02 / 08 · /code

Type. Click. It runs.

Repositories at github.com/synbioexplorer, grouped by domain. Click any card → architecture diagram + honest abstract.

// 27 repos · grouped by domain · click any card

The catalogue, organised.

// peer-reviewed · pipelines · model-driven design 9 repos

Published research & bioinformatics

// llms · multi-agent · orchestration 3 repos

AI · agentic systems

// aws · cognito · cloudformation · 31 instruments 5 repos

AGF platform · production infrastructure

// desktop apps · data migration · plate counting 3 repos

Lab tools

// weekend curiosity · personal ML · web experiments 7 repos

Side projects & explorations

→ see all 27+ on github

// stack

What's on the work machine.

Languages

  • Python
  • TypeScript
  • JavaScript
  • R
  • Shell
  • SQL

NGS · short reads

  • fastp
  • FastQC · MultiQC
  • BWA
  • Bowtie2
  • Salmon
  • STAR
  • HISAT2
  • SortMeRNA
  • samtools
  • bcftools
  • snpEff
  • Bedtools
  • deepTools

NGS · long reads

  • Dorado
  • Flye
  • Minimap2
  • NanoPlot
  • Porechop
  • QUAST
  • pysam

Downstream · DE / enrichment

  • DESeq2
  • edgeR
  • tximport
  • clusterProfiler
  • goseq
  • gseapy
  • complexHeatmap
  • EnhancedVolcano

Structural biology · protein

  • AlphaFold
  • ColabFold
  • Boltz-2
  • PyMOL
  • exonerate
  • MAFFT
  • BioPython

Systems · misc

  • COBRA · FBA
  • Opentrons API
  • GATK · Delly
  • NetworkX
  • NLP on sci-lit

Lab tools

  • LIMS design
  • Lab automation · MCP servers
  • Plate-reader analysis (Welly)
  • Microfluidics CAD
  • CRISPR / SCRaMbLE design

Cloud · DevOps

  • AWS Lambda
  • DynamoDB
  • S3
  • EventBridge
  • Cognito
  • CloudFormation
  • Amplify
  • API Gateway
  • GitHub Actions
  • Docker

AI · agents

  • Claude Code
  • LangGraph
  • LangChain
  • ChromaDB
  • Anthropic SDK
  • OpenAI SDK
  • MCP servers

Frontend · Backend

  • React
  • Next.js
  • Astro
  • Electron
  • Vite
  • Tailwind
  • FastAPI
  • Flask
  • PostgreSQL
  • Redis

Data viz

  • Plotly
  • Dash
  • Matplotlib
  • Seaborn
  • D3
  • pandas
  • Jupyter
repo

// repository