{"entity": "researcher", "timestamp": "2026-08-20T21:12:02.916Z", "family": "Kramer", "given": "Andrei", "initials": "A", "orcid": "0000-0002-3828-6978", "affiliations": ["Science for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 10044, Stockholm, Sweden. andreikr@kth.se."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/8181305816dc47afbd6a2bb17b9bab63.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/8181305816dc47afbd6a2bb17b9bab63"}}, "publications": [{"entity": "publication", "iuid": "11a0dcc1f898408fbf3563cc8e393d23", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/11a0dcc1f898408fbf3563cc8e393d23.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/11a0dcc1f898408fbf3563cc8e393d23"}}, "title": "Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows.", "authors": [{"family": "Eriksson", "given": "Olivia", "initials": "O", "orcid": "0000-0003-0740-4318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50ed8ead3a804dd28e4e7d5d3b3556d8.json"}}, {"family": "Bhalla", "given": "Upinder Singh", "initials": "US", "orcid": "0000-0003-1722-5188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdffabe50ea9416c81b99c91f5b42983.json"}}, {"family": "Blackwell", "given": "Kim T", "initials": "KT", "orcid": "0000-0003-4711-2344", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c810676e03014f6389d2cc79889e77d4.json"}}, {"family": "Crook", "given": "Sharon M", "initials": "SM", "orcid": "0000-0003-1659-0749", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b169ae29de4474a271926f09e8889f.json"}}, {"family": "Keller", "given": "Daniel", "initials": "D", "orcid": "0000-0003-3280-6255", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/815355e0fa8f4a02913e758c3d296bf5.json"}}, {"family": "Kramer", "given": "Andrei", "initials": "A", "orcid": "0000-0002-3828-6978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8181305816dc47afbd6a2bb17b9bab63.json"}}, {"family": "Linne", "given": "Marja-Leena", "initials": "ML", "orcid": "0000-0003-2577-7329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bb446e2144a4f22afc2bb5c38769282.json"}}, {"family": "Saudargien\u0117", "given": "Ausra", "initials": "A", "orcid": "0000-0003-2768-3334", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd194515e38a4230a32c995136ab2395.json"}}, {"family": "Wade", "given": "Rebecca C", "initials": "RC", "orcid": "0000-0001-5951-8670", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/502d793871ee450e9b3961a027d3199d.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "journal article", "published": "2022-07-06", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "11", "issn-l": "2050-084X"}, "abstract": "Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system works or why certain phenomena are observed. Data-driven modeling, on the other hand, follows a more unbiased approach, with model construction informed by the computationally intensive use of data. At the same time, researchers employ models at different biological scales and at different levels of abstraction. Combining these models while validating them against experimental data increases understanding of the multiscale brain. However, a lack of interoperability, transparency, and reusability of both models and the workflows used to construct them creates barriers for the integration of models representing different biological scales and built using different modeling philosophies. We argue that the same imperatives that drive resources and policy for data - such as the FAIR (Findable, Accessible, Interoperable, Reusable) principles - also support the integration of different modeling approaches. The FAIR principles require that data be shared in formats that are Findable, Accessible, Interoperable, and Reusable. Applying these principles to models and modeling workflows, as well as the data used to constrain and validate them, would allow researchers to find, reuse, question, validate, and extend published models, regardless of whether they are implemented phenomenologically or mechanistically, as a few equations or as a multiscale, hierarchical system. To illustrate these ideas, we use a classical synaptic plasticity model, the Bienenstock-Cooper-Munro rule, as an example due to its long history, different levels of abstraction, and implementation at many scales.", "doi": "10.7554/eLife.69013", "pmid": "35792600", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9259018"}, {"db": "pii", "key": "69013"}], "notes": [], "created": "2026-08-20T13:53:50.356Z", "modified": "2026-08-20T13:53:51.537Z"}, {"entity": "publication", "iuid": "9d48d65709524fd7a4a4de2acd909918", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9d48d65709524fd7a4a4de2acd909918.