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<h1 id="logo"><a href="#">Darshan Mandge</a></h1>
<p> Cells / Neuromathematics <br />
Open Brain Institute <br />
Computational Neuroscience <br />
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<li><a href="#one" class="active">About</a></li>
<li><a href="#two">Research & Education</a></li>
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<h2>Welcome</h2>
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<p>Hi ! I am Darshan, a Cells/Neuromathematics scientist at the <a href="https://openbraininstitute.org/">Open Brain Institute</a> (OBI), Laussane, Switzerland.
OBI is a open-source simulation neuroscience platform developed by the <a href="https://www.epfl.ch/research/domains/bluebrain/"> EPFL-Blue Brain Project</a> (BBP). OBI's goal is to advance the understanding of the brain by providing access to state-of-the-art data exploration, modeling, and simulation techniques. Before joining OBI, I was a postdoctoral reseracher at BBP, Geneva. I construct and simulate <i> detailed mathematical models of biological neurons and glial cells </i>to hypothesise and predict the causes of unanswered biological phenomena.</p>
<p>At present, I am the lead scientist building detailed single neuron electrical models at OBI for large-scale brain simulations. I also develop and maintain <a href="https://github.com/darshanmandge"> open source software</a> used for these <a href="https://github.com/BlueBrain/singlecell-emodel-suite"> single cell models</a> such as <a href="https://github.com/BlueBrain/BluePyEModel"> BluePyEModel</a>, <a href="https://github.com/BlueBrain/BlueCelluLab"> BlueCelluLab</a>, <a href="https://github.com/BlueBrain/eFEL"> eFEL</a> and <a href="https://github.com/BlueBrain/BluePyOpt"> BluePyOpt</a>.</p>
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<h3>Research and Education</h3>
<p>
I did my PhD in Computational Neurophysiology at <a href="https://www.iitb.ac.in/">Indian institute of Technology (IIT) Bombay</a> under <a href="http://www.bio.iitb.ac.in/people/faculty/manchanda-r"> Dr. Rohit Manchanda </a>. My doctoral and masters thesis work involved the use of computational tools like <a href="http://www.neuron.yale.edu/neuron/">NEURON</a> and <a href="http://www.scilab.org/"> Scilab</a> to model the peripheral sensory neurons – Dorsal Root Ganglion (DRG) Neurons – supplying the urinary bladder. I built biophysically detailed single cell and coupled computational models of Neurons and Satellite Glial Cells, and simplified neural network for the bladder relfex pathway.
</p>
<p>
I have a <a href="http://www.bio.iitb.ac.in">Masters</a> (IIT Bombay) and <a href="http://www.nitrr.ac.in/">Bachelors </a>(NIT Raipur) in Technology in Biomedical Engineering. I also had a brief stint as a market research analyst at <a href="http://www.cognizant.com/">Cognizant</a>.
I have guided several undergraduates, postgraduates and doctoral students in their research projects during my research career. I have also been a teaching assistant for international and institute courses on Computational Neuroscience and Biomedical Instrumentation.
</p>
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<h4> Publications</h4>
<b>Journal</b>
<ul style="list-style-type:disc">
<li>
<a href="https://doi.org/10.1101/2024.12.10.627740">A multiscale electro-metabolic model of a rat neocortical circuit reveals the impact of ageing on central cortical layers.</a> bioRxiv, 2024-12.
</li>
<li>
<a href="https://doi.org/10.21105/joss.07026">BlueCelluLab: Biologically Detailed Neural Network Experimentation API</a>
A high-level python API for the NEURON simulator to perform simulations and experiments on individual cells or groups of cells.
</li>
<li>
<a href="https://doi.org/10.1162/neco_a_01672">A Multimodal Fitting Approach to Construct Single-Neuron Models With Patch Clamp and High-Density Microelectrode Arrays</a>
A novel computational approach to use Extracellular and Intracellular electrophysiology data to construct detailed single neuron models.
(<a href="https://direct.mit.edu/neco/issue/36/7">Journal Issue Cover</a>)
</li>
<li>
<a href="https://doi.org/10.1016/j.patter.2023.100855">A universal workflow for creation, validation, and generalization of detailed neuronal models</a>
A workflow to create detailed single neuron models for large-scale brain simulations.
(<a href="https://www.sciencedirect.com/journal/patterns/vol/4/issue/11">Journal Issue Cover</a>)
</li>
<li>
<a href="https://doi.org/10.1101/2023.05.17.541168">Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part II: Physiology and Experimentation</a> (Preprint)
Rat Somatosensory Cortex Microcircuit Model.
</li>
<li>
D. Mandge and R. Manchanda, <a href="https://doi.org/10.1371/journal.pcbi.1006293">A biophysically detailed computational model of urinary bladder small DRG neuron soma</a> PLOS Computational Biology, 14(7): e1006293. 2018. (Model Links: <a href="https://modeldb.yale.edu/243448">ModelDB</a>, <a href="https://github.com/ModelDBRepository/243448">GitHub</a>).
