= 2009-04-06 =

== Hadoop / !MapReduce ==

 * 關於 !MapReduce:
   * [http://developer.amazonwebservices.com/connect/entry.jspa?externalID=2297&categoryID=265 Introduction to Amazon Elastic MapReduce]
   * [http://developer.amazonwebservices.com/connect/entry.jspa?externalID=2294&categoryID=265 Finding Similar Items with Amazon Elastic MapReduce, Python, and Hadoop Streaming] - 用 Hadoop 做相似度分析，可應用在生物資訊領域。
   * [http://hadoop.apache.org/core/docs/current/cn/mapred_tutorial.html Hadoop Map/Reduce 教程]
   * [http://www.eecs.berkeley.edu/Pubs/TechRpts/2008/EECS-2008-99.html Improving MapReduce Performance in Heterogeneous Environments] - Map/Reduce 在異質環境下的效能改良研究
   * [http://labs.google.com/papers/mapreduce.html MapReduce: Simplified Data Processing on Large Clusters] - Google 的 Map/Reduce 論文
 * [http://wiki.apache.org/hadoop/AmazonEC2 Hadoop Wiki 上關於 Amazon EC2 的使用說明]

 * [限制] Hadoop 0.18.3 不支援 Stream 下的數值排序 - [https://issues.apache.org/jira/browse/HADOOP-2302 Streaming should provide an option for numerical sort of keys]

== Cloud Computing and Science ==

 * 去年在 [wiki:jazz/09-01-10 eScience 2008] 看的一些演講錄影，現在論文也已經可以在 [http://ieeexplore.ieee.org/xpl/tocresult.jsp?isnumber=4736722 IEEE Xplore] 上找到了。
 * 這兩篇是講述將 !MapReduce 運用在生物資訊領域的實例。
   * [http://www.cs.umd.edu/Grad/scholarlypapers/papers/MichaelSchatz.pdf BlastReduce: High Performance Short Read Mapping with MapReduce]
   * [http://www.ece.rutgers.edu/~parashar/Classes/08-09/ece572/readings/cloudblast-escience-08.pdf CloudBLAST: Combining MapReduce and Virtualization on Distributed Resources for Bioinformatics Applications]
 * 跟虛擬化、生物影像、生物資訊、Mircoarray有關：
   * [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736753&isnumber=4736722 BioVLAB-Microarray: Microarray Data Analysis in Virtual Environment]
 * 有幾篇則跟 MapReduce 有關,如: [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736768&isnumber=4736722 MapReduce for Data Intensive Scientific Analyses]
 * 跟虛擬化有關的
   * [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736771&isnumber=4736722 Contextualization: Providing One-Click Virtual Clusters]
   * [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736759&isnumber=4736722 Characterizing User-level Network Virtualization: Performance, Overheads and Limits]
 * 跟生物統計 / R 相關
   * [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736775&isnumber=4736722 Biocep, Towards a Federative, Collaborative, User-Centric, Grid-Enabled and Cloud-Ready Computational Open Platform]
 * 此外，在 !SourceForge 上也有一些應用專案:
   * [http://apps.sourceforge.net/mediawiki/cloudburst-bio/ CloudBurst] - [http://developer.amazonwebservices.com/connect/entry.jspa?externalID=2272&categoryID=263 Amazon 上的 CloudBurst 專案介紹]
 * 當然我最關切的是"[http://blog.wired.com/wiredscience/2008/12/massive-amounts.html Amazon 提供公共資料庫]"的舉動對整個學術生態所造成的影響。此舉跟國網中心提供科學資料庫的定位十分相似，雖然 Amazon 在台灣區推廣有本土化方面的阻撓，但是如果真的有心朝國際化發展的話，台灣的學生應該要多學著使用這些服務，去做更大型的運算才對。[http://news.ycombinator.com/item?id=543069 這邊的討論]提供了許多參考連結。