Evidence map›Paper›PMID 35792600›Full record

ArticleeLife2022

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows.

Olivia Eriksson, Upinder Singh Bhalla, Kim T Blackwell, Sharon M Crook, Daniel Keller, Andrei Kramer, Marja-Leena Linne, Ausra Saudargienė, Rebecca C Wade, Jeanette Hellgren Kotaleski

Abstract read
In one paragraph

Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.

0numbers the graph read from it
0cells of the map it votes in
18citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

18 citing papers in PubMed.

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  18. Cracking the genetic code with neural networks.Frontiers in artificial intelligence · 2023
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Olivia ErikssonScience for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.ORCID 0000-0003-0740-4318
Upinder Singh BhallaNational Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.ORCID 0000-0003-1722-5188
Kim T BlackwellDepartment of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, United States.ORCID 0000-0003-4711-2344
Sharon M CrookSchool of Mathematical and Statistical Sciences, Arizona State University, Tempe, United States.ORCID 0000-0003-1659-0749
Daniel KellerBlue Brain Project, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.ORCID 0000-0003-3280-6255
Andrei KramerScience for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.ORCID 0000-0002-3828-6978
Marja-Leena LinneFaculty of Medicine and Health Technology, Tampere University, Tampere, Finland.ORCID 0000-0003-2577-7329
Ausra SaudargienėNeuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania.ORCID 0000-0003-2768-3334
Rebecca C WadeMolecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.ORCID 0000-0001-5951-8670
Jeanette Hellgren KotaleskiScience for Life Laboratory, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.ORCID 0000-0002-0550-0739

Funding

CRCNS: Spatio-temporal Dynamics of Dopamine Activated 2nd Messenger PathwaysR01AA016022 · NIAAA · GEORGE MASON UNIVERSITY · PI BLACKWELL, KIM L, LOVINGER, DAVID · 2005 to 2017
$2.6M
Tools for Model Discovery, Validation and Selection in Neuroscience with NeuroMLR01MH106674 · NIMH · ARIZONA STATE UNIVERSITY-TEMPE CAMPUS · PI CROOK, SHARON MARIE · 2015 to 2018
$1.6M
CRCNS: Visual Modulation of Panoramic Auditory Spatial ProcessingR01DC019278 · NIDCD · ARIZONA STATE UNIVERSITY-TEMPE CAMPUS · PI ZHOU, YI · 2020 to 2023
$1.5M
CRCNS: US-French Collaboration: Dopamine modulation of calcium in STDPR01DA038890 · NIDA · GEORGE MASON UNIVERSITY · PI BLACKWELL, KIM L · 2014 to 2017
$637k
NIAAA NIH HHS R01 AA016022NIDA NIH HHS R01 DA038890NIDCD NIH HHS R01 DC019278NIMH NIH HHS R01 MH106674
6 · The paper itself

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.

Indexed as

NeurosciencesWorkflowcomputational biologyFAIRmathematical modelingmodeling workflowsneuroscienceparameter estimationsynaptic plasticitysystems biologyuncertainty quantification

Identifiers

PMID35792600
PMCPMC9259018

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.