https://m2.mtmt.hu/ eng 2026-10-23 18:03 JournalArticle 2722359 ADMIN_APPROVED true Laboratory of Cerebral Cortex Research, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary Péter Pázmány Catholic University, Budapest, Hungary Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom Cited By :19 Export Date: 14 March 2024 Correspondence Address: Káli, S.; Laboratory of Cerebral Cortex Research, Institute of Experimental Medicine, Hungarian Academy of Sciences, Szigony u. 43, Budapest H-1083, Hungary; email: kali@koki.hu Funding details: Seventh Framework Programme, FP7, 294313, 604102 0 2018-01-31T13:22:29.000+0000 false 2722359 2026-10-16T18:32:00.536+0000 2023-09-23T09:10:17.625+0000 2014-08-28T08:20:20.000+0000 true 10011500 Káli Szabolcs /api/author/10011500 Author true 10011500 2024-06-24T07:58:19.935+0000 2024-06-24T07:58:19.935+0000 2015-03-04T10:44:37.000+0000 true 10019567 Sifter Viktória /api/admin/10019567 Admin true 10019567 true false true 24 24 /api/publicationtype/24 PublicationType 1 true 24 JournalArticle true 10000059 Article true 24 24 /api/publicationtype/24 PublicationType 1 true 24 JournalArticle /api/subtype/10000059 Szakcikk SubType 101 true 10000059 true 1 /api/category/1 Category true 1 Friedrich, P A flexible, interactive software tool for fitting the parameters of neuronal models. true true /api/journal/10010774 REVIEWED true false 10010774 false 10010774 true 1662-5196 Journal FOREIGN 8 63 63 20 2014 The construction of biologically relevant neuronal models as well as model-based analysis of experimental data often requires the simultaneous fitting of multiple model parameters, so that the behavior of the model in a certain paradigm matches (as closely as possible) the corresponding output of a real neuron according to some predefined criterion. Although the task of model optimization is often computationally hard, and the quality of the results depends heavily on technical issues such as the appropriate choice (and implementation) of cost functions and optimization algorithms, no existing program provides access to the best available methods while also guiding the user through the process effectively. Our software, called Optimizer, implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios. Meanwhile, educated users can extend the capabilities of the program and customize it according to their needs with relatively little effort. Optimizer has been developed in Python, takes advantage of open-source Python modules for nonlinear optimization, and interfaces directly with the NEURON simulator to run the models. Other simulators are supported through an external interface. We have tested the program on several different types of problems of varying complexity, using different model classes. As targets, we used simulated traces from the same or a more complex model class, as well as experimental data. We successfully used Optimizer to determine passive parameters and conductance densities in compartmental models, and to fit simple (adaptive exponential integrate-and-fire) neuronal models to complex biological data. Our detailed comparisons show that Optimizer can handle a wider range of problems, and delivers equally good or better performance than any other existing neuronal model fitting tool. 2014 659345 true true true false true false GOLD 2026-10-16 true https://doi.org/10.3389/fninf.2014.00063 true 10050617 Nagy Sára /api/admin/10050617 Admin true 10050617 31 0 31 26 6 31 29 27 31 31 31 26 26 26 5 0 31 26 31 26 0 1 1 Folyóiratcikk Journal Article 24 24 Könyvrészlet Chapter in Book 25 6 Könyv Book 23 1 Egyéb konferenciaközlemény Conference paper 31 0 Egyéb konferenciakötet Conference proceedings 32 0 Oltalmi formák Protection forms 26 0 Disszertáció Thesis 28 0 Egyéb Miscellaneous 29 0 Alkotás Achievement 22 0 Kutatási adat Research data 33 0 Folyóiratcikk Journal Article 24 0 0 0 Könyvrészlet Chapter in Book 25 0 0 0 Könyv Book 23 0 0 0 Egyéb konferenciaközlemény Conference paper 31 0 0 0 Egyéb konferenciakötet Conference proceedings 32 0 0 0 Oltalmi formák Protection forms 26 0 0 0 Disszertáció Thesis 28 0 0 0 Egyéb Miscellaneous 29 0 0 0 Alkotás Achievement 22 0 0 0 Kutatási adat Research data 33 0 0 0 2015 0 1 1 1 1 2016 0 