This page hosts documentations of our PREWS cluster for Cryo EM data processing.
PREWS stands for PRocessing Environment With Storage. *prews- is also a reconstructed stem in Proto-Indo-European language that means frost and freeze. Modern words derived from it include freeze and frost in English, frieren in German and vriezen in Dutch. We hope this serves cryo EM well.
The cluster was physically installed on Mar 25th, 2024. We performed beta testing with selected CryoEM facilities in the 2024 fiscal year. We started serving general academic users in April, 2025. A usage fee of 100,000 JPY (+ VAT) per 6 months is charged to cover the running cost (the price may change in the future). Please contact us at prews-help AT protein DOT osaka-u DOT ac DOT jp for account creation after carefully reading the rules (in Japanese) and the manual (in English and Japanese).
PREWS クラスタは AMED/BINDS の支援のもと構築された、クライオ電子顕微鏡データ処理のためのコンピュータクラスタです。2024 年 3 月 25 日の納入後、2024 年度は BINDS 電顕共用施設を中心とした運用を行い、2025 年度より一般ユーザへの提供も開始しました。
アカウント作成希望の方は、内規と説明書を確認の上、prews-help AT protein DOT osaka-u DOT ac DOT jp にメールください。電気代など運転費用を捻出するため、半年ごと(4 - 9 月, 10 - 3 月)に税別 10 万円の利用料をいただいています。料金は今後変更になる可能性があります。期間の途中から利用する場合でも減額はありませんのでご了承ください。
Our cluster consists of 30 GPU nodes and 10 CPU-only nodes as well as one login node and one management node. Our CephFS storage has a capacity of ~ 1.9 PB.
The cluster jobs are managed by SLURM. Basic SPA processing programs (RELION, CTFFIND, Topaz etc) are pre-installed. Users are allowed to install other software in their user area. Web-based applications are not allowed on the login node. They must be launched on worker nodes.
The PREWS cluster must be used exclusively for cryo-electron microscopy (SPA, STA, MicroED) data processing. For a broader scope of structural biology/chemistry applications (e.g. structure prediction, protein design, molecular dynamics, quantum chemistry), please contact the cluster administrator. We might give permission on a case-by-case basis, based on the resource availability and scientific merits.
Users have to back up their own data themselves. We do not guarantee availability and security. We might shutdown the system for maintenance without prior announcement. Your data might be lost and/or stolen due to system failures or attack.
The cluster is funded by AMED/BINDS. This page is written by Takanori Nakane at PDBj, Institute for Protein Research, Osaka University. Last updated on 2026 Jan 17th.