This paper was awarded one of the Best Paper Award by Dept.of Biosciences and Bioengineering, IIT Bombay. The article was featured on the PLOS Computational Biology website <a href="images/plosCB_featured_20072018.JPG">(image)</a> and <a href="https://twitter.com/PLOSCompBiol/status/1022149478604853248">twitter</a> <a href="https://twitter.com/PLOSCompBiol/status/1022308022159388673">page</a>. A layman's description of important results of the paper can be found on the <a href="https://twitter.com/SciResMatters/status/1244831995986935808">Research Matters</a> webpage.
</li>
</ul>
<b>Books and Chapters</b>
<ul style="list-style-type:disc">
<li>
<a href="http://www.narosa.com/books_display.asp?catgcode=978-81-8487-750-2Modelling">
Sensory Neurons of the Urinary Bladder. Urinary Bladder Physiology: Computational Insights. 2024-02 (Book chapter)
</a>
</li>
</ul>
<b>Conferences</b>
<ul style="list-style-type:disc">
<li>D. Mandge, P.R. Shukla, A. Bhatnagar and R. Manchanda, (2019, July).<a href="https://doi.org/10.1109/EMBC.2019.8857153">"Computational Model for Cross-Depolarization in DRG Neurons via Satellite Glial Cells using [K]o: Role of Kir4.1 Channels and Extracellular Leakage"</a>. In <b> Engineering in Medicine and Biology Society (EMBC) </b>, 2019 41st Annual International Conference of the IEEE, Berlin, 2019, pp.2320-2023</li>
<li>D. Mandge, A. Bhatnagar and R. Manchanda,<a href="https://goo.gl/YMRJB3"> “Computational Model for Intercellular Communication between DRG Neurons via Satellite Glial Cells using ATP.” </a> 2017 8th International <b>IEEE/EMBS Conference on Neural Engineering (NER)</b>, Shanghai, 2017.</li>
<li>S. Aruljothi, D. Mandge, and R. Manchanda, <a href="https://goo.gl/pAM9rk"> “A Biophysical Model of Heat Sensitivity in Nociceptive C-Fiber Neurons.”</a> 2017 8th International <b> IEEE/EMBS Conference on Neural Engineering (NER)</b>, Shanghai, 2017.</li>
<li>D. Mandge and R. Manchanda, <a href="https://goo.gl/fiiS1Q">"Computational studies on bladder small dorsal root ganglion neurons: Modelling BK channels."</a> 2015 37th Annual International Conference of the <b>IEEE Engineering in Medicine and Biology Society (EMBC)</b>, Milan, 2015, pp. 5376-5379 </li>
</ul>
<h4> Presentation and Talks</h4>
<ul style="list-style-type:disc">
<li> <a href="https://github.com/darshanmandge/EITN_fall_school_2023"> EITN Fall School in Computational Neuroscience 2023</a> </li>
<li> <a href="https://github.com/darshanmandge/CompNeuroResources/blob/master/UsefulLinksinNeuroscience.docx"> List of some useful links in computational Neuroscience</a> </li>
<li> <a href="https://goo.gl/tpZfYL">"An Introductory Talk on Computational Neuroscience"</a> at BioTech Club, IIT Bombay (March 2016) </li>
<li> Talk on <a href="https://goo.gl/352sYl">"Network Level Models in Computational Neuroscience"</a> for students of Sophia College For Women, IIT Bombay (March 2014)</li>
<li> <a href="https://goo.gl/Zs2pcG">"Lecture on the Hodgkin-Huxley Model"</a> for a short course on Mathematical Modelling for Neurophysiology using Open Source Softwares at Govt. Engineering College, Chandrapur, Maharashtra (February 2014)</li>
<h4> Codes </h4>
<ul style="list-style-type:disc"> (<a href="https://github.com/darshanmandge">Github Profile</a>)
<li> Interactive tools to learn <a href="https://github.com/darshanmandge/python/blob/master/nernst_eqn_slider.py"> Nernst</a> and <a href="https://github.com/darshanmandge/python/blob/master/ghk_eqn_slider.py"> GHK equations </a> </li>
<li> <a href="https://modeldb.yale.edu/243448">ModelDb entry </a> and <a href="https://github.com/darshanmandge/DRGsomamodel/tree/master/pythonmodel"> NEURON-python code </a> for Mandge and Manchanda 2018 </li>
<li> <a href="https://github.com/darshanmandge/Tools/tree/master/ConcClamp">Ion Concentration Clamp in NEURON</a> </li>
<li> <a href="https://github.com/darshanmandge/Tools/tree/master/multipleSEClamps">Multiple Successive Voltage Clamps in NEURON</a> </li>
<li> <a href="https://github.com/darshanmandge/Tools/tree/master/rIClamp">Ramp Current Clamp in NEURON</a> </li>
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