João Pedro Gomes dos Santos

Curriculum vitae

João Pedro Gomes dos Santos

AI / Systems Engineer | Computational Neuroscience PhD

jpgs.12390@gmail.com +351 963264450 Copenhagen, Amsterdam or Remote EU Citizen joaosantos1992 jpgsantos Portuguese native, English C2 Current: Vectonomous Labs · Founder of Octidy

Summary

Scientific computing, modeling, and production-minded implementation.

I solve complex problems with algorithms and scientific software. I am strongest where mathematical rigor has to become software a team can understand, validate, and use.

I combine 8+ years of ODE-based modeling, parameter estimation, sensitivity analysis, and scientific programming with practical software engineering. I am an AI / Systems Engineer at Vectonomous Labs and founder of Octidy, a Firebase-first Android app for fair household chore coordination.

Experience

Research and software work

AI / Systems Engineer

Vectonomous Labs

Apr 2026 - Present

Working on applied AI systems across data, backend, machine learning, and agentic engineering workflows.

  • Contributing to AI/ML systems, backend infrastructure, data pipelines, and intelligence services.
  • Applying strong analytical and systems-thinking skills from computational neuroscience to practical engineering problems.
  • Operating in a high-autonomy environment where architecture, implementation quality, and end-to-end ownership matter.

Founder

Octidy

2025 - Present

Founded and built Octidy, a Firebase-first Android app for coordinating household chores through bidding, assignment, and progress tracking.

  • Built invite-code households, task creation, bidding deadlines, automatic assignment, tie handling, recurring chores, calendar views, and progress statistics.
  • Implemented Kotlin, Jetpack Compose, Navigation Compose, Hilt, Coroutines/Flow, Firebase Auth, Firestore, offline persistence, and WorkManager.
  • Owned product definition, architecture, UI/UX, debugging, documentation, production packaging, and Play Console testing.

PhD Researcher

University of Porto / Karolinska Institutet / KTH / SciLifeLab

Jan 2016 - Mar 2025

Thesis: A workflow for developing biochemical pathway models using ordinary differential equations.

  • Built Subcellular Workflow, a modular FAIR-compliant MATLAB framework for ODE-based pathway modeling with simulation, analysis, and parameterization capabilities.
  • Implemented parameter estimation, local/global sensitivity analysis, and profile likelihood analysis.
  • Validated on LIRMO, LIREM, TM-M, and G-PIPK models spanning ligand-receptor interactions, effector responses, CaMKII autophosphorylation dynamics, and basal ganglia signaling.
  • Published in Neuroinformatics.

Research Scholar

UCIBIO @ REQUIMTE, University of Porto

Apr 2015 - Dec 2015

Conducted research on porphyrin nanomaterials via ionic self-assembly.

  • Performed synthesis, purification, and characterization of materials.
  • Analyzed IR spectrograms for species concentrations.
  • Supervised two undergraduate students.
  • Published in Tetrahedron.

Selected software and research projects

Android product engineering

Octidy Android App

A Firebase-first Android app that uses bidding, assignment, and progress tracking to make household chores more transparent and fair.

Kotlin Jetpack Compose Navigation Compose Hilt
Case study

Scientific software

Subcellular Workflow

A modular, FAIR-compliant MATLAB framework for ODE biochemical pathway modeling, analysis, and parameterization.

MATLAB SimBiology Optimization Toolbox Python
Case study

Materials chemistry research

Porphyrin Materials Research

Master's-level wet-lab and analytical work on ionic self-assembly of a porphyrin octacation with TPPS-based anions.

Organic synthesis Ionic self-assembly Porphyrin chemistry UV-vis/IR spectroscopy
Case study

Skills

Technical toolkit

Programming

Python NumPy SciPy Pandas Matplotlib Kotlin MATLAB

Data Science

Statistical analysis Time-series analysis Visualization Parameter estimation Sensitivity analysis

Scientific Computing

ODE modeling SBML Algorithm development Profile likelihood analysis Reproducibility (FAIR)

Android (Kotlin)

Jetpack Compose Navigation Compose ViewModel + Hilt Firebase Auth Firestore Realtime listeners Offline persistence WorkManager Coroutines/Flow Notifications Play Console testing

Tools & Platforms

Git/GitHub GitHub Actions VS Code Codex Android Studio IntelliJ Firebase SimBiology Jupyter Notebooks Conda/Anaconda Sphinx LaTeX Overleaf Markdown

Productivity & Collaboration

Microsoft Office Excel PowerPoint Word Jira Zoom EndNote Draw.io Figma

Education

Academic background

PhD, Computational Neuroscience

University of Porto (FCUP/ICBAS/FMUP/GABBA)

Jan 2016 - Mar 2025

Completed doctoral coursework with a strong quantitative and computational focus through the GABBA doctoral program, including biostatistics, systems and synthetic bioinformatics, neurosciences, cellular and developmental biology, molecular microbiology and parasitology, and new therapies and technologies.

