Hi, my name is

Karthick Maniram

Senior Full-Stack & Research Software — Genomics, Healthcare & Cloud Data Systems

11+ years designing and building scalable, full-stack software systems — currently as a System Developer (Research Software Engineer) at Karolinska Institutet, turning large-scale genomic and clinical data into platforms researchers and clinicians rely on.

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About Me

Who I Am

Hi, I'm Karthick Maniram, a Senior Full-Stack and Research Software Engineer based in Stockholm, Sweden.

With over 11 years of experience in software development, I design and build scalable, full-stack systems across healthcare, genomics and cloud computing — working end to end across the front end, the back end, and the data pipelines underneath.

I am currently a System Developer (Research Software Engineer) at Karolinska Institutet, where I build full-stack platforms — including Curator, Genomic Leaderboard and iPCM Leaderboard — that turn complex genomic and clinical research data into tools researchers and clinicians actually use. I work day to day with React, TypeScript, Flask, PostgreSQL, Docker and AWS, translating open-ended research problems into reliable, maintainable software.

Passionate about:

  • Research Software Engineering
  • Full Stack Development
  • Cloud & Data Engineering

My Engineering Stack

Data Engineering & Warehousing

Pipelines, Big Data & Cloud Systems

  • ETL Pipelines
  • T-SQL
  • Fluentd
  • Cron Jobs

Front-End

UI & Client-Side

  • ReactJS
  • TypeScript
  • JavaScript
  • HTML5
  • CSS3
  • Bootstrap
  • jQuery
  • AngularJS

Back-End

APIs & Services

  • Python
  • Flask
  • Flask-RESTX
  • FastAPI
  • Bottle
  • Node.js
  • Express
  • PHP

Databases & Storage

Storage & Persistence

  • PostgreSQL
  • MySQL
  • SQLite
  • MongoDB

Data Science & Visualization

Analysis & Insights

  • Pandas
  • NumPy
  • Scikit-learn
  • Matplotlib
  • Shiny
  • R
  • D3.js
  • Tableau
  • Kibana
  • amCharts
  • FusionCharts

Cloud & DevOps

Infrastructure & Delivery

  • AWS (S3, EC2, Lambda)
  • Azure SQL Warehouse
  • Docker
  • Git
  • Linux

Where I've Worked

System Developer

Aug 2020 - Present

Karolinska Institutet
  • Designed and built full-stack biomedical research platforms — Curator (genomic variant curation), Genomic Leaderboard (sample tracking) and iPCM Leaderboard (pathology workflow tracking) — using React, TypeScript, Flask and PostgreSQL.
  • Led migration of legacy AngularJS applications to modern React, improving performance and maintainability.
  • Automated data management tasks and built ETL pipelines and cron jobs for the Smart Trial API, plus secure patient-data workflows syncing AWS S3 and PostgreSQL.
  • Led sprint planning, deployment and release management, and provided technical mentorship across several projects.
  • Administered Dockerized environments and CI/CD pipelines for in-house applications and databases.

Selected Projects

Expo Google Sign-In Firebase

  • Expo
  • React Native
  • Firebase Authentication
  • Google Sign-In

Cross-platform Expo app demonstrating Firebase Authentication with Google Sign-In, for Android and Web.

Curator

  • React
  • AngularJS
  • Node.js
  • NPM
  • Python
  • Flask
  • Flask-RESTx
  • PostgreSQL
  • Apache

What I Built

  • Configured the Apache web server as the front door — reverse proxy, firewall rules and routing — in front of the application.
  • Built the frontend (HTML, CSS, AngularJS/React, Node.js, NPM) and led its migration from AngularJS to React to improve maintainability and performance.
  • Built the Python3/Flask/Flask-RESTx backend API, backed by PostgreSQL for variant and curation records and the NFS file system for underlying data files.

Architecture

Browser

Researcher

Web Server

Apache · reverse proxy · firewall

Frontend

HTML, CSS, AngularJS/React, Node.js, NPM

Backend

Python3, Flask, Flask-RESTx

File System

NFS

PostgreSQL Database

Variant & curation records

Apache fronts the app as a reverse proxy, routing to a React frontend that calls a Flask/Flask-RESTx backend, which reads and writes PostgreSQL and the NFS file system.

Curator Data Migrator

  • Python
  • PostgreSQL
  • NFS
  • YAML

What I Built

  • Built migrate_sample_data.py to migrate sample information from NFS into the database, and migrate_genomic_profiles.py to move genomic profiles from the old database to the new one.
  • Built genomic_data_processor.py for shared genomic data processing utilities, and update_sample_status.py to keep sample status in sync with file availability on NFS.
  • Made the toolchain config-driven (config.yml) so database connections can be changed without touching code.

Architecture

/nfs

Sample files

Legacy Database

Old genomic profiles

Migration Scripts

Python · config.yml

PostgreSQL

Sample & genomic profile records

Config-driven Python scripts read sample and genomic profile data from NFS and the legacy database, transform it, and write it into the current Curator PostgreSQL database.

local-s3-sync

  • Python
  • Bash
  • AWS S3
  • BAM/CRAM

What I Built

  • Built BAM → CRAM conversion tooling to optimise storage footprint before upload.
  • Built statistics scripts to retrieve object counts and sizes across local/NFS storage and S3.
  • Built sync scripts to upload raw and processed data to S3, plus cleanup scripts to remove redundant or unwanted files from S3.

Architecture

Local Storage / NFS

BAM/CRAM files

Sync Scripts

Python · Bash

Amazon S3

Raw & processed data

Bash/Python scripts convert BAM to CRAM locally, then sync raw and processed data to S3, with separate scripts for usage statistics and cleanup.

