【Schedular】

1. 2009-09-09 測試資料。
2. 2009-09-04 15:30 跟陽明視訊開會。
3. 2009-09-11 第一階段軟體安裝。
4. 2009-09-16 系統測試、種子學員~教學大綱。
5. 2009-11-11 openPBS torque ~教學大綱。
6. 2010-05-17 bio2 叢集重新設定

【Environment】

• OS:Ubuntu 8.04.3 LTS

【Software list】

PART 1 : Bioinformatics related Software / Applications

1. AutoFACT
   • 缺資料庫。
2. BLAST
   • 測試完成。已安裝版本：1:2.2.17.20070822-3。
3. SIM4
   • 測試完成。
4. Clustal
   • 測試完成。
5. PipMaker
   • 已安裝。
6. Phylip
   • 測試完成。
7. Velvet
   • 測試完成。
8. Bowtie
   • 測試完成。
9. SOAP
   • 測試完成。
10. wwwBLAST

PART 2 : Cluster Management related Software

1. OpenPBS : torque - Ubuntu 套件:
   • ​TORQUE Admin Manual
   • 不希望使用者直接到 compute node 執行動作，先前民哥建議的做法是參考 ​prologue and epilogue for PBS - using PAM to enforce PBS node assignments，這個作法在 Torque 可能要研究一下​管理手冊 附錄 G Prologue & Epilogue Scripts。
2. ​DRBL - 無碟開機系統
3. ​Lustre - 硬碟合併機制
4. Ganglia - 叢集監控系統(CPU/RAM/DISK/排程) - Debian 套件: ​ganglia-monitor, ​gmetad, ​ganglia-webfrontend
5. ​Nagios - 網路狀態監控與事件通報系統(Ex.發簡訊SMS) - Debian 套件: ​nagios3
   • ​collectd - 可以跟 Nagios 結合的本機監控軟體 - Debian 套件: ​collectd
   • ​scalable monitoring with collectd and nagios
   • ​The term “monitoring” needs clarification - 確實監控分成很多種，這篇文章列舉了三種不同監控的定義
6. VNC - 遠端桌面 - 需要 ​vnc-java, ​vnc-reflector, some kind of message queue (MQ)
7. LDAP - 統一帳號管理機制
   • ​使用 Active Directory 對 Linux 用戶端進行身份驗證
   • ​adLDAP - LDAP Authentication with PHP for Active Directory - LGPL 授權 PHP AD 整合函式庫 (參考以前當 maicl 顧問的 code @ sensor)
8. Web Server - ​lighttpd 或 ​apache2
9. zterm - Java SSH Client

【Database list】

1. Human dbEST database
2. Human UniGene database
3. Protein interaction database
4. Gene ontology database
5. Homologene database

【Reference】

• ​http://www.bioinformatics.org/
• ​http://biowulf.nih.gov/

• ​http://www.biosino.org/~gwding/R/R-Learn/ - 一些 R 語言的學習資源 (簡體)

【Cloud Computing Related】

• ​CloudBurst - a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.

【Recent Changes】

Mar 11, 2011

• biocluster (diff)

Jan 12, 2011

• biocluster/Velvet (diff)

Aug 22, 2010

• biocluster/10-05-28 (diff)

May 24, 2010

• biocluster/10-05-24

May 17, 2010

• biocluster/10-05-17 (diff)

Dec 10, 2009

• biocluster/AutoFACT (diff)

Nov 30, 2009

• biocluster/SOAP (diff)
• biocluster/Bowtie (diff)
• biocluster/Clustal (diff)

Nov 18, 2009

• biocluster/wwwblast (diff)

Nov 11, 2009

• biocluster/BLAST (diff)

Sep 16, 2009

• biocluster/教學大綱 (diff)

Sep 15, 2009

• biocluster/Phylip (diff)
• biocluster/SIM4 (diff)

Sep 12, 2009

• biocluster/Eland (diff)

Sep 4, 2009

• biocluster/PipMaker (diff)