A customer involved in the development of organic fertilizers asked us about a workstation for data processing of amplicon sequence analysis and integrated analysis of multi-omics.
Mainly uses R packages (WGCNA, lavaan, ggplot, arules, imager, etc.), igraph, and QIIME2, and some photo processing is also expected (about 450MB per week). Since it is assumed that processing and analysis will be performed on the CPU, I have heard that they would like to place emphasis on CPU performance.
Your requirements are as follows.
・CPU: Emphasis on performance ・Memory: 128GB or more ・Storage: Approximately 512GB ・OS: None ・Software used: R package (WGCNA, lavaan, ggplot, arules, imager, etc.), igraph, QIIME2 ・Budget: About 80 million yen |
Based on the information you provided, we have prepared the following structure.
CPU | Intel Xeon W5-2465X (3.10GHz 16 cores) |
memory | 128GB REG ECC |
storage | 500GB SSD M.2 |
video | NVIDIA T400 4GB |
network | on board (2.5GbE x1, 10GbE x1) |
Housing + power supply | Tower type housing + 1000W |
OS | None |
As of August 2023, the configuration is equipped with the latest Xeon W-10 series.
We chose the Intel Xeon W5-2465X (16 cores), which is the highest-end model that fits within your budget.
Note that in order to perform multi-threaded operations in R, it is necessary to install a parallelization package.Please note that if you run an R program without the parallelization package installed, it will run single-threaded and you will not be able to effectively utilize the number of cores.
The installed memory capacity is 128GB, but there are 4 empty slots, so it is possible to add more memory in the future.
If you are analyzing around 450MB of images per week, it is thought that very high GPU performance is not required.
Therefore, we chose the NVIDIA T400 4GB, an entry model for workstations, as the video card, but you can change it if you wish.
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 different conditions than what is listed.
■ Keywords・What is amplicon sequence analysis? Amplicon sequencing is a molecular biology method that rapidly sequences specific DNA or RNA regions.Genes, gene regions, or fragments are amplified in a PCR reaction using specific primers and sequenced using a next-generation sequencer.It is used in many fields, including microbiology, genetics, and ecology, and has applications in investigating genetic polymorphism, microbial identification, disease-related mutations, and environmental diversity.The obtained data will be analyzed using bioinformatics tools to obtain biological information. ・What is Omics analysis? Omics analysis is a data-driven approach widely used in biology and medicine. Omics is a general term for technologies for collecting and analyzing biological data, such as genomics, proteomics, and transcriptomics. ・What is R? R is an open source and free software programming language/development execution environment for statistical analysis.Used in calculations and graphing for statistical processing.
・What is igraph? igraph is an open source library for graph creation and network analysis. It supports programming in C/C++, R, Python, and Mathematica.
・What is QIIME2? QIIME2 is an open source software package for microbiome analysis.We emphasize transparency in data and analysis, and you can easily check the analysis data from the dedicated website "QIIME2 View".New features are added regularly through plugins. |
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