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Specification For A Computational Bioinformatics Lab Setup

a course for computational bioinformatics

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Desye Melese
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25 views

Specification For A Computational Bioinformatics Lab Setup

a course for computational bioinformatics

Uploaded by

Desye Melese
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Specification for a Computational Bioinformatics Lab Setup

To set up a computational bioinformatics lab, here are the recommended specifications for:

1. Two High-Performance Workflow Computers


2. A Dedicated Server
3. Six Desktops for General Computational Work
4. TV for Displaying

Each component is selected for computational tasks in bioinformatics, such as data analysis,
molecular simulations, machine learning, and software development.

1. Two High-Performance Workflow Computers

Purpose: These systems are designed for high-end computational tasks such as molecular docking,
simulations, large-scale data analysis, and machine learning model training.

Specifications:

 Processor: AMD Ryzen 9 7950X or Intel Core i9-13900K (16 cores, 24 threads) for high
multi-core performance.
 RAM: 64 GB DDR5 (2 x 32 GB, expandable to 128 GB) with high-speed, 4800+ MHz for
handling large datasets and parallel computations.
 Storage:
o Primary: 2 TB NVMe SSD for fast access to active project files and datasets.
o Secondary: 4 TB SATA SSD or HDD for additional storage.
 GPU: NVIDIA RTX 4090 (24 GB GDDR6X) or NVIDIA A5000 for GPU-accelerated
tasks (deep learning and molecular dynamics).
 Cooling: Liquid cooling to maintain stable performance under heavy loads.
 Operating System: Linux-based OS (Ubuntu 22.04 LTS or CentOS) for optimal
compatibility with bioinformatics tools.
 Network: 10 Gigabit Ethernet card for fast data transfer to the server.
 Display: Dual 27" monitors (4K resolution) for multi-tasking.

2. Dedicated Server

Purpose: A powerful server for hosting shared databases, running centralized applications, and
managing computational resources for tasks submitted by lab users.

Specifications:

 Processor: Dual AMD EPYC 7763 or Intel Xeon Gold 6348 processors (2x32 cores, 64
threads each) for extensive parallel processing capability.
 RAM: 512 GB DDR4 ECC RAM for high memory bandwidth and error correction.
 Storage:
o Primary Storage: 4 TB NVMe SSD for OS, databases, and frequently accessed
datasets.
o Backup Storage: 20 TB RAID 5/6 (HDD) for large storage with redundancy for
data protection.
 Network: Dual 10 Gigabit Ethernet ports with failover support.
 GPU (Optional for heavy ML/AI tasks): NVIDIA A100 Tensor Core GPU (40 GB) for
large-scale AI computations.
 Operating System: Ubuntu Server 22.04 LTS or CentOS 8 Stream for robust server support.
 Power Supply: Redundant hot-swappable power supply units for fault tolerance.
 Cooling: Rack-mounted liquid cooling system for maintaining server performance.
 Chassis: Rack-mounted 2U or 4U chassis for easy data center integration.
 Additional Software: SLURM or OpenPBS for job scheduling, RAID management tools,
backup software, and security packages.
3. Six Desktop Computers

Purpose: Designed for day-to-day computational work, code development, running lighter
bioinformatics software, and performing data analysis.

Specifications:

 Processor: AMD Ryzen 7 7700X or Intel Core i7-13700K (8 cores, 16 threads).


 RAM: 32 GB DDR5 (2 x 16 GB) for standard bioinformatics applications.
 Storage:
o Primary: 1 TB NVMe SSD for OS and project files.
o Secondary (Optional): 2 TB SATA HDD for additional data storage.
 GPU: NVIDIA RTX 3060 (12 GB) or AMD Radeon RX 6700 XT for moderate
computational tasks.
 Cooling: Air-cooled with ample ventilation.
 Operating System: Ubuntu 22.04 LTS or Windows 11 Pro (if specific software requires it).
 Network: 1 Gigabit Ethernet for stable LAN connectivity.
 Display: Single 24" monitor (1080p or 1440p resolution).

4 .TV for Displaying

 Size: 65-inch 4K UHD Smart TV with HDMI and wireless connectivity for presentations
and collaborative work.

Additional Considerations

 Networking Equipment: Ensure a high-speed switch (10 Gbps) for connecting all devices,
along with a secure firewall to protect against network vulnerabilities.
 Backup Solution: Network-attached storage (NAS) with RAID configuration for regular
data backups.
 Uninterruptible Power Supply (UPS): For the server and workflow computers to prevent
data loss during power outages.

This setup provides a balanced, scalable infrastructure for bioinformatics computations, ensuring
robust performance, data protection, and high-speed access across all lab systems.

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