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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Neuroinform.</journal-id>
<journal-title>Frontiers in Neuroinformatics</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Neuroinform.</abbrev-journal-title>
<issn pub-type="epub">1662-5196</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fninf.2024.1534396</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Neuroscience</subject>
<subj-group>
<subject>Editorial</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Editorial: Addressing large scale computing challenges in neuroscience: current advances and future directions</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" corresp="yes">
<name><surname>Nguyen</surname> <given-names>Tam V.</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="corresp" rid="c001"><sup>&#x0002A;</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/2239805/overview"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Wang</surname> <given-names>Min</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/828264/overview"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Maisto</surname> <given-names>Domenico</given-names></name>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/144963/overview"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
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</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Department of Computer Science, University of Dayton</institution>, <addr-line>Dayton, OH</addr-line>, <country>United States</country></aff>
<aff id="aff2"><sup>2</sup><institution>School of Information Technology and Systems, University of Canberra</institution>, <addr-line>Canberra, ACT</addr-line>, <country>Australia</country></aff>
<aff id="aff3"><sup>3</sup><institution>Institute of Cognitive Sciences and Technologies, National Research Council of Italy</institution>, <addr-line>Rome</addr-line>, <country>Italy</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited and reviewed by: Michael Denker, J&#x000FC;lich Research Centre, Germany</p></fn>
<corresp id="c001">&#x0002A;Correspondence: Tam V. Nguyen <email>tamnguyen&#x00040;udayton.edu</email></corresp>
</author-notes>
<pub-date pub-type="epub">
<day>17</day>
<month>12</month>
<year>2024</year>
</pub-date>
<pub-date pub-type="collection">
<year>2024</year>
</pub-date>
<volume>18</volume>
<elocation-id>1534396</elocation-id>
<history>
<date date-type="received">
<day>25</day>
<month>11</month>
<year>2024</year>
</date>
<date date-type="accepted">
<day>03</day>
<month>12</month>
<year>2024</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x000A9; 2024 Nguyen, Wang and Maisto.</copyright-statement>
<copyright-year>2024</copyright-year>
<copyright-holder>Nguyen, Wang and Maisto</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p></license>
</permissions>
<related-article id="RA1" related-article-type="commentary-article" xlink:href="https://www.frontiersin.org/research-topics/57446/addressing-large-scale-computing-challenges-in-neuroscience-current-advances-and-future-directions" ext-link-type="uri">Editorial on the Research Topic <article-title>Addressing large scale computing challenges in neuroscience: current advances and future directions</article-title></related-article>
<kwd-group>
<kwd>neuroscience</kwd>
<kwd>neural network</kwd>
<kwd>large-scale computing systems</kwd>
<kwd>high-performance computing (HPC)</kwd>
<kwd>neuroinformatics infrastructure</kwd>
</kwd-group>
<counts>
<fig-count count="0"/>
<table-count count="0"/>
<equation-count count="0"/>
<ref-count count="5"/>
<page-count count="3"/>
<word-count count="1346"/>
</counts>
</article-meta>
</front>
<body>
<sec sec-type="intro" id="s1">
<title>1 Introduction</title>
<p>Neuroscience research generates vast amounts of data, requiring advanced computing resources for storage, management, analysis, and simulation (Glasser et al., <xref ref-type="bibr" rid="B3">2016</xref>). Efficient utilization of high-performance computing architectures to process these massive datasets poses significant challenges, demanding the development of innovative computational methods and algorithms (Gorgolewski et al., <xref ref-type="bibr" rid="B4">2011</xref>; Ding et al., <xref ref-type="bibr" rid="B1">2018</xref>). Integrating advanced techniques is essential to address these issues, the integration of enabling researchers to overcome barriers and uncover new insights into brain function and structure (Markram et al., <xref ref-type="bibr" rid="B5">2015</xref>; Eickenberg et al., <xref ref-type="bibr" rid="B2">2017</xref>). This Research Topic highlights recent advancements and future directions in large-scale computing for neuroscience. The scope of this Research Topic included, among others</p>
<list list-type="bullet">
<list-item><p>Interdisciplinary strategies and collaborations to address issues related to data sharing, integration, and analysis.</p></list-item>
<list-item><p>Security and privacy challenges, such as ethical issues, regulation, and government policies, and the potential for harmful or accidental data breaches.</p></list-item>
<list-item><p>Reproducibility and transparency concerns in large-scale computing, including data sharing, standards, and best practices for data collection, analysis, and archival.</p></list-item>
<list-item><p>Novel strategies and algorithms to exploit large-scale computing architectures and cloud technologies in neuroscience, e.g., for simulation, analysis, and data presentation.</p></list-item>
</list>
<p>This Research Topic provides a broad overview of the current challenges and emerging solutions, offering guidance for improving the scalability, efficiency, and accessibility of computational tools in this field. Four papers have ultimately been included; each one deals with one currently challenging aspect of large-scale computing in neuroscience.</p>
