\u044b\u0445 \u0441\u0442\u0440\u0443\u043a\u0442\u0443\u0440 SCOP \u0438 CATH. \u0417\u043d\u0430\u043a\u043e\u043c\u0441\u0442\u0432\u043e \u0441 \u0441\u0435\u0440\u0432\u0435\u0440\u0430\u043c\u0438, \u043f\u043e\u043c\u043e\u0433\u0430\u044e\u0449\u0438\u043c\u0438 \u043f\u043e\u0441\u0442\u0440\u043e\u0438\u0442\u044c \u043c\u043e\u0434\u0435\u043b\u0438 \u0431\u0435\u043b\u043a\u043e\u0432 (Genesilico metaserver, Swiss-Model, I-tasser). \u0417\u0430\u043f\u0443\u0441\u043a \u043f\u043e\u0441\u043b\u0435\u0434\u043e\u0432\u0430\u0442\u0435\u043b\u044c\u043d\u043e\u0441\u0442\u0435\u0439 \u0431\u0443\u0434\u0443\u0449\u0438\u0445 \u043c\u043e\u0434\u0435\u043b\u0435\u0439 \u043d\u0430 \u0440\u0430\u0437\u043b\u0438\u0447\u043d\u044b\u0445 \u0441\u0435\u0440\u0432\u0435\u0440\u0430\u0445.<\/li>\n<li>\u0420\u0430\u0431\u043e\u0442\u0430 \u0441 \u043f\u0440\u043e\u0433\u0440\u0430\u043c\u043c\u0430\u043c\u0438 \u043f\u0440\u043e\u0441\u043c\u043e\u0442\u0440\u0430 \u043f\u0440\u043e\u0441\u0442\u0440\u0430\u043d\u0441\u0442\u0432\u0435\u043d\u043d\u044b\u0445 \u0441\u0442\u0440\u0443\u043a\u0442\u0443\u0440 \u0431\u0435\u043b\u043a\u043e\u0432 \u0432 \u0444\u043e\u0440\u043c\u0430\u0442\u0435 PDB (Accelrys Visualizer, PyMOL) \u2014 \u043e\u0441\u043d\u043e\u0432\u043d\u044b\u0435 \u0432\u043e\u0437\u043c\u043e\u0436\u043d\u043e\u0441\u0442\u0438. \u0418\u0437\u0443\u0447\u0435\u043d\u0438\u0435 \u0444\u043e\u0440\u043c\u0430\u0442\u0430 PDB.<\/li>\n<li>\u0421\u0442\u0440\u0443\u043a\u0442\u0443\u0440\u043d\u043e\u0435 \u0432\u044b\u0440\u0430\u0432\u043d\u0438\u0432\u0430\u043d\u0438\u0435. \u0421\u0440\u0430\u0432\u043d\u0435\u043d\u0438\u0435 \u043c\u043e\u0434\u0435\u043b\u0435\u0439, \u043f\u043e\u043b\u0443\u0447\u0435\u043d\u043d\u044b\u0445 \u0440\u0430\u0437\u043d\u044b\u043c\u0438 \u0441\u043f\u043e\u0441\u043e\u0431\u0430\u043c\u0438, \u0438 \u0440\u0435\u0430\u043b\u044c\u043d\u044b\u0445 \u0441\u0442\u0440\u0443\u043a\u0442\u0443\u0440.<\/li>\n<\/ol>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #800000;\"><strong>\u0412\u043b\u0430\u0441\u043e\u0432 \u041f\u0451\u0442\u0440 \u041a\u043e\u043d\u0441\u0442\u0430\u043d\u0442\u0438\u043d\u043e\u0432\u0438\u0447<\/strong><\/span>,<br \/>\nInstitute of Science and Technology, \u0410\u0432\u0441\u0442\u0440\u0438\u044f<br \/>\n<strong>\u041f\u0440\u0430\u043a\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0435 \u0437\u0430\u043d\u044f\u0442\u0438\u0435<\/strong>:<br \/>\n<span style=\"color: #0000ff;\">\u0420\u0430\u0446\u0438\u043e\u043d\u0430\u043b\u044c\u043d\u044b\u0439 \u0434\u0438\u0437\u0430\u0439\u043d \u043b\u0435\u043a\u0430\u0440\u0441\u0442\u0432: \u0441\u0435\u0440\u0435\u0431\u0440\u044f\u043d\u043e\u0439 \u043f\u0443\u043b\u0438 \u043d\u0435\u0442 &#8212; \u041d\u041e \u043e\u0445\u043e\u0442\u0430 \u043d\u0430 \u0421\u043d\u0430\u0440\u043a\u0430 \u0437\u0430\u043a\u043e\u043d\u0447\u0438\u043b\u0430\u0441\u044c.