Genomic Leaderboard

  • HTML
  • CSS
  • Javascript
  • Flask-RESTx
  • PostgreSQL
  • Cron

What I Built

  • Built a crontab-scheduled script that fetches and matches sequencing and curation information from NFS storage and the Smart-Trial API (now greenlight guru Clinical), creating and updating sample records in PostgreSQL.
  • Modelled sample state across two databases — a Referral DB and a Genomic DB — reflecting the pipeline from inclusion through to randomization.
  • Built the Genomic Leaderboard dashboard (React, React-Bootstrap, Chart.js) and a dedicated Genomic Leaderboard API to surface that tracking data to research teams.

Architecture

/nfs

Sequence & sample files

Smart-Trial API

greenlight guru Clinical

Crontab Script

Fetch & match sequence + curation info

Referral DB

Inclusion & referral records

Genomic DB

Sequencing, analysis & curation records

Genomic Leaderboard API

Genomic Leaderboard

Sample-tracking dashboard

Browser

Research team

A crontab job matches sequencing and curation data from NFS and the Smart-Trial API (greenlight guru Clinical) into PostgreSQL. The Genomic Leaderboard API then serves that data to the dashboard researchers use to track samples from inclusion to randomization.

iPCM Leaderboard

  • React
  • TypeScript
  • Flask-RESTx
  • PostgreSQL
  • Cron

What I Built

  • Built a crontab-scheduled script that fetches and matches sequencing and curation information from NFS storage, creating and updating sample records in PostgreSQL.
  • Modelled sample state across two databases — a Referral DB and an IPCM DB — reflecting the pipeline from inclusion through pathology, BioBank, sequencing, data delivery, analysis and curation, to the final report.
  • Built the iPCM Leaderboard dashboard and a dedicated iPCM Leaderboard API to surface that tracking data to research and pathology teams.

Architecture

/nfs

Sequence & sample files

Crontab Script

Fetch & match sequence + curation info

Referral DB

Inclusion & referral records

IPCM DB

Pathology, sequencing & curation records

iPCM Leaderboard API

iPCM Leaderboard

Sample-tracking dashboard

Browser

Research team

A crontab job matches sequencing and curation data from NFS into PostgreSQL (Referral DB, IPCM DB). The iPCM Leaderboard API then serves that data to the dashboard teams use to track samples from inclusion to report.

Quiz Application

  • AngularJS
  • TypeScript
  • Bootstrap

Configurable quiz and assessment tool with timed sessions and scoring.

NGS Analysis Software

  • PHP
  • JavaScript
  • Bottle
  • AWS
  • MySQL

Cloud-based next-generation-sequencing analysis suite supporting multiple genomic file formats.

Genome Functional Toolkit

  • JavaScript
  • PHP
  • AWS SDK
  • MySQL

Toolkit for functional annotation and interpretation of genomic variants.

AWS Cloud Monitoring Tool

  • JavaScript
  • PHP
  • amCharts
  • AWS

Monitoring dashboard surfacing AWS resource health and spend in a single view.

Research Interests

Where I Want to Take This

My day-to-day work already sits at the intersection of software engineering and scientific research — building and maintaining the platforms and data tooling behind genomic and clinical research at Karolinska Institutet. These are the areas of that work I'd like to go deeper on:

  • Research software engineering for genomics

    Designing and maintaining the platforms researchers and clinicians depend on daily — Curator for clinical variant curation, Genomic Leaderboard for sample tracking from inclusion to randomization, and iPCM Leaderboard for pathology workflow tracking from inclusion to report.

  • Data engineering & migration for clinical and genomic data

    Building the pipelines and tooling that keep research data trustworthy — crontab-driven ETL syncing external trial APIs into PostgreSQL, Curator Data Migrator moving sample and genomic profile records between databases and NFS, and local-s3-sync converting BAM to CRAM and syncing processed data to S3.

  • Scalable, secure architecture for research platforms

    Full-stack system design across the whole stack — Apache reverse proxies, React/TypeScript front ends, Flask/Flask-RESTx APIs and PostgreSQL — plus migrating legacy AngularJS systems and designing secure workflows for sensitive patient data.

  • Applied data science & visualization for research decisions

    Using Pandas, NumPy, Scikit-learn and visualization tools like D3.js, Tableau and amCharts to turn raw genomic and operational data into dashboards researchers and teams can act on.

  • Cloud infrastructure for reproducible research pipelines

    Applied cloud engineering for research workloads — Docker and CI/CD for platform delivery, NFS/S3 storage optimisation, and benchmarking data-warehouse platforms (Redshift Spectrum, Azure SQL Warehouse, Snowflake) to choose the right tool for a dataset.

Resume / CV

The Short Version

A one-page summary of my experience, for anyone who wants the short version alongside the full case studies above.

  • 11+ years building full-stack and data platforms across healthcare, genomics and cloud computing
  • System Developer (Research Software Engineer), Karolinska Institutet — genomics & clinical research software
  • Full-stack: React, TypeScript, Python/Flask, PostgreSQL, AWS, Docker

Education

  • M.E., Computer Science and Engineering — 2016 - 2018
  • B.E., Computer Science and Engineering — 2010 - 2014
Download Full Resume (PDF)

Get In Touch

I'm a Senior Full-Stack and Research Software Engineer focused on building reliable systems for research and data-intensive products. My work spans front-end and back-end development, data engineering and cloud computing — I'm always glad to talk about engineering roles or research collaborations.

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