Zakir Alibhai

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Merging computational innovation and life sciences at UCSD. Passionate about using machine learning and data analysis to solve complex biological challenges. Bioinformatics student, developer, computational biologist, and aspiring researcher.

9+
Projects
12+
Skills
20+
Courses
150+
Hours of Coding

About Me

Academic Background

First-year Bioinformatics student at UCSD, combining computer science with biological research. Focused on developing algorithms, tools, and analyzing data to solve various complex genetic, viral, and bio-chemical problems.

Research Interests

Passionate about biotechnology, medical research, and the intersection of computing with genetics. Exploring applications of machine learning in genomic analysis. Interested in developing tools for epigenetic analysis and personalized medicine for the average consumer.

Future Goals

Aspiring to contribute to breakthrough research in computational biology and develop innovative solutions for healthcare challenges through technology. Planning to leverage existing genomic tools and solutions to augment our knowledge and understanding of the human genome.

As a Biology major specializing in Bioinformatics at UCSD, I'm exploring the cutting-edge intersection of using computational methods to perform genomic research. More relevant than ever today, my program combines the depth of understanding in epigenetics, molecular and chemical biology, and phylogenetics with the power of modern computing, preparing me to tackle next-generation challenges in personalized medicine, viral data analysis, and other genomic research.

Beyond coursework, I'm actively developing extracurricular expertise in both cellular and molecular biology techniques within the wet lab; and expanding my repertoire of programming languages and relevant technologies, with a particular focus on:

Python
Java
JavaScript
Jupyter Notebooks
R Programming
Web Development
Genomics
Epigenetics
Phylogenetics
Viral Research
API Integration
Protein Modeling

My Tech Stack

Operating Systems

Primary: macOS (M1 MacBook Air)
Secondary: Linux - Ubuntu (UTM VM)

I’ll always prefer the polished ecosystem and UNIX-based developer environment of macOS, but the various Linux distros are always a nice challenge. Virtualizing Ubuntu sacrifices some performance, but lets me practice my CLI skills and test packages cross-platform.

Development Environment

Code Editor: VS Code, Cursor.sh, Zed
Terminal: iTerm2 + Oh My Zsh
Package Managers: Homebrew, Flatpak

I started — and will probably end — with VS Code, but Cursor’s agentic AI beats Copilot by a mile, and Zed makes some interesting design decisions too. iTerm2 (and the ZSH shell) are by far the smartest choices on a Mac and I’d hate to work without them. I’d highly recommend installing everything you can with Homebrew, and avoiding the Snap store is always a safe bet with Flatpaks.

Productivity Tools

Notes: Obsidian.MD, Apple Notes
Calendar: Apple Calendar (ICS)
Task Management: TickTick
Password Manager: Bitwarden

Obsidian is quite possibly the best power tool for lightweight note-taking I’ve ever used. The plugin ecosystem is an actual marvel, where I can run my code-snippets within a Markdown document, sync with Git, organize with data frames, and symlink concepts, lectures, and assignments. I haven’t even begun to unlock its full potential, but I’m already impressed with how genuinely powerful it is.

I’m still heavily embedded in the Apple ecosystem with no intentions of escaping, so I’ll occasionally write in the native apps when I’m not on Linux. TickTick has recommendations from some of the most reputable people in the tech space, and you don’t need me to tout how versatile or efficient it is, but what I personally love is converting my task lists to time-blocked ICS files and importing into Apple Calendar.

Lastly, Bitwarden is free and open source, reliable, cross-platform software that truly “just works”.

Daily Applications

Browser: Arc Browser, Zen Browser
PDF Viewer: Apple Preview, Edge PDF
Media: Apple Music, IINA, Plex
Communication: Discord

So far, Arc is by far the best browser for actually managing a productive workspace of programming, hobbies, courses, and research. As soon as Zen Browser — the FOSS alternative built on Gecko — starts supporting some essential features and gains the polish and sophistication that makes Arc’s organization just a genuine joy to use, I will happily switch away from Chromium. Until then, Arc remains unparalleled for productivity in every way, from its spaces and pinned tabs UI to my keyboard shortcuts and many nested folders.

