IRCMS International Research Center for Medical Sciences

Service

Service

Bioinformatics

IRCMS provides to eligible students and interested staff of Kumamoto University access to its mini-cluster for bioinformatics research and education.
The four-node cluster has 80 cores. Two nodes consist of four standard Intel Xeon E5-2680 v4, 2.40 GHz 14-core processors, 32 DDR4 (2400 MHz) 32 GB memory modules and two NVIDIA Tesla K80 GPUs. The other two nodes are composed of four older Intel Xeon E5-2630 v2, 2.30 GHz 6-core processors, 48 DDR3 (1866 MHz) 16 GB memory modules and two NIVIDA Quadro K4000 GPUs. A tape library system is used for archiving. A G-SPEED Studio XL 42 TB storage server that is mounted to the front-end of the cluster facilates data transfer from PCs linked with instruments to the storage server and access of the stored data from the cluster or networked PCs.
Users are permitted to install their own tools in their home directory and create web-accessible databases. General available tools and packages include AmberTools, Bioconductor, BioPerl, BioRuby, Bowtie2, Cytoscape, HMMER, GATK, MODELLER, MySQL, NCBI toolkit, Perl, PHP, PyMOL, Python, RStudio Server, Tophat2, SAMtools, and Trinity among others.
In addition to collaborative research involving bioinformatics IRCMS offers routine bioinformatics support on a Fee For Service (FFS) agreement basis. User account requests and inquiries regarding services should be directed to bioinfoservice@kumamoto-u.ac.jp. For inquiries on collaborative research contact bioinforesearch@kumamoto-u.ac.jp.