Computational NeuroscienceActive
Barn Owl Auditory Neural Pipeline
Automated spike sorting and population coding analysis for barn owl inferior colliculus recordings.
PythonNumPySciPy+4
2025Lead Developer
Research Portfolio
Rupak
Ghosh
Cell and molecular biology researcher working across computational neuroscience, bioinformatics, biophysics, climate technology, and scientific software.
Seattle UniversityB.S. Cell & Molecular BiologyHonors Program
Currently
Neural data analysis at UT Austin · ERW modeling at Equilibrium Earth · Membrane-protein MD at Seattle University
Research Identity
Interdisciplinary
by design
The common thread: quantitative methods applied to biological questions across scale — from molecular interactions to neural populations to ecosystem processes. Select a domain to explore the connections.
Select a domain
to explore connections
Experience
Research &
professional record
A chronological record of research appointments, technical roles, laboratory work, and campus leadership. Select a category to filter.
Projects
Selected
project archive
Research projects, scientific software, and data analysis work. Select any project to view context, methods, results, and limitations.
Computational NeuroscienceActive
Neural Pathway Simulation Platform
Interactive browser-based platform for visualizing and simulating auditory and visual neural pathway models.
Next.jsTypeScriptPython+4
2024Lead Developer
Scientific Machine LearningCompleted
Multi-Hit Cancer Progression Simulation
Stochastic simulation of somatic mutation accumulation and clonal expansion dynamics under the multi-hit hypothesis.
PythonNumPySciPy+3
2024Developer
Geospatial AnalysisCompleted
Urban Wildlife Corridor Analysis
Habitat connectivity modeling and camera-trap image analysis for urban wildlife in the Seattle metropolitan area.
PythonQGISGeoPandas+4
2024Data Analyst
Molecular BiologyCompleted
DNA Computational Logic Circuits
Design and experimental validation of Boolean logic gates implemented using DNA strand displacement reactions.
NUPACKPythongel electrophoresis+3
2024Research Contributor
Climate TechnologyActive
Enhanced Rock Weathering CDR Modeling
Geochemical and remote sensing analysis to estimate carbon dioxide removal potential of enhanced rock weathering across Pacific Northwest farmland.
PythonRQGIS+4
2024–2025Research & Data Analyst
Full-Stack EngineeringCompleted
College Transfer Application Platform
Full-stack web application supporting college transfer students through document tracking, deadline management, and institutional research.
Next.jsTypeScriptFastAPI+4
2024Lead Developer
BiophysicsActive
Membrane Protein Molecular Dynamics
Atomistic simulation and experimental validation of lipid bilayer interactions with membrane-associated peptides.
Materials StudioGROMACSPython+4
2023–2025Research Assistant
Current Work
Active &
in progress
What I am actively working on right now. Each entry reflects current research questions, open problems, and next steps rather than polished outcomes.
PrototypingUpdated Jun 2025
Population Coding Analysis — Barn Owl IC
Do inferior colliculus neuron populations encode ITD through rate coding, temporal coding, or a mixed strategy across frequency channels?
Current MilestoneImplementing cross-correlation analysis across 40 sorted unit pairs from 3 recording sessions.
Open Problems
- Drift correction for extended recordings not yet implemented
- Unclear whether sorted units represent single units or multi-unit activity in lower SNR electrodes
PythonMountainSort4SciPy
RepoNext → Compute signal and noise correlations across frequency-matched and -unmatched unit pairs.
ValidatingUpdated May 2025
ERW Field Validation & MRV Data Products
Do geochemical weathering rate models calibrated on laboratory kinetics accurately predict field-measured soil alkalinity changes after basalt application?
Current MilestoneComparing modeled vs. measured alkalinity across 6 field sites with 12-month basalt application history.
Open Problems
- Soil pH and moisture data collection has gaps for two sites
- Uncertainty propagation in multi-step geochemical model not yet fully characterized
PythonRgeochemical modeling
Next → Complete field data integration and produce site-level CDR estimate with confidence intervals.
ExploringUpdated Apr 2025
Enhanced Sampling MD for Membrane Peptides
Can replica exchange molecular dynamics (REMD) resolve slow membrane insertion conformational transitions missed by conventional 500 ns simulations?
Current MilestoneLiterature review of REMD protocols for lipid bilayer systems; evaluating GPU cluster access for production runs.
Open Problems
- Computational resource access for REMD scale is not confirmed
- Optimal replica temperature ladder for POPC systems not established
GROMACSREMDMaterials Studio
Next → Submit GPU cluster allocation request; run test REMD on peptide in water to validate protocol.
DeployedUpdated Jun 2025
Research Portfolio Website
How do you build a research portfolio that communicates scientific depth without resorting to résumé formatting?
Current MilestoneInitial deployment with all major sections complete.
Open Problems
- Case study pages need richer media and citations
- Current work section needs automated "last updated" from GitHub activity
Next.jsTypeScriptTailwind CSS
RepoNext → Add MDX-based case study pages with full citations and methodology diagrams.
Methods & Tools
A structured
methods index
Organized by domain rather than proficiency. Each method links to the projects and positions where it was applied.
