= 2009-04-06 =

 * 演講準備 - 蒐集 HPC, Cloud Computing, MapReduce 與生物資訊相關運用參考資料

 * [https://sourceforge.net/projects/octaveoncloud/ Octave as Cloud Service] -  Octave 是一套類似 Matlab 的自由軟體，其實這個專案的 idea 挺不錯的，教學上如果多採用 Octave 的話，就不會造成學校或實驗室在 Matlab 授權/非法侵權的問題。當然我覺得如果熟悉網頁設計跟 VNC 這個服務應該不難做出來才對。

 * [http://developer.amazonwebservices.com/connect/entry.jspa?externalID=609&categoryID=88 Elasticfox] - Firefox Extension for Amazon EC2

 * [http://www.debian.org/devel/wnpp/ Debian Work-Needing and Prospective Packages] - 提報 Debian 打包需求的做法

== Clustering / Distributed Computing / Bioinformatics ==

 * [https://sourceforge.net/search/index.php?words=trove%3A(252)+AND+trove%3A(141)&type_of_search=soft&pmode=0&filtermanip=1&gfload=&gfnew=&inex=1&sortselect=has_file%3Atrue&registration_date__0=&trove__225=456&trove__274=369&trove__160=584&trove__199=426&trove__13=14&trove__1=534&trove__6=7&trove__496=499&newfilter=Apply 同時歸類在 Bioinformatics 與 Clustering 又有檔案可以下載的 SourceForge 專案]
   * [http://lucene.apache.org/java/2_3_1/queryparsersyntax.html SourceForge 搜尋關鍵字的語法是用 Lucene]

 * [http://hubris.ucsd.edu/dapper/ Dapper] - The Distributed and Parallel Program Execution Runtime
   * 在 !SourceForge 的 Clustering Topic 軟體中，Ranking 算蠻高的。
 * [http://proactive.inria.fr/ ProActive] - Open Source middleware (OW2 consortium) for parallel, distributed, multi-core computing. - 法國的一個專案，目的似乎在簡化建立平行/分散/多核心叢集的工作
 * [http://gridder.sourceforge.net/ Gridder] - 基於 Globus 的 Web Service Portlet ... 跟 Grid Portal 很像 :p
 * [http://www.uscms.org/SoftwareComputing/Grid/WMS/glideinWMS/ glideinWMS] - The glidein based WMS

== Open Source : Bioinformatics ==

 * [http://libseq.sourceforge.net/  C++ Bio Sequence Library] - C++ 版本的序列分析函式庫
 * [http://biospice.sourceforge.net/ Bio-SPICE] - Biological Simulation Program for Intra- and Inter-Cellular Evaluation
   * 在電子電機領域，SPICE 是非常重要的一套模擬軟體。Bio-SPICE 應該是一套希望在生物方面佔有一席之地的模擬軟體。
 * [http://bioera.net/ BioEra] is DSP visual designer that can be used to create interfaces between human being and a machine with using bio signals like EEG, QEEG, HEG, EMG, ECG, GSR, EOG, visual/sound entrainment and others. - !BioEra 跟腦科學應該有蠻強的關聯性，主要功能是在做訊號處理。
 * [https://sourceforge.net/projects/ncbiviewer/ NCBI Viewer] - [http://ncbiviewer.bravehost.com/ 新的官方網站] - NCBI 
 * 從 [http://www.bioinformatics.org/ Bioinformatics Organization] 又找到好幾個生物資訊的自由軟體專案
   * [http://www.open-bio.org/ Open Bioinformatics Foundation]
   * [http://www.bioperl.org/ BioPerl]
   * [http://biopython.org/ Biopython]
   * [http://biophp.org/ BioPHP] - PHP for Bioinformatics
   * [http://www.bioruby.org/ BioRuby] - Open source bioinformatics library for Ruby
   * [http://biojava.org/ BioJava]

== 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 MapReduce 教程]
   * [http://www.eecs.berkeley.edu/Pubs/TechRpts/2008/EECS-2008-99.html Improving MapReduce Performance in Heterogeneous Environments] - MapReduce 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 MapReduce 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]
   * [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736757&isnumber=4736722 An Extensible, Scalable Architecture for Managing Bioinformatics Data and Analyses]
   * [http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4736722&arnumber=4736800&count=180&index=70 Imagery Data Mining: The IDEC Experiment]
   * [http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4736722&arnumber=4736741&count=180&index=11 Lowering the Barriers to Cancer Imaging]
 * 有幾篇則跟 !MapReduce 有關,如: 
   * [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736760&isnumber=4736722 MRPGA: An Extension of MapReduce for Parallelizing Genetic Algorithms]
   * [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736768&isnumber=4736722 MapReduce for Data Intensive Scientific Analyses]
   * [http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4736722&arnumber=4736879&count=180&index=149  MRGIS: A MapReduce-Enabled High Performance Workflow System for GIS] - 拿 MapReduce 來處理 GIS 的 Workflow
 * 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]
 * 有講 Web 2.0 與生物資訊的關係
   * [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736827&isnumber=4736722 BioMashups: the new world of exploratory bioinformatics?]
   * [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736842&isnumber=4736722 Bio-Sense: A System for Supporting Sharing and Exploration in Bioinformatics Using SemanticWeb Services]
 * 其他有趣的主題
   * [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736849&isnumber=4736722  An Educator's Perspective on Cyberinfrastructure] - 站在教育者的立場來看 Cyberinfrastructure，他們是如何在教室裡運用這些資源呢??
   * [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4736747&isnumber=4736722 Scalable Semantics – the Silver Lining of Cloud Computing] - 純講 Cloud Computing 的商業未來
   * [http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4736722&arnumber=4736810&count=180&index=80  Mobile e-Lab: A Mobile Personalized Virtual Research Computing Environment] - Mobile Computing 相關
   * '''[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4736722&arnumber=4736854&count=180&index=124 Why Good Software Sometimes Dies – And How to Save It]''' - 這一篇我覺得最有趣，為什麼好的軟體有時候會死掉呢?!在商業競爭的環境下，很多軟體叫好但是不叫座，往往重視行銷的'次級品'反而大行其道，佔據非常高比例的市場佔有率。
   * [http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4736722&arnumber=4736855&count=180&index=125  Towards Making BOINC and EGEE Interoperable] - 講述如何整合 BOINC (Desktop Grid) 與 EGEE (Service Grid) 的做法
 * 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。