I may be an Apple shill, but I’ll maintain that their native PDF viewer can almost match Edge, and their Music client — at least when you’re deep in the ecosystem — far surpasses the alternative. Of course, I self-host most of my media on a Plex server through a VM on the cloud that I port-forward and SSH into with some janky but working automated scripts. The rest is self-explanatory.

Additional Tools

Bookmarking: Raindrop.io
VPN: Cloudflare WARP

Lastly, Raindrop is an (oft-neglected) must for saving anything useful that crosses any platform you browse, and Cloudflare — especially if you own a domain and can tunnel your traffic — is probably the best (RD-compatible) VPN, even if you only want a DNS change.

Extensions: uBlock Origin, SingleFile, TickTick, DraftBack, Raindrop.io, Unclutter, Bitwarden, Form History Control, Redirector, Obsidian Web Clipper, PrintFriendly, Unpaywall, JSON Formatter, Copyfish, Perplexity, Translate, TaperMonkey, SponsorBlock, Arc

Thanks for reading about my tech stack, and feel free to request other categories I can add and talk about!

Projects & Research

GPTPortal - Advanced LLM Interface

Comprehensive Node.js platform integrating 10+ leading AI providers including OpenAI, Anthropic, Google, Meta AI, and Mistral. Features multi-modal interactions (text, voice, images), custom instructions, prompt templates, automated cost tracking, and multiple specialized modes including RAG and Jupyter environments.

Node.js AI/ML Full Stack

EpiGenAI - Epigenetic Analysis Portal

Specialized Node.js portal for epigenetic data analysis using vector embeddings and LLMs. Features DNA methylation analysis, pattern recognition, and natural language interpretation of genetic data.

Bioinformatics ML Node.js

Crime Analysis Data Pipeline

Detailed data pipeline for visualizing the relationships between political leaning, incarceration rates, and crime rates across US states. Utilizes advanced R programming techniques and real collected data from original sources.

R Data Analysis Research

WebReg Auto-Enroller

A robust Rust application that monitors UCSD's WebReg system for course openings and automatically enrolls in classes. Features asynchronous execution with Tokio, intelligent retry mechanisms, multi-channel notifications (email/Discord), detailed health monitoring, and configurable course tracking with TOML.

Rust Async Programming API Integration

AO3 History Exporter Extension

Cross-compatible TaperMonkey script and Chrome/Firefox extension to export and download your AO3 history as a JSON file. Features include network fetch requests, dynamic DOM parsing, data extraction, and JSON formatting. Error handling with partial results, pausing for rate-limits, and web app integration included.

JavaScript JSON Data DOM Parsing

AO3 History Explorer Web App

A full-featured React Web Application to explore and analyze your AO3 history with an interactive filterable table, custom statistics, and dynamic visualizations from a JSON file. Integrates with my extension using TypeScript and local data processing.

TypeScript ReactJS Tailwind CSS

BILD4 Final Research Project

Comprehensive Obsidian vault exploring epigenetic effects of alcohol consumption in Asian populations. Research focuses on DNA hypomethylation patterns and the ALDH2*rs671 variant's role in acetaldehyde metabolism. Displays final poster.

Markdown Obsidian Research

BILD5 Obsidian Vault

Complete Obsidian vault of notes, research, and projects for BILD5: Biostatistics R programming assignments, concepts, and final project.

Markdown Obsidian Research

React To-Do App

An advanced React-based To-Do application featuring task categorization, priority settings, due dates, and integrated voice command capabilities. Developed as a peer-programming test of Claude-3.7-Sonnet-Thinking capabilities with single-file constraints.

React TypeScript Voice Integration

Personal Portfolio Website

Modern portfolio website built with HTML5, Tailwind CSS, and Alpine.js. Features responsive design, dark mode, and interactive elements like visualizations and navigational animations to showcase projects and skills.

HTML Tailwind CSS Alpine.js

Genomic Data Analysis Tool

Python-based genomic analysis tool for processing and visualizing DNA sequence data. Features include sequence alignment, pattern recognition, and interactive visualizations.

