Empowering Bangladesh's Bioinformatics Revolution
Establishing the first open-access High-Performance Computing cluster dedicated to genomic surveillance, pathogen research, and computational biology in Bangladesh.
The Computational Bottleneck in
Bangladeshi Genomics
Bangladesh's genomic research is currently restricted by a lack of local, high-performance computing resources. Researchers are forced to rely on limited cloud credits or foreign collaborations, leading to significant delays in critical public health responses.
- Delayed Outbreak Response
- During dengue or cholera outbreaks, waiting weeks for external compute can cost lives. Local HPC enables real-time pathogen tracking.
- Data Sovereignty & Privacy
- National genomic data should be analyzed locally to maintain strict ethical standards and ensure the security of sensitive biological information.
Scientific Limitations
- Inability to run large-scale WGS pipelines locally
- Limited capacity for de novo assembly of local species
- High cost of commercial cloud providers for long-term projects
- Brain drain as computational biologists seek foreign infrastructure
$ hpc-status --check-resource
[WARN] Local cluster not found.
[INFO] Latency to foreign nodes: 280ms
[INFO] Queue time: 14 hours
CRITICAL: Insufficient local capacity for outbreak modeling.
The Infrastructure
Visualizing the BioHPC Lab
This isn't just hardware; it's the engine of scientific progress for Bangladesh.
Scalable Compute Power
High-density server racks designed for massive parallel processing of genomic sequences.
Data Sovereignty
Local storage infrastructure ensuring Bangladeshi genomic data stays within national borders.
Accelerated Discovery
GPU-accelerated nodes that reduce analysis time from weeks to hours.
The Workflow
How HPC Accelerates Discovery
From raw genetic data to life-saving insights, BioHPC Lab orchestrates a complex computational journey.
Massive Data Input
Gigabytes of raw genomic sequences and biological data are uploaded to the secure facility.
Smart Job Scheduling
Our scheduler (SLURM) prioritizes tasks, allocating memory and CPU cores to maximize efficiency.
Parallel Processing
Hundreds of processor nodes work in unison to perform complex calculations in minutes instead of weeks.
Insight & Discovery
Visualized results empower scientists to identify disease variants and design new treatments.
Scientific Impact
Transforming Public Health with HPC
BioHPC Lab provides the computational foundation for a wide spectrum of advanced research domains, driving breakthroughs in national health and biological science.
Pathogen Surveillance
Real-time tracking of Dengue, Cholera, and COVID variants to predict outbreaks and inform national health policy.
Single-Cell Genomics
Decoding cellular heterogeneity to understand complex diseases, developmental biology, and immune responses at individual cell resolution.
Neurogenomics
Investigating the genetic basis of neurological disorders and brain function through large-scale neural data analysis.
Cancer Bioinformatics
Identifying genetic markers specific to the Bangladeshi population for personalized oncology and precision medicine.
Drug Discovery & Design
Accelerating the identification of novel drug targets for multi-drug resistant (MDR) pathogens using molecular docking.
Agricultural Genomics
Enhancing climate resilience and yield of local crops like Jute and Rice through advanced genomic selection.
Metagenomics & AMR
Studying environmental microbiomes to track the spread of Antimicrobial Resistance (AMR) in the community.
AlphaFold & Proteomics
Running protein structure predictions locally to understand molecular mechanisms and accelerate biochemical research.
Population Genetics
Mapping the genetic diversity of the Bangladeshi population to study evolutionary history and disease susceptibility.
Endorsements
Supported by National Leaders
BioHPC Lab is supported by prominent researchers across Bangladesh's leading academic institutions.
"The establishment of a local HPC cluster is a critical step towards scientific self-reliance for Bangladesh. It will transform how we conduct genomic research and train our students."
"High-performance computing is the backbone of modern genomics. BioHPC Lab will provide the necessary infrastructure to accelerate our research in infectious diseases and molecular biology."
"BioHPC Lab addresses the most significant barrier in our research: the computational bottleneck. This initiative is essential for the future of microbiology and pathogen surveillance."
"Modern agricultural genomics and aquatic health management require massive computational power. A national HPC cluster will be a game-changer for food security and biodiversity research in Bangladesh."
Initiator
Md. Jubayer Hossain
Bioinformatician & Educator
A visionary bioinformatician and educator who founded DeepBio Limited and CHIRAL Bangladesh to advance bioinformatics research and training.
His work spans genomics, transcriptomics, and cancer bioinformatics, with a primary focus on democratizing research skills and making them accessible to all researchers and students across Bangladesh.
Infrastructure Vision
A Strategic Roadmap for National HPC
A phased approach to building world-class genomic infrastructure, from starter nodes to full-scale production clusters.
Phase 1 — Starter Node
Month 1–2One refurbished compute server. Can already run BWA-MEM2, GATK, Snakemake pipelines.