<\/span><\/p>\n<p>\u0413\u043b\u0430\u0432\u043d\u0430\u044f \u0446\u0435\u043b\u044c \u043f\u0440\u043e\u0435\u043a\u0442\u0430 &#8212; \u0434\u0430\u0442\u044c \u0443\u0447\u0430\u0441\u0442\u043d\u0438\u043a\u0430\u043c \u043f\u0440\u0435\u0434\u0441\u0442\u0430\u0432\u043b\u0435\u043d\u0438\u0435 \u043e \u0441\u043e\u0432\u0440\u0435\u043c\u0435\u043d\u043d\u043e\u0439 \u043c\u043e\u043b\u0435\u043a\u0443\u043b\u044f\u0440\u043d\u043e\u0439 \u0431\u0438\u043e\u043b\u043e\u0433\u0438 \u0438 \u0433\u0435\u043d\u0435\u0442\u0438\u043a\u0435 \u0432 \u043a\u043e\u043d\u0442\u0435\u043a\u0441\u0442\u0435 \u0438\u0445 \u00ab\u043f\u0440\u043e\u0435\u043a\u0446\u0438\u0438\u00bb \u043d\u0430 \u0440\u0430\u0437\u0440\u0430\u0431\u043e\u0442\u043a\u0443 \u043b\u0435\u043a\u0430\u0440\u0441\u0442\u0432\u0435\u043d\u043d\u044b\u0445 \u043f\u0440\u0435\u043f\u0430\u0440\u0430\u0442\u043e\u0432 \u0438 \u043d\u0430 \u043f\u0435\u0440\u0441\u043e\u043d\u0430\u043b\u0438\u0437\u0438\u0440\u043e\u0432\u0430\u043d\u043d\u0443\u044e \u0431\u0438\u043e\u043c\u0435\u0434\u0438\u0446\u0438\u043d\u0443. \u0412 \u043f\u0440\u043e\u0435\u043a\u0442\u0435 \u043e\u0431\u044a\u0435\u0434\u0438\u043d\u044f\u044e\u0442\u0441\u044f \u043a\u043e\u043c\u043f\u044c\u044e\u0442\u0435\u0440\u043d\u044b\u0435 \u043c\u0435\u0442\u043e\u0434\u044b \u0433\u0435\u043d\u0435\u0442\u0438\u043a\u0438, \u0441\u0438\u0441\u0442\u0435\u043c\u043d\u043e\u0439 \u0431\u0438\u043e\u043b\u043e\u0433\u0438\u0438 \u0438 \u0440\u0430\u0446\u0438\u043e\u043d\u0430\u043b\u044c\u043d\u043e\u0433\u043e \u0434\u0438\u0437\u0430\u0439\u043d\u0430 \u043b\u0435\u043a\u0430\u0440\u0441\u0442\u0432. \u041f\u0440\u043e\u0435\u043a\u0442 \u0432\u043a\u043b\u044e\u0447\u0430\u0435\u0442 (1) \u0442\u0435\u043e\u0440\u0435\u0442\u0438\u0447\u0435\u0441\u043a\u0438\u0439 \u043a\u0443\u0440\u0441: \u043e\u0431\u0441\u0443\u0436\u0434\u0435\u043d\u0438\u0435 \u0440\u0430\u0437\u043d\u043e\u043e\u0431\u0440\u0430\u0437\u043d\u044b\u0445 \u0440\u0430\u0437\u0434\u0435\u043b\u043e\u0432 \u0438 \u0442\u0435\u0445\u043d\u043e\u043b\u043e\u0433\u0438\u0439 \u043c\u043e\u043b\u0435\u043a\u0443\u043b\u044f\u0440\u043d\u043e\u0439 \u0438 \u043a\u043b\u0435\u0442\u043e\u0447\u043d\u043e\u0439 \u0431\u0438\u043e\u043b\u043e\u0433\u0438\u0438, \u043f\u0435\u0440\u0435\u043d\u043e\u0441\u0438\u043c\u044b\u0445 \u0432 \u043c\u0435\u0434\u0438\u0446\u0438\u043d\u0443, \u043f\u0440\u0430\u043a\u0442\u0438\u043a\u0443 \u0441\u0438\u0441\u0442\u0435\u043c\u043d\u043e\u0433\u043e \u043f\u043e\u0434\u0445\u043e\u0434\u0430 \u0432 \u043f\u043e\u0438\u0441\u043a\u0435 \u0442\u0435\u0440\u0430\u043f\u0435\u0432\u0442\u0438\u0447\u0435\u0441\u043a\u0438\u0445 \u043c\u0438\u0448\u0435\u043d\u0435\u0439, \u0441\u0430\u043c\u043e\u0441\u0442\u043e\u044f\u0442\u0435\u043b\u044c\u043d\u044b\u0439 \u043f\u043e\u0438\u0441\u043a \u0438 \u0430\u043d\u0430\u043b\u0438\u0437 \u0441\u043e\u043e\u0442\u0432\u0435\u0442\u0441\u0442\u0432\u0443\u044e\u0449\u0435\u0439 \u0438\u043d\u0444\u043e\u0440\u043c\u0430\u0446\u0438\u0438 \u0438 \u043f\u0440\u2026 \u0438 (2) \u043f\u0440\u0430\u043a\u0442\u0438\u0447\u0435\u0441\u043a\u0443\u044e \u0440\u0430\u0431\u043e\u0442\u0443: \u043e\u0441\u0432\u043e\u0435\u043d\u0438\u0435 \u0441\u043e\u0432\u0440\u0435\u043c\u0435\u043d\u043d\u044b\u0445 \u043c\u0435\u0442\u043e\u0434\u043e\u0432 \u043c\u043e\u0434\u0435\u043b\u0438\u0440\u043e\u0432\u0430\u043d\u0438\u044f \u0431\u0435\u043b\u043a\u043e\u0432\u044b\u0445 \u0441\u0442\u0440\u0443\u043a\u0442\u0443\u0440 \u0438 \u0431\u0435\u043b\u043e\u043a-\u043b\u0438\u0433\u0430\u043d\u0434\u043d\u044b\u0445 \u0432\u0437\u0430\u0438\u043c\u043e\u0434\u0435\u0439\u0441\u0442\u0432\u0438\u0439. \u0412 \u043f\u0440\u043e\u0435\u043a\u0442\u0435 \u0431\u0443\u0434\u0443\u0442 \u043f\u0440\u0435\u0434\u0441\u0442\u0430\u0432\u043b\u0435\u043d\u044b \u043e\u0431\u0449\u0430\u044f \u0438\u0434\u0435\u043e\u043b\u043e\u0433\u0438\u044f \u0438 \u00ab\u0442\u0440\u0430\u0435\u043a\u0442\u043e\u0440\u0438\u044f\u00bb \u0440\u0430\u0446\u0438\u043e\u043d\u0430\u043b\u044c\u043d\u043e\u0433\u043e \u0434\u0438\u0437\u0430\u0439\u043d\u0430 \u043b\u0435\u043a\u0430\u0440\u0441\u0442\u0432, \u0440\u0430\u0437\u043e\u0431\u0440\u0430\u043d\u044b \u043a\u043e\u043d\u043a\u0440\u0435\u0442\u043d\u044b\u0435 \u043f\u0440\u0438\u043c\u0435\u0440\u044b \u0432\u044b\u0431\u043e\u0440\u0430 \u043d\u043e\u0432\u044b\u0445 \u0438\u043d\u0442\u0435\u0440\u0435\u0441\u043d\u044b\u0445 \u00ab\u043c\u0438\u0448\u0435\u043d\u0435\u0439\u00bb \u0434\u043b\u044f (\u043f\u043e\u0442\u0435\u043d\u0446\u0438\u0430\u043b\u044c\u043d\u043e\u0433\u043e) \u0442\u0435\u0440\u0430\u043f\u0435\u0432\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0433\u043e \u0432\u043e\u0437\u0434\u0435\u0439\u0441\u0442\u0432\u0438\u044f \u0438, \u043d\u0430\u043a\u043e\u043d\u0435\u0446,\u00a0\u043e\u0431\u0441\u0443\u0436\u0434\u0435\u043d\u0430 \u0432\u0430\u0436\u043d\u043e\u0441\u0442\u044c \u043e\u0446\u0435\u043d\u043a\u0438 \u0432\u043b\u0438\u044f\u043d\u0438\u044f \u0432\u0430\u0440\u0438\u0430\u0442\u0438\u0432\u043d\u043e\u0441\u0442\u0438 \u0433\u0435\u043d\u043e\u043c\u0430 \u0447\u0435\u043b\u043e\u0432\u0435\u043a\u0430 \u043d\u0430 \u0441\u0442\u0440\u0443\u043a\u0442\u0443\u0440\u044b\/\u0444\u0443\u043d\u043a\u0446\u0438\u0438 \u043a\u043e\u043d\u043a\u0440\u0435\u0442\u043d\u044b\u0445 \u0431\u0435\u043b\u043a\u043e\u0432 \u0438 \u043d\u0430 \u0445\u043e\u0434 \u0441\u043e\u043e\u0442\u0432\u0435\u0442\u0441\u0442\u0432\u0443\u044e\u0449\u0438\u0445 \u0431\u0438\u043e\u0445\u0438\u043c\u0438\u0447\u0435\u0441\u043a\u0438\u0445 \u043a\u0430\u0441\u043a\u0430\u0434\u043e\u0432. \u041e\u0442\u0434\u0435\u043b\u044c\u043d\u043e\u0435 \u0432\u043d\u0438\u043c\u0430\u043d\u0438\u0435 \u0431\u0443\u0434\u0435\u0442 \u0443\u0434\u0435\u043b\u0435\u043d\u043e \u0442\u043e\u043c\u0443, \u043a\u0430\u043a \u043d\u0430 \u043c\u043e\u043b\u0435\u043a\u0443\u043b\u044f\u0440\u043d\u043e\u043c \u0443\u0440\u043e\u0432\u043d\u0435 \u0432\u043e\u043f\u043b\u043e\u0449\u0430\u0435\u0442\u0441\u044f \u0441\u0432\u044f\u0437\u044c \u0433\u0435\u043d\u0435\u0442\u0438\u043f-\u0444\u0435\u043d\u043e\u0442\u0438\u043f, \u0432 \u0442.\u0447. \u0432 \u043a\u043e\u043d\u0442\u0435\u043a\u0441\u0442\u0435 \u0440\u0430\u0437\u043b\u0438\u0447\u043d\u044b\u0445 \u043f\u0430\u0442\u043e\u0433\u0435\u043d\u0435\u0437\u043e\u0432 \u2013 \u0438 \u0442\u043e\u043c\u0443, \u043a\u0430\u043a \u0441\u043e\u0432\u0440\u0435\u043c\u0435\u043d\u043d\u044b\u0435 \u043f\u0440\u0435\u0434\u0441\u0442\u0430\u0432\u043b\u0435\u043d\u0438\u044f \u043e\u0431 \u044d\u0442\u043e\u0439 \u0441\u0432\u044f\u0437\u0438 \u0438\u0441\u043f\u043e\u043b\u044c\u0437\u0443\u044e\u0442\u0441\u044f \u0432 \u0441\u043e\u0437\u0434\u0430\u043d\u0438\u0438 \u043d\u043e\u0432\u044b\u0445 \u043b\u0435\u043a\u0430\u0440\u0441\u0442\u0432\u0435\u043d\u043d\u044b\u0445 \u043f\u0440\u0435\u043f\u0430\u0440\u0430\u0442\u043e\u0432.<\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #800000;\"><strong>\u041a\u0440\u0435\u0431\u0441\u00a0\u041e\u043b\u044c\u0433\u0430<\/strong><\/span>,<br \/>\n\u0418\u043d\u0441\u0442\u0438\u0442\u0443\u0442 \u0442\u0435\u043e\u0440\u0435\u0442\u0438\u0447\u0435\u0441\u043a\u0438\u0445 \u0438\u0441\u0441\u043b\u0435\u0434\u043e\u0432\u0430\u043d\u0438\u0439, \u0413\u0435\u0439\u0434\u0435\u043b\u044c\u0431\u0435\u0440\u0433, \u0413\u0435\u0440\u043c\u0430\u043d\u0438\u044f (HITS gGmbH, Heidelberg, Germany)<strong><br \/>\n<\/strong><strong>\u041f\u0440\u0430\u043a\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0435 \u0437\u0430\u043d\u044f\u0442\u0438\u0435:<br \/>\n<\/strong><span style=\"color: #0000ff;\">Data, operations and models in SEEK: storing, interlinking, finding, and reusing.