Python BioPython Data Analysis

Research Data Visualization

R-based visualization toolkit for biological research data. Creates interactive plots and statistical analyses for genomic and proteomic datasets.

R ggplot2 Bioconductor

Personal Brand Website

Custom-designed personal brand website showcasing professional achievements and services. Features responsive design, modern aesthetics, and optimized user experience across devices.

HTML CSS JavaScript

Personal Brand Website

Custom-designed personal brand website showcasing professional achievements and services. Features responsive design, modern aesthetics, and optimized user experience across devices.

HTML CSS JavaScript

PLACEHOLDER: UCSD Research Project

Undergraduate research project focusing on genetic markers in cancer cells. Combining wet lab techniques with computational analysis to study gene expression patterns.

Research Genetics Lab Work

PLACEHOLDER: Bioinformatics Course Project

Advanced computational analysis of protein structures using machine learning techniques. Developed predictive models for protein-protein interactions.

Machine Learning Proteins Analysis

PLACEHOLDER: Independent Research Study

Self-directed study on emerging technologies in biotechnology and their applications in medical research and treatment development.

Biotech Research Medicine

Future Projects & Interests: Placeholders

AI in Genomics Research

Developing machine learning models for genomic data analysis and prediction of genetic variations. Extending AlphaFold with other cutting-edge models for protein structure prediction in a user-friendly manner.

Drug Discovery Platform

Creating a computational platform for predicting drug-protein interactions and potential therapeutic targets. Utilizing deep learning models in the cloud and on local hardware for new drug discovery and repurposing.

Automated Lab Analysis

Developing automation tools for processing and analyzing laboratory data using computer vision and machine learning. Implementing algorithms to identify and quantify biological samples, automate data entry, and enhance the accuracy and efficiency of laboratory workflows.

Real-time Genomic Analysis

Developing a real-time system for processing and analyzing genomic sequencing data as it's generated. Create a pipeline that can handle high-throughput sequencing data, perform quality control, align sequences, and identify variants in real-time.

Skills & Technologies

Programming Languages

Python
Advanced
BioPython Pandas NumPy
JavaScript
Advanced
ES6+ Node.js ReactJS API Integration
R Programming
Intermediate
ggplot2 Bioconductor tidyverse
Java
Learning
Core Java OOP Data Structures
Rust
Learning
Async/Tokio Error Handling Memory Safety
TypeScript
Learning
Type Systems React Integration Interface Design

Biotechnology Skills

Lab Techniques
Intermediate
PCR Gel Electrophoresis Cell Culture
Genomic Analysis
Learning
DNA Sequencing BLAST Sequence Analysis

Clinical Experience

Neurology Department Volunteer
1 Year
Patient Care Medical Procedures Clinical Operations

Volunteered at Cedars-Sinai Medical Center's Neurology Ward, gaining hands-on experience in patient care and medical procedures while developing a deep understanding of clinical operations and healthcare delivery.

Healthcare Competencies
  • Patient Interaction & Care
  • Medical Documentation
  • Healthcare Protocols
  • Clinical Environment Experience

DevOps & Infrastructure

Cloud Infrastructure
Active
Oracle Cloud Linux Server SSH Management Cloudflare
  • Oracle Cloud Infrastructure Management
  • Linux Server Administration via CLI
  • Docker Container Management
  • Cloudflare Tunneling
  • DNS Management and Routing
Hosted Services
Discord Bot Plex Server Web Projects Shell Scripting
  • Custom Discord Bot Development & Hosting
  • Media Server Configuration & Management
  • Automated Deployment Workflows
  • Virtual Machine Upkeep
  • Custom Shell Scripts & Automation

Tools & Frameworks

Development

  • Git & GitHub
  • VS Code & Obsidian.md
  • Command Line

Web Technologies

  • HTML & CSS
  • JavaScript
  • Tailwind CSS

Data Analysis

  • Jupyter Notebooks
  • RStudio
  • Data Visualization

Additional Competencies

Research Skills

  • Scientific Literature Review
  • Data Collection & Analysis
  • Experimental Design
  • Technical Documentation

Operating Systems

  • MacOS (Primary)
  • Ubuntu/Linux
  • Windows (VMs)
  • Command Line Proficiency

Soft Skills

  • Problem Solving
  • Team Collaboration
  • Technical Writing
  • Project Management

Currently Learning

  • Machine Learning
  • Advanced Bioinformatics
  • Database Management
  • Cloud Computing

Education

University of California, San Diego

B.S. Biology with Specialization in Bioinformatics

2024 - 2028
First Year Student at John Muir College
Current University GPA: 3.8

Pursuing a comprehensive program combining biological sciences with computational approaches, focusing on bioinformatics applications in medical research and genomics.