Technical Configuration & Pricing
| Component / Item | Est. Cost |
|---|---|
| Refurbished Dell R6525 (AMD EPYC 7313, 16c) | $1,800 |
| 256 GB DDR4 ECC RAM (8× 32 GB used) | $900 |
| 4× 4 TB NVMe SSD (Samsung 980 Pro) | $800 |
| 10 GbE NIC (Mellanox ConnectX-4) | $200 |
| UPS (APC 1500VA) | $280 |
| OS, cables, rack shelf | $320 |
| 1-year cloud backup (Backblaze B2) | $120 |
| Shipping to Dhaka + import duties (~30%) | $2,400 |
| Experiment.com platform fee (8%) | $680 |
| Contingency buffer (10%) | $1,000 |
Capabilities & Unlocks
- BWA-MEM2 / STAR alignment
- GATK4 variant calling
- FastQC / MultiQC
- Snakemake / Nextflow
- BLAST / Diamond
- ~20 WGS samples/day
Strategic Goal
Establish initial local capacity.
Phase 2 — Small Cluster
Month 3–6Add a second compute node + shared NAS storage. Run parallel pipelines, scRNA-seq.
Technical Configuration & Pricing
| Component / Item | Est. Cost |
|---|---|
| Refurbished Dell R6525 (AMD EPYC 7443, 24c) | $2,800 |
| 512 GB DDR4 ECC RAM | $1,600 |
| TrueNAS server + 8× 12 TB HDD (96 TB raw) | $4,200 |
| 25 GbE switch (Mikrotik CRS305) | $380 |
| Additional NVMe SSDs × 4 | $800 |
| SLURM + BeeGFS setup & admin (3 months) | $2,400 |
| Shipping + import duties | $3,200 |
| Experiment.com fee + contingency | $2,100 |
| Power conditioning / stabilizer | $450 |
| Annual maintenance reserve | $4,070 |
Capabilities & Unlocks
- scRNA-seq (Seurat/Scanpy)
- Metagenomics (Kraken2/MetaPhlAn)
- Trinity de novo assembly
- Multi-sample GWAS
- ~60 WGS samples/day
- 2-node SLURM queue
Strategic Goal
Establish parallel workflow capabilities.
Phase 3 — GPU Accelerated
Month 7–18Add GPU node for AlphaFold2, DeepVariant, AI-based pathogen surveillance.
Technical Configuration & Pricing
| Component / Item | Est. Cost |
|---|---|
| Used A100 40 GB PCIe GPU × 2 (eBay / LambdaLabs) | $14,000 |
| GPU workstation (Supermicro AS-4124GS) | $6,500 |
| 512 GB RAM + NVMe for GPU node | $2,200 |
| InfiniBand HDR switch (used/refurb) | $5,800 |
| Shipping + import (GPU classified as research equipment) | $5,500 |
| Annual NVIDIA Parabricks license | $2,500 |
| IT staff training (bioinformatics HPC) | $2,000 |
| Infrastructure / cooling upgrade | $3,500 |
| Platform fees + contingency | $3,000 |
Capabilities & Unlocks
- AlphaFold2/3 protein prediction
- DeepVariant deep learning caller
- AI-based antimicrobial resistance
- COVID / dengue surveillance ML
- scRNA GPU acceleration (RAPIDS)
- ~200 WGS samples/day
Strategic Goal
Establish AI/ML acceleration.
Phase 4 — Full Production HPC
Year 2–3Scale to full cluster matching original spec. Serve multiple universities across Bangladesh.
Technical Configuration & Pricing
| Component / Item | Est. Cost |
|---|---|
| 4× compute nodes (EPYC 9554 dual socket) | $45,000 |
| 2× GPU nodes (H100 SXM5 ×4) | $56,000 |
| Parallel storage (Lustre, 576 TB) | $18,000 |
| HDR InfiniBand fabric | $12,000 |
| Professional rack + power + UPS | $9,000 |
| Import duties + installation | $10,000 |
Capabilities & Unlocks
- National genomics infrastructure
- Regional disease surveillance hub
- AI drug discovery
- International collaboration node
- Open access for all BD universities
Strategic Goal
Establish national-scale production.
Investing in Human Capital
Beyond hardware, BioHPC Lab is a commitment to the next generation of Bangladeshi scientists. We are building a center of excellence for training MSc and PhD students in computational biology.
Students Trained Annually
Research Labs Served
Access for All Universities
Support the Initiative
Enable the Future of Science
BioHPC Lab is a collaborative, open-access project. Your support helps us bridge the computational gap for Bangladeshi researchers.
Experiment.com
Science-specific
Best for Phase 1. Science audience, high credibility. All-or-nothing model means donors trust you won't pocket partial funds.
GoFundMe
General public
Share in Bangladeshi diaspora communities (UK, USA, Canada). Tell the human story: diseases, patients, local researchers.
Indiegogo
Tech community
Use InDemand mode after initial goal — keep collecting indefinitely. Good for tech-savvy international donors.
Open Collective
Open source / research
Transparent fund management. Great for institutional donors who want audit trails. Register as a Fiscal Host.
Recognition & Rewards
Contributor Tiers
Supporter
Need 50+
🎁Name in README + digital thank-you certificate
Lab Friend
Need 40+
🎁All above + mention in first publication acknowledgements
Genome Patron
Need 20+
🎁All above + acknowledgement in methods paper
Sequence Sponsor
Need 8+
🎁All above + named server partition + priority access