Thesis: A workflow for developing biochemical pathway models using ordinary differential equations.

  • Designed an integrated ODE modeling workflow for model initialization, simulation, parameter estimation, sensitivity analysis, and profile likelihood analysis.
  • Validated the framework across models of increasing complexity, from simple ligand-receptor systems to G-PIPK, a striatal signaling model integrating glutamatergic and cholinergic inputs.
  • Coordinated collaborative development across three institutions using Git/GitHub and delivered end-user documentation.
  • Published in Neuroinformatics and funded by Fundação para a Ciência e Tecnologia (FCT).

MSc, Biochemistry

University of Porto (FCUP, ICBAS)

2013 - 2015

Grade: 16/20. Specialized in computational and analytical approaches to biochemistry, with coursework in computational biochemistry, bioinformatics, instrumental analysis, and bioanalytical chemistry.

Thesis: Exploring the Boundaries of Porphyrin Materials Synthesis by Ionic Self-Assembly.

  • Performed synthesis, purification, and spectroscopic characterization of porphyrin nanostructures.
  • Quantified spectroscopic data to determine species concentrations.
  • Supervised two undergraduate students during extracurricular research internships.
  • Research contributed to a publication in Tetrahedron.

BSc, Biochemistry

University of Porto (FCUP, ICBAS)

2010 - 2013

Grade: 16/20. Completed a three-year program combining biological sciences with quantitative and analytical methods, including coursework in mathematics, statistical methods, and mathematical models.

Completed a research internship at the Institute for Molecular and Cell Biology (i3S) on protein depletion and cell cycle regulation in Drosophila melanogaster wing disc development.

Publications

Peer-reviewed work

2022

A modular workflow for model building, analysis, and parameter estimation in systems biology and neuroscience

Santos, JPG, Pajo, K., Trpevski, D., Stepaniuk, A., Eriksson, O., Nair, AG., Keller, D., Hellgren Kotaleski, J., & Kramer, A.

Neuroinformatics, 20(1), 241–259.

DOI: 10.1007/s12021-021-09546-3
2016

Ionic self-assembly reactions of a porphyrin octacation

Frigerio, C., Santos, JPG, Quaresma, P., Rebelo, SLH., Gomes, A., Eaton, P., Pereira, E., Carvalho, PA., Shelnutt, JA., Jiang, L., Medforth, CJ.

Tetrahedron, 72(44), 6988–6995.

DOI: 10.1016/j.tet.2016.09.030

Curriculum vitae

João Pedro Gomes dos Santos

AI / Systems Engineer / Computational Neuroscience PhD

João Pedro Gomes dos Santos
Emailjpgs.12390@gmail.com Phone+351 963264450 LocationCopenhagen, Amsterdam or Remote CitizenshipEU Citizen LinkedInjoaosantos1992 GitHubjpgsantos LanguagesPortuguese native, English C2 CurrentVectonomous Labs · Founder of Octidy

Summary

Scientific computing, modeling, and production-minded implementation.

I solve complex problems with algorithms and scientific software. I am strongest where mathematical rigor has to become software a team can understand, validate, and use.

I combine 8+ years of ODE-based modeling, parameter estimation, sensitivity analysis, and scientific programming with practical software engineering. I am an AI / Systems Engineer at Vectonomous Labs and founder of Octidy, a Firebase-first Android app for fair household chore coordination.

Experience

Research and software work

Apr 2026 -> Present

AI / Systems Engineer

Vectonomous Labs

Working on applied AI systems across data, backend, machine learning, and agentic engineering workflows.

  • Contributing to AI/ML systems, backend infrastructure, data pipelines, and intelligence services.
  • Applying strong analytical and systems-thinking skills from computational neuroscience to practical engineering problems.
  • Operating in a high-autonomy environment where architecture, implementation quality, and end-to-end ownership matter.

2025 -> Present

Founder

Octidy

Founded and built Octidy, a Firebase-first Android app for coordinating household chores through bidding, assignment, and progress tracking.

  • Built invite-code households, task creation, bidding deadlines, automatic assignment, tie handling, recurring chores, calendar views, and progress statistics.
  • Implemented Kotlin, Jetpack Compose, Navigation Compose, Hilt, Coroutines/Flow, Firebase Auth, Firestore, offline persistence, and WorkManager.
  • Owned product definition, architecture, UI/UX, debugging, documentation, production packaging, and Play Console testing.

Jan 2016 -> Mar 2025

PhD Researcher

University of Porto / Karolinska Institutet / KTH / SciLifeLab

Thesis: A workflow for developing biochemical pathway models using ordinary differential equations.

  • Built Subcellular Workflow, a modular FAIR-compliant MATLAB framework for ODE-based pathway modeling with simulation, analysis, and parameterization capabilities.
  • Implemented parameter estimation, local/global sensitivity analysis, and profile likelihood analysis.
  • Validated on LIRMO, LIREM, TM-M, and G-PIPK models spanning ligand-receptor interactions, effector responses, CaMKII autophosphorylation dynamics, and basal ganglia signaling.
  • Published in Neuroinformatics.

