Cell Ranger/QuPath workstation | Information dissemination media for research and development TEGAKARI

A customer involved in genetic research asked us to install a bioinformatics workstation with a budget of around 100 million yen.
Currently, we are mainly conducting genome analysis such as single-cell RNA analysis, and I have heard that there are plans to conduct spatial genetic analysis in conjunction with high-quality pathological images in the future.

Regarding machine specs, we received a request to focus on the number of CPU cores and memory capacity.
The software to be used is assumed to be Cell Ranger or QuPath, and the preferred OS is Linux.
We have received inquiries from customers saying, ``I'm not used to using Linux, so if possible, I'd like Cell Ranger and QuPath to be shipped with Cell Ranger and QuPath installed.''

Based on this information, we proposed the following configuration.

CPU	AMD Ryzen Threadripper 7960X (4.20GHz 24 cores)
memory	256GB REG ECC
storage	2TB SSD M.2 NVMe Gen4
Video	NVIDIA T400 4GB
network	on board(2.5GbE x1 10GBase-T x1) Wi-Fi x1
Housing + power supply	Tower type housing + 1000W
OS	Ubuntu 22.04
Other	Cell Ranger, QuPath installation

Configuration that emphasizes the number of CPU cores and memory capacity within the budget

We proposed a configuration that emphasizes the number of CPU cores and memory capacity within your budget.
The CPU is equipped with the latest AMD Ryzen Threadripper 2024 series 5-core model as of May 7000.
Memory is 64 x 4GB modules for a total of 256GB.
With a 24-core CPU and 256GB memory capacity, you can expect high performance during analysis.

Please note that Cell Ranger and QuPath currently have limited support for GPU acceleration, so if you do not use GPU acceleration, it is thought that there will be no problem with operation even with an entry-class video card. Therefore, we chose the entry-class NVIDIA T400 4GB video card for workstations, keeping the budget in mind and not considering the use of GPU acceleration.

Please note that the power supply capacity of this machine is selected for the current configuration, and does not take into account future additions or upgrades of devices such as GPU expansion.
If you are planning to add devices that consume a lot of power, such as adding GPUs, please feel free to contact us as we can change the configuration.

Cell Ranger・QuPath pre-installation service

We will ship the product with Cell Ranger/QuPath pre-installed according to the customer's request.
Note that QuPath also works on Linux, but some issues have been reported.
Please refer to the official manual below for details.

Reference: Installation — QuPath 0.5.1 documentation

Additionally, if you wish, you can create a dual-boot configuration with Cell Ranger installed on Linux and QuPath installed on Windows.
If you would like to pre-install other software, please feel free to let us know.

The configuration of this case study is based on the conditions given by the customer.
We will flexibly propose machines according to your conditions, so please feel free to contact us even if you are considering conditions different from those listed.

■ Keywords

・What is Cell Ranger?
Cell Ranger is a software pipeline from 10x Genomics.Single-cell RNA-sequencing data can be processed, clustered, and gene expression quantified. Process single-cell RNA-seq data generated using 1x Genomics Chrome and perform gene expression clustering to identify single-cell subpopulations.In addition, it also supports creation of expression matrix by mapping to virtual reference and quantifying genes.

Reference: Cell Ranger (10x Genomics) *Jumps to an external site

・What is QuPath?

QuPath is open source software for biological image analysis. Equipped with a wealth of analysis functions, it is possible to comprehensively visualize and analyze the entire slide image.