4 4 4 4 2017 0 3 3 3 3 2018 0 7 7 7 7 2019 0 1 1 1 1 2020 0 2 1 2 1 2021 0 2 1 2 1 2022 0 2 1 2 1 2023 0 2 2 2 2 2024 0 5 3 5 3 2025 0 2 2 2 2 Q1 false 10011500 false false false 2015-03-04T10:44:37.000+0000 2014-08-28T08:23:17.000+0000 Agykéreg Kutatócsoport (KOKI / CHO); Információs Technológiai és Bionikai Kar (PPKE) 3 16 2 5 0 true Language 10002 /api/language/10002 Angol English true 2 true PersonAuthorship 5443072 /api/authorship/5443072 1 0.2 true false Friedrich P true false false AuthorshipType 1 /api/authorshiptype/1 0 true 0 true false 20212522 true PersonAuthorship 5443073 /api/authorship/5443073 2 0.2 false false Vella M true false false AuthorshipType 1 /api/authorshiptype/1 0 true 0 true false 20212521 true PersonAuthorship 5443074 /api/authorship/5443074 3 0.2 false false Author 10009114 /api/author/10009114 Gulyás Attila true 10009114 true Gulyas AI true false false AuthorshipType 1 /api/authorshiptype/1 0 true 0 true false 20212520 true PersonAuthorship 5443075 /api/authorship/5443075 4 0.2 false false Author 10000275 /api/author/10000275 Freund Tamás true 10000275 true Freund TF true false false AuthorshipType 1 /api/authorshiptype/1 0 true 0 true false 20212519 true PersonAuthorship 5443076 /api/authorship/5443076 5 0.2 false true Author 10011500 /api/author/10011500 Káli Szabolcs true 10011500 true Kali S true false false AuthorshipType 1 /api/authorshiptype/1 0 true 0 true false 20212518 true PublicationIdentifier 883110 /api/publicationidentifier/883110 PlainSource 6 /api/publicationsource/6 PublicationSourceType 10001 /api/publicationsourcetype/10001 true true true DOI DOI https://doi.org/@@@ true true 6 true GOLD true IDENTICAL 10.3389/fninf.2014.00063 https://doi.org/10.3389/fninf.2014.00063 false 934194 true PublicationIdentifier 883108 /api/publicationidentifier/883108 PlainSource 1 /api/publicationsource/1 PublicationSourceType 10003 /api/publicationsourcetype/10003 false true true WoS WoS https://www.webofscience.com/wos/woscc/full-record/@@@ true true 1 true false IDENTICAL 000348113500001 https://www.webofscience.com/wos/woscc/full-record/000348113500001 false 1165816 true PublicationIdentifier 883109 /api/publicationidentifier/883109 PlainSource 3 /api/publicationsource/3 PublicationSourceType 10003 /api/publicationsourcetype/10003 false true true Scopus Scopus http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-@@@ true true 3 true false IDENTICAL 84904185582 http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-84904185582 false 1710649 true PublicationIdentifier 883111 /api/publicationidentifier/883111 PlainSource 17 /api/publicationsource/17 PublicationSourceType 10003 /api/publicationsourcetype/10003 false true true PubMed PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=@@@&dopt=Abstract true true 17 true false NO 25071540 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=25071540&dopt=Abstract false 934195 true Classification 10034 /api/classification/10034 true true SjrRating 11064068 /api/sjrrating/11064068 26 0.24 journal RatingType 10002 /api/ratingtype/10002 sjr true true ClassificationExternal 2204 /api/classificationexternal/2204 true 2204 true Q1 DIRECT true true /api/publication/2722359 <div class="JournalArticle Publication long-list"> <div class="authors"> <img title="Forrásközlemény" style="float: left" src="/frontend/resources/grid/publication-core-icon.png"> <img title="Idézőközlemény" style="float: left" src="/frontend/resources/grid/publication-citation-icon.png"> <div class="autype autype0"> <span class="author-name" >Friedrich P </span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" >Vella M </span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" mtid="10009114"><a href="/gui2/?type=authors&mode=browse&sel=10009114" target="_blank">Gulyas AI (<span class="authorship-author-name">Gulyás Attila</span> <span class="authorAux-mtmt"> Neurobiológia</span>) </a> </span> <span class="author-affil"><span title="MTA Kísérleti Orvostudományi Kutatóintézet">IEMHAS</span>/<span title="Department of Cellular and Network Neurobiology">DCNN</span>/Laboratory of Cerebral Cortex Research</span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" mtid="10000275"><a