Software Architecture & Web Infrastructure
I engineer reproducible computational pipelines, high-performance command-line packages, and production databases that empower scientists worldwide to analyze complex omics data.
Production Pipelines & Command-Line Tools
Containerized Nextflow DSL2 workflows and open Python packages built for high-throughput diagnostic clusters.
MetaNextViro
Nextflow DSL2 • Slurm • SingularityA modular Nextflow pipeline for virus identification, taxonomic classification, host depletion, de novo assembly, viral genome quality assessment, and coverage analysis across local, containerized, and HPC environments.
# Run MetaNextViro on high-performance compute cluster with Slurm & Singularity nextflow run navduhan/metanextviro \ -profile slurm,singularity \ --input samplesheet_avian_swabs.csv \ --reference h5n1_clade2344b_reference.fasta \ --host_depletion true \ --host_index /hpc/ref/host_indices/gallus_gallus \ --kraken2_db /hpc/ref/kraken2_viral_2026 \ --min_depth 100 \ --call_isnv true \ --min_var_freq 0.05 \ --outdir ./results_hpai_surveillance
Production Software Packages (9)
Nextflow DSL2 pipelines, Python CLI utilities, Zenodo-checksummed models & deep learning frameworks
MetaNextViro
Modular Nextflow pipeline for virus identification and metagenomic analysis, including de novo assembly, taxonomic classification, viral genome quality assessment, coverage analysis, and interactive reporting across local, containerized, and HPC environments.
PyVirSeq
Production CLI parser for viral read classification, reference-guided consensus generation, amplicon sequencing, genome reconstruction, and open-ended virome discovery with local and SLURM execution support.
PRGminer
Deep learning package for predicting and classifying plant resistance genes into eight functional categories; also deployed as an interactive web server at kaabil.net/prgminer.
CodonAdaptPy
Python package for coding-sequence validation, codon-usage and host-adaptation analysis, molecular-evolution diagnostics, phylogenetics, and constrained codon optimization.
miPyRNA
Automated python package for small RNA sequencing data analysis, novel microRNA discovery, and target site prediction. Adopted by 100+ research groups worldwide.
SNVguru
Automated python package for single nucleotide variation (SNV) interpretation, analyzing codon bias, secondary structure effects, and splice alterations. Adopted by 50+ research groups.
pySeqRNA
Complete automated package for next-generation RNA sequencing data analysis from quality control to differential gene expression. Complete documentation website with 500+ users.
MINpred v1.0.0
Alignment-free, four-phase deep learning package for ten-class nitrogen mineralization enzyme and EC prediction, using checksum-verified TFLite models archived on Zenodo.
deepNEC 2.0
Alignment-free protein language model for hierarchical enzyme and EC classification across ten nitrogen-metabolism pathways and 24 terminal outputs. Published in Briefings in Bioinformatics.
19 Deployed Web Platforms • 24,000+ Researchers
Production bioinformatics databases and AI servers deployed across kaabil.net and bioinfo.usu.edu, powering biological discovery in 140+ countries.
deepHPI
Deep learning framework for predicting host-pathogen protein interactions with the interactive Deepteractomer visualization interface.
covidTracker
Real-time infection statistics tracker and evolutionary tracking portal for COVID-19 pandemic epidemiology.
GreeningDB
Interactive database of host-pathogen interactions and comparative omics of citrus and citrus greening disease (Huanglongbing).
TritiKBdb
Host-pathogen interaction database for understanding Karnal Bunt disease infection and defense mechanisms in wheat.
legumeSSRdb
Comprehensive microsatellite marker database and comparative genomic resource across major legume species.
deepNEC Web Server
Alignment-free web platform for identifying and classifying nitrogen mineralization-related enzymes from sequence alone.
AtSubP-2.0
Deep learning platform for predicting single, dual, and membrane-protein subcellular localization across the Arabidopsis proteome.
ranchSATdb
Curated database of microsatellite markers and genomic variation across ranch animals and livestock breeds.
citSATdb
Citrus species microsatellite marker repository and functional annotation database.
RSLpred2
Web server for predicting and annotating protein subcellular localization across the rice proteome.
HuCoPIA
Atlas of Human vs. SARS-CoV-2 interactome and comparative interactomic analysis with other Coronaviridae family viruses.
deepNEC-2.0 Web Server
Multistage web server for functional classification of nitrogen mineralization enzymes using protein language embeddings.
LegumeLoc
Deep learning web server for predicting single and dual subcellular localization of legume crop proteins.
PRGminer Web Server
Interactive web interface for predicting and classifying plant disease resistance genes into 8 structural classes.
HuPoxNET
Host-pathogen protein-protein interaction database for Human-Monkeypox virus (Mpox, Variola) pathogenesis.
APinet
Interactive portal for predicting and visualizing protein-protein interactions in the Arabidopsis-Pseudomonas host-pathogen system.
MINpred Web Server
Online deep neural network server for multi-class nitrogen mineralization enzyme prediction.
HPInet
Cereal crops and fungal pathogen protein-protein interaction database and network visualization platform.
myDockDB
Cancer-focused molecular docking database prioritizing natural compounds against multiple myeloma therapeutic protein targets.