</sec>
<sec id="s2">
<title>2 The Papers</title>
<p>The four papers featured in this Research Topic explore these themes from different angles, presenting diverse strategies to advance data processing, simulation, and modeling in neuroscience. Two papers were Original Research papers, and two were Methods papers.</p>
<p>In the first Method paper, <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.3389/fninf.2023.1208073">Villarreal-Haro et al.</ext-link> introduced CACTUS (Computational Axonal Configurator for Tailored and Ultradense Substrates), a computational workflow for generating white-matter substrates with predefined histological features of interest. The proposed three-step algorithmic procedure can generate synthetic axon populations with unprecedented biological fidelity. Achieving packing densities up to 95% of intracellular volume fractions and supporting voxel sizes up to 500 &#x003BC;m, CACTUS reproduces complex synthetic fibre configurations with biological plausibility that can be used as a numerical phantom to validate diffusion-weighted magnetic resonance images (DW-MRI) models. This enables more accurate modeling of diffusion-weighted magnetic resonance images. CACTUS represents a vital step toward bridging the gap between microscopic tissue properties and macroscopic imaging data.</p>
<p>Classifying neuron types from extracellular recordings is a cornerstone of neuroscience but remains constrained by traditional waveform-based methods. In the first Original Research paper, <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.3389/fninf.2024.1303993">Haynes et al.</ext-link> introduce a machine learning-based approach to demix extracellularly recorded action potentials (EAPs), uncovering underlying spatial and temporal features that reflect neuronal morphology and electrophysiology. The authors developed a hierarchical classification system which, by applying a tensor components analysis to the features extracted through multiresolution wavelet analysis, furnishes a low-dimensional representation for recorded units that best characterizes waveform patterns shared across a diverse population of cortical neuron-type families. This method provides robust, interpretable features for neuron-type identification, and it highlights the potential of machine learning to tackle long-standing challenges in neuronal classification, making it a powerful tool for large-scale neuronal studies.</p>
<p>Simulating biologically realistic brain models at scale is essential for advancing our understanding of neural dynamics. Despite their utility the current platforms often fall short in flexibility, scalability, and ease of use. In the second Original Research paper, <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.3389/fninf.2024.1330875">Miedema and Strydis</ext-link> introduce ExaFlexHH which addresses limitations above with an exascale-ready, flexible library for simulating Hodgkin-Huxley (HH) models on Field-Programmable Gate Array (FPGA) platforms. Leveraging the dataflow programming paradigm, ExaFlexHH achieves high scalability and energy efficiency for simulating large-scale brain models with HH-like neurons. Interestingly, ExaFlexHH is designed to consider user-friendliness and compliance with NeuroML, an XML brain model description prominent in computational neuroscience. The tests demonstrated near-linear performance gains across multiple FPGAs and exceptional resource efficiency in GFLOPS per watt concerning the classical High-Performance Computing approaches ExaFlexHH sets the stage for future computational neuroscience breakthroughs by enabling scalable, high-performance brain simulations.</p>
<p>Finally, in the second Method paper, <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.3389/fninf.2024.1448161">M&#x000F6;nke et al.</ext-link> introduce SyNCoPy, short for Systems Neuroscience Computing in Python, a Python package for analyzing large-scale electrophysiological data. Its trial-parallel workflows and out-of-core computation techniques make it suitable for both small-scale and high-performance computing systems. SyNCoPy&#x00027;s seamless interoperability with other software and adherence to established conventions like FieldTrip&#x02014;a widely diffused open-source Matlab toolbox for advanced analysis of electrophysiological data - enhance its accessibility for scholars. Consequently, this package represents an effective merge of the importance of user-friendly with powerful tools for large-scale data analysis, following a design paradigm that could reveal crucial in accelerating progress in systems neuroscience.</p>
</sec>
<sec sec-type="conclusions" id="s3">
<title>3 Conclusion</title>
<p>The papers featured in this Research Topic demonstrate how advanced computational methods and algorithms could overcome some critical challenges in large-scale neuroscience research. At broader level, this Research Topics could serve as a means for addressing the demands of large-scale neuroscience and anticipate future directions in this research field will continue to evolve, focusing on developing interoperable, scalable, and energy-efficient computational tools.</p>
</sec>
</body>
<back>
<sec sec-type="author-contributions" id="s4">
<title>Author contributions</title>
<p>TN: Writing &#x02013; original draft, Writing &#x02013; review &#x00026; editing. MW: Writing &#x02013; review &#x00026; editing. DM: Writing &#x02013; review &#x00026; editing.</p>
</sec>
<sec sec-type="COI-statement" id="conf1">
<title>Conflict of interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec sec-type="disclaimer" id="s5">
<title>Publisher&#x00027;s note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
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