Apr 2015 -> Dec 2015

Research Scholar

UCIBIO @ REQUIMTE, University of Porto

Conducted research on porphyrin nanomaterials via ionic self-assembly.

  • Performed synthesis, purification, and characterization of materials.
  • Analyzed IR spectrograms for species concentrations.
  • Supervised two undergraduate students.
  • Published in Tetrahedron.

Selected software and research projects

01 / Android product engineering

Octidy Android App

A Firebase-first Android app that uses bidding, assignment, and progress tracking to make household chores more transparent and fair.

Kotlin Jetpack Compose Navigation Compose
Case study

02 / Scientific software

Subcellular Workflow

A modular, FAIR-compliant MATLAB framework for ODE biochemical pathway modeling, analysis, and parameterization.

MATLAB SimBiology Optimization Toolbox
Case study

03 / Materials chemistry research

Porphyrin Materials Research

Master's-level wet-lab and analytical work on ionic self-assembly of a porphyrin octacation with TPPS-based anions.

Organic synthesis Ionic self-assembly Porphyrin chemistry
Case study

Skills

Technical toolkit

01

Programming

Python NumPy SciPy Pandas Matplotlib Kotlin MATLAB
02

Data Science

Statistical analysis Time-series analysis Visualization Parameter estimation Sensitivity analysis
03

Scientific Computing

ODE modeling SBML Algorithm development Profile likelihood analysis Reproducibility (FAIR)
04

Android (Kotlin)

Jetpack Compose Navigation Compose ViewModel + Hilt Firebase Auth Firestore Realtime listeners Offline persistence WorkManager Coroutines/Flow Notifications Play Console testing
05

Tools & Platforms

Git/GitHub GitHub Actions VS Code Codex Android Studio IntelliJ Firebase SimBiology Jupyter Notebooks Conda/Anaconda Sphinx LaTeX Overleaf Markdown
06

Productivity & Collaboration

Microsoft Office Excel PowerPoint Word Jira Zoom EndNote Draw.io Figma

Education

Academic background

Jan 2016 -> Mar 2025

PhD, Computational Neuroscience

University of Porto (FCUP/ICBAS/FMUP/GABBA)

Completed doctoral coursework with a strong quantitative and computational focus through the GABBA doctoral program, including biostatistics, systems and synthetic bioinformatics, neurosciences, cellular and developmental biology, molecular microbiology and parasitology, and new therapies and technologies.

Thesis: A workflow for developing biochemical pathway models using ordinary differential equations.

  • Designed an integrated ODE modeling workflow for model initialization, simulation, parameter estimation, sensitivity analysis, and profile likelihood analysis.
  • Validated the framework across models of increasing complexity, from simple ligand-receptor systems to G-PIPK, a striatal signaling model integrating glutamatergic and cholinergic inputs.
  • Coordinated collaborative development across three institutions using Git/GitHub and delivered end-user documentation.
  • Published in Neuroinformatics and funded by Fundação para a Ciência e Tecnologia (FCT).

2013 -> 2015

MSc, Biochemistry

University of Porto (FCUP, ICBAS) / Grade 16/20

Grade: 16/20. Specialized in computational and analytical approaches to biochemistry, with coursework in computational biochemistry, bioinformatics, instrumental analysis, and bioanalytical chemistry.

Thesis: Exploring the Boundaries of Porphyrin Materials Synthesis by Ionic Self-Assembly.

  • Performed synthesis, purification, and spectroscopic characterization of porphyrin nanostructures.
  • Quantified spectroscopic data to determine species concentrations.
  • Supervised two undergraduate students during extracurricular research internships.
  • Research contributed to a publication in Tetrahedron.

2010 -> 2013

BSc, Biochemistry

University of Porto (FCUP, ICBAS) / Grade 16/20

Grade: 16/20. Completed a three-year program combining biological sciences with quantitative and analytical methods, including coursework in mathematics, statistical methods, and mathematical models.

Completed a research internship at the Institute for Molecular and Cell Biology (i3S) on protein depletion and cell cycle regulation in Drosophila melanogaster wing disc development.

Publications

Peer-reviewed work

2022

A modular workflow for model building, analysis, and parameter estimation in systems biology and neuroscience

Santos, JPG, Pajo, K., Trpevski, D., Stepaniuk, A., Eriksson, O., Nair, AG., Keller, D., Hellgren Kotaleski, J., & Kramer, A.

Neuroinformatics, 20(1), 241–259.

DOI: 10.1007/s12021-021-09546-3
2016

Ionic self-assembly reactions of a porphyrin octacation

Frigerio, C., Santos, JPG, Quaresma, P., Rebelo, SLH., Gomes, A., Eaton, P., Pereira, E., Carvalho, PA., Shelnutt, JA., Jiang, L., Medforth, CJ.

Tetrahedron, 72(44), 6988–6995.

DOI: 10.1016/j.tet.2016.09.030