href="/gui2/?type=authors&mode=browse&sel=10000275" target="_blank">Freund TF (<span class="authorship-author-name">Freund Tamás</span> <span class="authorAux-mtmt"> Neurobiológia, idegtudomány</span>) </a> </span> <span class="author-affil"><span title="MTA Kísérleti Orvostudományi Kutatóintézet">IEMHAS</span>/<span title="Department of Cellular and Network Neurobiology">DCNN</span>/Laboratory of Cerebral Cortex Research; <span title="Pázmány Péter Catholic University">PPCU</span>/Információs Technológiai és Bionikai Kar</span> ;&nbsp;&nbsp;&nbsp; <span class="author-name" mtid="10011500"><a href="/gui2/?type=authors&mode=browse&sel=10011500" target="_blank">Kali S (<span class="authorship-author-name">Káli Szabolcs</span> <span class="authorAux-mtmt"> Elméleti neurobiológia</span>) </a> </span> <span class="author-affil"><span title="MTA Kísérleti Orvostudományi Kutatóintézet">IEMHAS</span>/<span title="Department of Cellular and Network Neurobiology">DCNN</span>/Laboratory of Cerebral Cortex Research; <span title="Pázmány Péter Catholic University">PPCU</span>/Információs Technológiai és Bionikai Kar</span> </div> </div> <div class="title"><a href="/gui2/?mode=browse&params=publication;2722359" target="_blank">A flexible, interactive software tool for fitting the parameters of neuronal models.</a></div> <div> <span class="journal-title">FRONTIERS IN NEUROINFORMATICS</span> <span class="journal-issn">( <a target="_blank" href="https://portal.issn.org/resource/ISSN/1662-5196">1662-5196</a>)</span>: <span class="journal-volume">8</span> <span class="page"> Paper 63. 20 p. </span> <span class="year">(2014)</span> </div> <div class="pub-footer"> <span class="language" xmlns="http://www.w3.org/1999/html">Language: English | </span> <span class="identifiers"> <span class="id identifier oa_GOLD" title=" Gold "> <a style="color:blue" title="10.3389/fninf.2014.00063" target="_blank" href="https://doi.org/10.3389/fninf.2014.00063"> DOI </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="000348113500001" target="_blank" href="https://www.webofscience.com/wos/woscc/full-record/000348113500001"> WoS </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="84904185582" target="_blank" href="http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-84904185582"> Scopus </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:black" title="25071540" target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=25071540&dopt=Abstract"> PubMed </a> </span> </span> <OnlyViewableByAuthor><div class="ratings"> <div class="journal-subject">Journal subject: Scopus - Biomedical Engineering&nbsp;&nbsp;&nbsp;Rank:&nbsp;Q1</div> <div class="journal-subject">Journal subject: Scopus - Computer Science Applications&nbsp;&nbsp;&nbsp;Rank:&nbsp;Q1</div> <div class="journal-subject">Journal subject: Scopus - Neuroscience (miscellaneous)&nbsp;&nbsp;&nbsp;Rank:&nbsp;Q2</div> </div></OnlyViewableByAuthor> <div class="publication-citation" style="margin-left: 0.5cm;"> <span title="" class="citingPub-count">Citing papers: 31</span> | Independent citation: 26 | Self citation: 5 | Unknown citation: 0 | Number of citations in WoS: 27 | Number of citations in Scopus:&nbsp;31 | WoS/Scopus assigned:&nbsp;31 | Number of citations with DOI:&nbsp;29 </div> <div class="publication-citation"> <a target="_blank" href="/api/publication?cond=citations.related;eq;2722359&sort=publishedYear,desc&sort=title"> Number of cited publications: 1 </a> </div> <div class="mtid"><span class="long-pub-mtid">Publication: 2722359</span> | <span class="status-data status-ADMIN_APPROVED"> Admin approved </span> <span class="oldId">Old id: 2722359</span> | Core Citing | <span class="type-subtype">Journal Article ( Article ) </span> | <span class="pub-category">Scientific</span> | <span class="publication-sourceOfData">MEDLINE</span> </div> <div class="lastModified">Last Modified: 2023.09.23. 11:10 Gusztáv Ladányi (MTMT API user, admin) </div> <pre class="comment" style="margin-top: 0; margin-bottom: 0;"><u>Comments</u>: Laboratory of Cerebral Cortex Research, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary Péter Pázmány Catholic University, Budapest, Hungary Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom Cited By :19 Exp...</pre> </div></div>