<\/span><\/p>\n<p><em>Docu can be found here<\/em><br \/>\n<a href=\"http:\/\/docs.seek4science.org\/help\/user-guide\/index.html\" target=\"_blank\" rel=\"noopener noreferrer\"><em>http:\/\/docs.seek4science.org\/help\/user-guide\/index.html<\/em><\/a><br \/>\n<em>Register here (local SEEK instance)<\/em><br \/>\n<a href=\"http:\/\/seekdb.bionet.nsc.ru\/\" target=\"_blank\" rel=\"noopener noreferrer\"><em>http:\/\/seekdb.bionet.nsc.ru\/<\/em><\/a><br \/>\n<em>FAIRDOMHub (public instance) with real projects<\/em><br \/>\n<a href=\"https:\/\/fairdomhub.org\/\" target=\"_blank\" rel=\"noopener noreferrer\"><em>https:\/\/fairdomhub.org\/<\/em><\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong><span style=\"color: #800000;\">\u041b\u0430\u0448\u0438\u043d \u0421\u0435\u0440\u0433\u0435\u0439 \u0410\u043b\u0435\u0441\u0430\u043d\u0434\u0440\u043e\u0432\u0438\u0447, \u041c\u0443\u0441\u0442\u0430\u0444\u0438\u043d \u0417\u0430\u0445\u0430\u0440 \u0421\u0435\u0440\u0433\u0435\u0435\u0432\u0438\u0447<\/span>,<br \/>\n<\/strong>\u0418\u0426\u0438\u0413 \u0421\u041e \u0420\u0410\u041d, \u041d\u0413\u0423, \u041d\u043e\u0432\u043e\u0441\u0438\u0431\u0438\u0440\u0441\u043a, \u0420\u043e\u0441\u0441\u0438\u044f<br \/>\n<strong>\u041f\u0440\u0430\u043a\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0435 \u0437\u0430\u043d\u044f\u0442\u0438\u0435<\/strong>:<br \/>\n<span style=\"color: #0000ff;\">\u041f\u043e\u0441\u0442\u0440\u043e\u0435\u043d\u0438\u0435 \u0438 \u0430\u043d\u0430\u043b\u0438\u0437 \u0431\u0438\u043e\u043b\u043e\u0433\u0438\u0447\u0435\u0441\u043a\u0438\u0445 \u0441\u0435\u0442\u0435\u0439 \u0441 \u043f\u043e\u043c\u043e\u0449\u044c\u044e \u043f\u0440\u043e\u0433\u0440\u0430\u043c\u043c\u044b Cytoscape.<\/span><strong><br \/>\n<\/strong><\/p>\n<p>\u0412 \u0440\u0430\u043c\u043a\u0430\u0445 \u043f\u0440\u0430\u043a\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0433\u043e \u0437\u0430\u043d\u044f\u0442\u0438\u044f \u043c\u044b \u043f\u043e\u0437\u043d\u0430\u043a\u043e\u043c\u0438\u043c\u0441\u044f \u0441 \u043e\u0434\u043d\u0438\u043c \u0438\u0437 \u0441\u0430\u043c\u044b\u0445 \u043f\u043e\u043f\u0443\u043b\u044f\u0440\u043d\u044b\u0445 \u0441\u0440\u0435\u0434\u0441\u0442\u0432 \u0434\u043b\u044f \u0440\u0430\u0431\u043e\u0442\u044b \u0441 \u0433\u0435\u043d\u043d\u044b\u043c\u0438 \u0441\u0435\u0442\u044f\u043c\u0438 \u2013 Cytoscape. \u0411\u0443\u0434\u0443\u0442 \u0440\u0430\u0437\u043e\u0431\u0440\u0430\u043d\u044b \u0441\u043f\u043e\u0441\u043e\u0431\u044b \u0441\u043e\u0437\u0434\u0430\u043d\u0438\u044f \u0441\u0435\u0442\u0435\u0439 \u0432\u0440\u0443\u0447\u043d\u0443\u044e, \u0441 \u043f\u043e\u043c\u043e\u0449\u044c\u044e \u0438\u043c\u043f\u043e\u0440\u0442\u0430 \u0438\u0437 \u0442\u0430\u0431\u043b\u0438\u0446, \u0430 \u0442\u0430\u043a\u0436\u0435 \u0433\u0435\u043d\u0435\u0440\u0430\u0446\u0438\u0438 \u0441 \u043f\u043e\u043c\u043e\u0449\u044c\u044e \u043f\u043e\u0434\u043a\u043b\u044e\u0447\u0430\u0435\u043c\u044b\u0445 \u043c\u043e\u0434\u0443\u043b\u0435\u0439. \u0411\u0443\u0434\u0443\u0442 \u0440\u0430\u0441\u0441\u043c\u043e\u0442\u0440\u0435\u043d\u044b \u043f\u043e\u043f\u0443\u043b\u044f\u0440\u043d\u044b\u0435 \u043d\u0430 \u0441\u0435\u0433\u043e\u0434\u043d\u044f\u0448\u043d\u0438\u0439 \u0434\u0435\u043d\u044c \u0441\u043f\u043e\u0441\u043e\u0431\u044b \u043f\u043e\u0441\u0442\u0440\u043e\u0435\u043d\u0438\u044f \u0441\u0435\u0442\u0435\u0439 \u043d\u0430 \u043e\u0441\u043d\u043e\u0432\u0435 \u0438\u043c\u0435\u044e\u0449\u0435\u0433\u043e\u0441\u044f \u0441\u043f\u0438\u0441\u043a\u0430 \u0433\u0435\u043d\u043e\u0432. \u0411\u0443\u0434\u0443\u0442 \u0440\u0430\u0437\u043e\u0431\u0440\u0430\u043d\u044b \u0432\u043e\u0437\u043c\u043e\u0436\u043d\u043e\u0441\u0442\u0438 \u0440\u0430\u0431\u043e\u0442\u044b \u0441 \u0432\u043d\u0435\u0448\u043d\u0438\u043c \u0432\u0438\u0434\u043e\u043c \u0441\u0435\u0442\u0438, \u0430 \u0438\u043c\u0435\u043d\u043d\u043e \u2013 \u0446\u0432\u0435\u0442\u043e\u0432\u044b\u0435 \u0441\u0445\u0435\u043c\u044b, \u0441\u0445\u0435\u043c\u044b \u043a\u043e\u043c\u043f\u043e\u043d\u043e\u0432\u043a\u0438, \u0433\u0440\u0443\u043f\u043f\u0438\u0440\u043e\u0432\u043a\u0430 \u0443\u0437\u043b\u043e\u0432. \u0411\u0443\u0434\u0443\u0442 \u0440\u0430\u0437\u043e\u0431\u0440\u0430\u043d\u044b \u0432\u043e\u0437\u043c\u043e\u0436\u043d\u043e\u0441\u0442\u0438 \u0431\u0438\u043e\u043b\u043e\u0433\u0438\u0447\u0435\u0441\u043a\u043e\u0433\u043e \u0430\u043d\u0430\u043b\u0438\u0437\u0430 \u0441\u0435\u0442\u0435\u0439 \u0441 \u043f\u043e\u043c\u043e\u0449\u044c\u044e \u043f\u043e\u0434\u043a\u043b\u044e\u0447\u0430\u0435\u043c\u044b\u0445 \u043c\u043e\u0434\u0443\u043b\u0435\u0439.<\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #800000;\"><strong>\u041c\u0438\u0440\u043e\u043d\u043e\u0432\u0430 \u0412\u0438\u043a\u0442\u043e\u0440\u0438\u044f\u00a0 \u0412\u043b\u0430\u0434\u0438\u043c\u0438\u0440\u043e\u0432\u043d\u0430<\/strong><\/span>,<br \/>\n\u0418\u0426\u0438\u0413 \u0421\u041e \u0420\u0410\u041d, \u041d\u0413\u0423, \u041d\u043e\u0432\u043e\u0441\u0438\u0431\u0438\u0440\u0441\u043a, \u0420\u043e\u0441\u0441\u0438\u044f<br \/>\n<strong>\u041f\u0440\u0430\u043a\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0435 \u0437\u0430\u043d\u044f\u0442\u0438\u0435<\/strong>:<br \/>\n<span style=\"color: #0000ff;\">Functional annotation of differentially expressed genes.<\/span><\/p>\n<p>On the practice we will functionally annotate several transcriptome datasets united by the same problem (abiotic stresses). We will learn which processes are affected, which transcription factors likely are the most important regulators and how the abiotic stress recruits developmental programs to help an organism coping with the stress. Students will work with R Studio, FoldGO, DAVID, AgriGO, MetaRE and Cytoscape softwares.