Programming & Computation
TypeScript
Bash / Shell scripting
Git & GitHub
Jupyter Notebooks
Quarto
Education
Academic
formation
Seattle University
Seattle, WA · 2021 — 2025
B.S. Cell and Molecular Biology
Minor in Data Science & Neuroscience
Distinctions
- Honors Program
- Dean's List
- Undergraduate Research Scholar
Research Themes
Computational neuroscienceMembrane biophysicsMolecular biologyScientific softwareData science
Selected Coursework
Biochemistry · Molecular Biology · Biophysics · Cell Biology · Biostatistics · Scientific Computing · Organic Chemistry · Genetics · Ecology · Data Science
Navkis Group of Institutions
India · Pre-university
Pre-University — Science Stream
Biology, Chemistry, Physics, Mathematics
Foundation
Rigorous pre-university science training in biology, chemistry, and mathematics, providing the disciplinary foundation for undergraduate research in life sciences.
Leadership & Service
Mentorship
& institutional work
Peer mentorship, advisory participation, and library instruction reflect a consistent commitment to supporting other students and contributing to departmental and campus community.
Peer Academic Advocate
Seattle University Student Success Center
2022 — 2024
Provided peer academic coaching to undergraduate students on study strategies, scientific writing, and course planning. Developed and led a workshop on reading primary scientific literature for first-year biology students. Mentored 25+ students per semester, with a focus on STEM retention.
Research & Instruction Library Assistant
Lemieux Library, Seattle University
2022 — Present
Supports library research instruction and information literacy workshops. Assists with systematic review methodology, citation database navigation, and literature search strategy. Led 14+ drop-in research workshops annually and supported 200+ students.
Student Advisory Board Member
Seattle University Biology Department
2023 — 2024
Participated in departmental curriculum review and student feedback processes. Represented undergraduate research student perspectives on course design, laboratory access, and mentorship programming.
Research Workshop Facilitator
Seattle University
2023 — Present
Developed and delivered standalone workshops on scientific literature reading, citation management, and research methodology for undergraduate students across disciplines. Materials available through the university library.
Writing & Research Outputs
Posters, reports
& documentation
Research outputs including posters, technical reports, research summaries, and instructional materials. Filterable by output type and year.
Poster2024
Stochastic Simulation of Multi-Hit Cancer Progression: Parameter Sensitivity Analysis
Seattle University Undergraduate Research Symposium
Presented stochastic simulation results for multi-hit carcinogenesis models. Highlighted parameter regimes where Armitage-Doll power law breaks down and discussed implications for cancer epidemiology.
Research Summary2024
Urban Wildlife Corridor Connectivity in the Seattle Metropolitan Area: A Geospatial Analysis
Seattle Urban Wildlife Research Initiative — Internal Report
Technical summary of habitat connectivity modeling methods and results. Includes least-cost path maps, species-specific connectivity scores, and policy recommendations for greenway prioritization.
Research Summary2024
Design and Experimental Validation of 3-Input DNA Boolean Logic Gates
IISc Molecular Biophysics Unit — Internship Report
Technical report documenting NUPACK-based design workflow, experimental validation protocol, and performance characterization of DNA strand displacement logic gates.
Technical Report2025
Enhanced Rock Weathering CDR Potential Assessment: Methods and Data Sources
Equilibrium Earth — Internal Methodology Document
Internal documentation of data sources (SSURGO, POLARIS, PRISM), geochemical weathering rate model implementation, and uncertainty quantification approach for CDR potential estimation.
Documentation2025
Barn Owl IC Recording Pipeline: Analysis Notebook
UT Austin — Laboratory Documentation
Quarto-rendered reproducible analysis notebook documenting the full preprocessing, spike sorting, and cross-correlation pipeline for barn owl inferior colliculus recordings.
Documentation2024
College Transfer Platform: Technical Architecture and User Research Summary
Project Documentation
Technical documentation covering system architecture, database schema, API design, and user research findings from pilot deployment.
Presentation2024
Building Accessible Neural Simulation Tools for Undergraduate Education
Seattle University STEM Faculty Seminar
Presentation on the design rationale, technical architecture, and pedagogical outcomes of the browser-based neural pathway simulation platform.
Lab Manual2023
Reading Primary Scientific Literature: A Workshop for First-Year Biology Students
Seattle University — Peer Academic Advocate Program
A guided workshop curriculum for undergraduate students learning to read, annotate, and critically evaluate primary research articles in the life sciences.
Contact
Get in
touch
I am available for research collaborations, graduate program discussions, and conversations about scientific software. Direct email is the most reliable way to reach me.
Areas of potential collaboration
- Computational neuroscience — electrophysiology analysis, spike sorting, neural modeling
- Bioinformatics pipelines — reproducible analysis workflows, data processing
- Scientific software — research tools, simulation interfaces, data platforms
- Climate and geospatial analysis — ERW, habitat modeling, remote sensing
- Biophysics — molecular dynamics, protein characterization
Current availability
Available for research conversations, graduate program discussions, and technical collaborations. Response time: 48–72 hours.