Current Coursework

Fall Quarter 2025
  • • CHEM 40A - Organic Chemistry I
  • • BILD 2 - Multicellular Life
  • • PHYS 2A - Physics I
  • • MATH 20B - Calculus II
  • • HITO 87 - Tourism Seminar
Spring Quarter 2025
  • • BILD 1 - The Cell
  • • CHEM 6C - General Chemistry III
  • • CHEM 7L - General Chemistry Lab
  • • VIS 10 - Computing in the Arts
  • • POLI 87 - Data Literacy
Winter Quarter 2025
  • • BILD 5 - Data Analysis/Design for Bio
  • • MCWP 50 - Critical Writing II
  • • CHEM 6A - General Chemistry II
  • • PHIL 10 - Introduction to Logic
  • • HITO 87 - European Seminar
  • • ANTH 87 - Mapping Capitalism
Fall Quarter 2024
  • • MATH 10A - Calculus I
  • • CHEM 6A - General Chemistry I
  • • CSE 8A - Intro to Programming
  • • BILD 4 - Introductory Biology Lab
  • • MCWP 40 - Critical Writing I
  • • CSE 87 - Bioinformatics Seminar

Advanced Placement Courses

  • Biology
  • Chemistry
  • U.S. History
  • Calculus
  • Computer Science
  • Government & Politics
  • English Literature
  • English Language
  • Human Geography
  • Academic Background & Experience

    High School GPA: 4.4
    Medical Science Academy - 3 Years
    • • Advanced Physiology
    • • Biotechnology
    • • Biomedical Innovations
    Certifications
    • Laboratory Safety Certification
      • - MSA & BILD 4
    • CPR and First on the Scene
      • - Cedars-Sinai Certified Training
    Clinical Experience

    1 Year Volunteer Experience at Cedars-Sinai Medical Center

    Neurology Department • Patient Care & Clinical Support

    Academic Timeline

    Medical Science Academy

    2020 - 2023

    Advanced medical & biological sciences training

    First Year

    2024 - Present

    Declared Biology Major with Bioinformatics Specialization

    Expected Graduation

    2028

    B.S. Biology with Specialization in Bioinformatics

    Academic Highlights

    • 40+ AP Credits Earned
    • Satisfied UC Entry-Level Writing Requirement
    • American History & Institutions Requirement Satisfied
    • 3.8 University GPA
    • 4.4 High School GPA
    • Medical Science Academy Graduate
    • CPR, & FOTS Certifications
    • 2+ Years Wet Lab Experience
    • Cedars-Sinai Clinical Experience

    Get In Touch

    Interested in collaboration or have questions about my research? I'd love to hear from you!

    Direct Contact

    University of California, San Diego

    Connect With Me

    Availability

    Currently open to research collaborations, internship opportunities, and academic discussions. I will also occasionally do web development for clients as a hobby, so if you like the look and feel of this portfolio or any of my personal brand projects, feel free to let me know, and we can get in touch!

    Contact Form

    Interactive Visualizations

    Skills Network

    Language Proficiency

    Interactive DNA Sequence

    Project Timeline & Progress

    Technical Features

    Exploring the technical capabilities and interactive elements that power this portfolio

    Interactive Elements

    • Smooth Scrolling Navigation
    • Dynamic Project Filtering
    • Dark/Light Mode Toggle
    • Scroll Animations

    Technical Features

    • SEO Optimized Structure
    • Performance Optimization
    • Responsive Design
    • Modern Web Technologies

    Bioinformatics Tools

    • Molecular Visualizations
    • Data Analysis Examples
    • Interactive Demonstrations
    • Research Visualizations
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