<\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #800000;\"><strong>\u0422\u0438\u0439\u0441 \u0415\u0432\u0433\u0435\u043d\u0438\u0439 \u0421\u0435\u0440\u0433\u0435\u0435\u0432\u0438\u0447,<\/strong><\/span><br \/>\n\u0418\u0426\u0438\u0413 \u0421\u041e \u0420\u0410\u041d, \u041d\u043e\u0432\u043e\u0441\u0438\u0431\u0438\u0440\u0441\u043a, \u0420\u043e\u0441\u0441\u0438\u044f<br \/>\n<strong>The practical training:<br \/>\n<\/strong><span style=\"color: #0000ff;\">Applying ANDSystem for reconstruction and analysis of molecular genetic networks, related to diseases and phenotypical traits.<\/span><strong><br \/>\n<\/strong> will include:<\/p>\n<ol>\n<li>Introduction to automatic text analysis techniques (text-mining);<\/li>\n<li>Analysis of over-represented gene Ontology biological processes by the PANTHER tool;<\/li>\n<li>Familiarity with the ANDSystem system, which allows for the reconstruction and analysis of molecular genetic networks associated with diseases and phenotypic traits;<\/li>\n<li>Mastering the methods of reconstruction and analysis of associative gene networks using the ANDSystem;<\/li>\n<li>Acquaintance with the methods assessing the centrality of vertices in graphs and gene network clustering.<\/li>\n<\/ol>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #800000;\"><strong>\u0429\u0435\u0440\u0431\u0430\u043a\u043e\u0432 \u0414\u043c\u0438\u0442\u0440\u0438\u0439 \u042e\u0440\u044c\u0435\u0432\u0438\u0447<\/strong><\/span>,<br \/>\n\u041b\u0418\u041d \u0421\u041e \u0420\u0410\u041d, \u0418\u0440\u043a\u0443\u0442\u0441\u043a, \u0420\u043e\u0441\u0441\u0438\u044f<br \/>\n<strong>\u041f\u0440\u0430\u043a\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0435 \u0437\u0430\u043d\u044f\u0442\u0438\u0435:<\/strong><br \/>\n<span style=\"color: #0000ff;\">\u0421\u0442\u0430\u0442\u0438\u0447\u0442\u0438\u0447\u0435\u0441\u043a\u0438\u0435 \u043c\u0435\u0442\u043e\u0434\u044b \u0441\u0440\u0430\u0432\u043d\u0435\u043d\u0438\u044f \u0433\u0438\u043f\u043e\u0442\u0435\u0437 \u043e \u0441\u0446\u0435\u043d\u0430\u0440\u0438\u044f\u0445 \u0441\u043b\u043e\u0436\u043d\u044b\u0445\u00a0 \u043c\u0438\u043a\u0440\u043e\u044d\u0432\u043e\u043b\u044e\u0446\u0438\u043e\u043d\u043d\u044b\u0445 \u043f\u0440\u043e\u0446\u0435\u0441\u0441\u043e\u0432.