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9d48d65709524fd7a4a4de2acd909918"}}, "title": "A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience.", "authors": [{"family": "Santos", "given": "Jo\u00e3o P G", "initials": "JPG", "orcid": "0000-0002-0395-039X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57b4d19321b146e4be78794b7ea69ad6.json"}}, {"family": "Pajo", "given": "Kadri", "initials": "K", "orcid": "0000-0003-2110-7889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7288dc0795e49129c8d5b79b0ff1f90.json"}}, {"family": "Trpevski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9068-6744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc.json"}}, {"family": "Stepaniuk", "given": "Andrey", "initials": "A", "orcid": "0000-0002-2543-4820", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e95615d8a854b60a3f70821cfeddb8c.json"}}, {"family": "Eriksson", "given": "Olivia", "initials": "O", "orcid": "0000-0003-0740-4318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50ed8ead3a804dd28e4e7d5d3b3556d8.json"}}, {"family": "Nair", "given": "Anu G", "initials": "AG", "orcid": "0000-0002-1952-9583", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a923f8455b54b32b90949faa67ea90c.json"}}, {"family": "Keller", "given": "Daniel", "initials": "D", "orcid": "0000-0003-3280-6255", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/815355e0fa8f4a02913e758c3d296bf5.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Kramer", "given": "Andrei", "initials": "A", "orcid": "0000-0002-3828-6978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8181305816dc47afbd6a2bb17b9bab63.json"}}], "type": "journal article", "published": "2022-01-00", "journal": {"title": "Neuroinformatics", "issn": "1559-0089", "volume": "20", "issue": "1", "pages": "241-259", "issn-l": null}, "abstract": "Neuroscience incorporates knowledge from a range of scales, from single molecules to brain wide neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two adjacent scales and researchers use a variety of different software tools in the model building and analysis process. Here we focus on the scale of biochemical pathways, which is one of the main objects of study in systems biology. While systems biology is among the more standardized fields, conversion between different model formats and interoperability between various tools is still somewhat problematic. To offer our take on tackling these shortcomings and by keeping in mind the FAIR (findability, accessibility, interoperability, reusability) data principles, we have developed a workflow for building and analyzing biochemical pathway models, using pre-existing tools that could be utilized for the storage and refinement of models in all phases of development. We have chosen the SBtab format which allows the storage of biochemical models and associated data in a single file and provides a human readable set of syntax rules. Next, we implemented custom-made MATLAB\u00ae scripts to perform parameter estimation and global sensitivity analysis used in model refinement. Additionally, we have developed a web-based application for biochemical models that allows simulations with either a network free solver or stochastic solvers and incorporating geometry. Finally, we illustrate convertibility and use of a biochemical model in a biophysically detailed single neuron model by running multiscale simulations in NEURON. Using this workflow, we can simulate the same model in three different simulators, with a smooth conversion between the different model formats, enhancing the characterization of different aspects of the model.", "doi": "10.1007/s12021-021-09546-3", "pmid": "34709562", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9537196"}, {"db": "pii", "key": "10.1007/s12021-021-09546-3"}], "notes": [], "created": "2026-08-20T06:40:27.397Z", "modified": "2026-08-20T06:40:27.743Z"}, {"entity": "publication", "iuid": "27b6126f8f3c4511acab6ef1075f069f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/27b6126f8f3c4511acab6ef1075f069f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/27b6126f8f3c4511acab6ef1075f069f"}}, "title": "A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience", "authors": [{"family": "Santos", "given": "Jo\u00e3o P G", "initials": "JPG", "orcid": "0000-0002-0395-039X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57b4d19321b146e4be78794b7ea69ad6.json"}}, {"family": "Pajo", "given": "Kadri", "initials": "K", "orcid": "0000-0003-2110-7889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7288dc0795e49129c8d5b79b0ff1f90.json"}}, {"family": "Trpevski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9068-6744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc.json"}}, {"family": "Stepaniuk", "given": "Andrey", "initials": "A", "orcid": "0000-0002-2543-4820", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e95615d8a854b60a3f70821cfeddb8c.json"}}, {"family": "Eriksson", "given": "Olivia", "initials": "O"}, {"family": "Nair", "given": "Anu G", "initials": "AG", "orcid": "0000-0002-1952-9583", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a923f8455b54b32b90949faa67ea90c.json"}}, {"family": "Keller", "given": "Daniel", "initials": "D", "orcid": "0000-0003-3280-6255", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/815355e0fa8f4a02913e758c3d296bf5.json"}}, {"family": "Kotaleski", "given": "Jeanette Hellgren", "initials": "JH", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Kramer", "given": "Andrei", "initials": "A", "orcid": "0000-0002-3828-6978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8181305816dc47afbd6a2bb17b9bab63.json"}}], "type": "posted-content", "published": "2020-11-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.11.17.385203", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:59:52.437Z", "modified": "2026-08-20T10:00:11.436Z"}]}