<\/span><\/p>\n<p>\u0412 \u043f\u0440\u0430\u043a\u0442\u0438\u0435 \u0431\u0443\u0434\u0443\u0442 \u0440\u0430\u0441\u0441\u043c\u043e\u0442\u0440\u0435\u043d\u044b \u043c\u0435\u0442\u043e\u0434\u044b \u0444\u043e\u0440\u0432\u0430\u0440\u0434\u043d\u043e\u0433\u043e \u0438 \u043f\u043e\u0441\u0442\u0435\u0440\u0438\u043e\u0440\u043d\u043e\u0433\u043e \u043c\u043e\u0434\u0435\u043b\u0438\u0440\u043e\u0432\u0430\u043d\u0438\u044f<br \/>\n\u043c\u0438\u043a\u0440\u043e\u044d\u0432\u043e\u043b\u044e\u0446\u0438\u043e\u043d\u043d\u044b\u0445 \u043f\u0440\u043e\u0446\u0435\u0441\u0441\u043e\u0432(\u0438\u0437\u043c\u0435\u043d\u0435\u043d\u0438\u044f \u0447\u0438\u0441\u043b\u0435\u043d\u043d\u043e\u0441\u0442\u0438, \u043c\u0438\u0433\u0440\u0430\u0446\u0438\u0438, \u0432\u0442\u043e\u0440\u0438\u0447\u043d\u044b\u0445<br \/>\n\u043d\u0430\u0440\u0443\u0448\u0435\u043d\u0438\u0439 \u0440\u0435\u043f\u0440\u043e\u0434\u0443\u043a\u0442\u0438\u0432\u043d\u043e\u0439 \u0438\u0437\u043e\u043b\u044f\u0446\u0438\u0438) \u0438 \u043f\u0440\u043e\u0433\u0440\u0430\u043c\u043c\u044b, \u0440\u0435\u0430\u043b\u0438\u0437\u0443\u044e\u0449\u0438\u0435 \u044d\u0442\u0438 \u043c\u0435\u0442\u043e\u0434\u044b.<\/p>","protected":false},"excerpt":{"rendered":"<p>\u0410\u043a\u0431\u0435\u0440\u0434\u0438\u043d \u0418\u043b\u044c\u044f \u0420\u0438\u043d\u0430\u0442\u043e\u0432\u0438\u0447, \u041e\u041e\u041e &#171;\u0411\u0418\u041e\u0421\u041e\u0424\u0422.\u0420\u0423&#187;, \u041d\u043e\u0432\u043e\u0441\u0438\u0431\u0438\u0440\u0441\u043a, \u0420\u043e\u0441\u0441\u0438\u044f http:\/\/biomodelsgroup.ru\/people\/akberdin\/, email: akberdinir@gmail.com \u041f\u0440\u0430\u043a\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0435 \u0437\u0430\u043d\u044f\u0442\u0438\u0435: HANDS-ON TRAINING: Constraint-based modeling of metabolic systems SHORT DESCRIPTION: Cellular metabolism constitutes a complex dynamical system and gives rise to a wide variety of dynamical phenomena, including multiple &hellip; <a href=\"https:\/\/conf.icgbio.ru\/sbb2019\/practice\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":17,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/conf.icgbio.ru\/sbb2019\/wp-json\/wp\/v2\/pages\/365"}],"collection":[{"href":"https:\/\/conf.icgbio.ru\/sbb2019\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/conf.icgbio.ru\/sbb2019\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/conf.icgbio.ru\/sbb2019\/wp-json\/wp\/v2\/users\/17"}],"replies":[{"embeddable":true,"href":"https:\/\/conf.icgbio.ru\/sbb2019\/wp-json\/wp\/v2\/comments?post=365"}],"version-history":[{"count":3,"href":"https:\/\/conf.icgbio.ru\/sbb2019\/wp-json\/wp\/v2\/pages\/365\/revisions"}],"predecessor-version":[{"id":741,"href":"https:\/\/conf.icgbio.ru\/sbb2019\/wp-json\/wp\/v2\/pages\/365\/revisions\/741"}],"wp:attachment":[{"href":"https:\/\/conf.icgbio.ru\/sbb2019\/wp-json\/wp\/v2\/media?parent=365"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}