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Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4.

by Holger Rohde, Junjie Qin, Yujun Cui, Dongfang Li, Nicholas J Loman, Moritz Hentschke, Wentong Chen, Fei Pu, Yangqing Peng, Junhua Li, Feng Xi, Shenghui Li, Yin Li, Zhaoxi Zhang, Xianwei Yang, Meiru Zhao, Peng Wang, Yuanlin Guan, Zhong Cen, Xiangna Zhao, Martin Christner, Robin Kobbe, Sebastian Loos, Jun Oh, Liang Yang, Antoine Danchin, George F Gao, Yajun Song, Yingrui Li, Huanming Yang, Jian Wang, Jianguo Xu, Mark J Pallen, Jun Wang, Martin Aepfelbacher, Ruifu Yang show all authors
The New England Journal of Medicine ()

Abstract

An outbreak caused by Shiga-toxinproducing Escherichia coli O104:H4 occurred in Germany in May and June of 2011, with more than 3000 persons infected. Here, we report a cluster of cases associated with a single family and describe an open-source genomic analysis of an isolate from one member of the family. This analysis involved the use of rapid, bench-top DNA sequencing technology, open-source data release, and prompt crowd-sourced analyses. In less than a week, these studies revealed that the outbreak strain belonged to an enteroaggregative E. coli lineage that had acquired genes for Shiga toxin 2 and for antibiotic resistance.

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Open-source genomic analysis of S...

0 7 4 0 - 7 4 5 9 / 0 5 / $ 2 0 . 0 0 �� 2 0 0 5 I E E E M a rc h / A p r i l 2 0 0 5 I E E E S O F T WA R E 1 1 E d i t o r : C h r i s t o f E b e r t ��� A l c a t e l ��� c h r i s t o f . e b e r t @ a l c a t e l . c o m W hen you work on a software project, you have to manage the bugs you find. At first, you might list them on a spreadsheet. But when the number of bugs becomes too large and a lot of people must access and input data on them, you have to give up the spreadsheet and instead use a bug- or issue-tracking system. Many software projects reach this point, espe- cially during testing and deployment when users tend to find an application���s bugs. Nowadays you can choose among dozens of bug-tracking systems. Some are commer- cial, others are open source projects such as the two we describe here. Bugzilla When Mozilla (www.mozilla.org), the large open source Web browser project, needed a bug- tracking system, its developers built their own��� Bugzilla, also an open source project. The first public release was written in Perl, and the open source community continues to improve it. Today, many users���including open source projects (Apache, Linux, Open Office) as well as private and public organizations (NASA, IBM)���are using Bugzilla. So, Bugzilla���s focus has changed from being a Mozilla tool to be- coming a general bug-tracking system. Using the tool Like any information system, Bugzilla���s main functions are for inputting and accessing data. When you log into the system, you can input new bugs or search for, track, or edit existing ones. Figure 1 shows part of the advanced-search win- dow, and Figure 2 shows a screen displaying a specific issue (a bug, enhancement, feature, task, or patch). To track a particular bug, you must be able to locate it. The Product, Component, Version, Status, and Reporter fields are related to track- ing, whereas the Summary, Status Whiteboard, Keywords, Severity, Attachments, and Depen- dencies fields are related to fixing it. These fields contain the data you must input when you���re reporting a bug and the data that helps you filter your searches. Another way to find information is through Bugzilla, ITracker, and Other Bug Trackers Nicol��s Serrano and Ismael Ciordia To err is human, and we learn from our mistakes. For software developers, this means knowing what the error is, resolving it, and learning from it. Bug-tracking systems help us do these tasks. This column looks at two specific open source products and provides useful hints for working with any bug-tracking tool. I look forward to hearing from you about this Open Source column and the products and tools you want to know more about. If you���d like to write for this column, see the author guide- lines at www.computer.org/software/author.htm or contact me. ���Christof Ebert
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1 2 I E E E S O F T WA R E w w w. c o m p u t e r. o r g / s o f t w a r e OPEN SOURCE Bugzilla���s reports, which describe the current state of the bugs, and charts, which describe an application���s state over time. Architecture Bugzilla is a Web application, so users interact only with its HTML pages. Al- though Bugzilla���s design principles state that it should support commercial data- bases, it works only with mySQL, a pop- ular open source database. Detailed in- formation about the installation process is available at www.bugzilla.org/docs. ITracker We���ve also worked with ITracker (http://sourceforge.net/projects/itracker), an issue-tracking system designed by Jason Carroll in 2002 to support mul- tiple projects with independent user bases. Its features resemble Bugzilla���s. The main difference is that it���s platform independent (because it���s a J2EE appli- cation) and database independent. Table 1 compares the two tools. Other tools Applied Testing and Technology���s Web site (www.aptest.com/bugtrack.html) of- fers a list of more than 70 bug-tracking tools���some commercial, some open source. Software configuration management applications provide several tools and methods to manage the life cycle of software products, so they contain bug- tracking systems as well as process management, configuration control, version control, and release manage- ment functions. Their prices and setup times are well above those of a focused bug-tracking tool, so SCM systems are actually applications of a different size. Example SCM systems include Clear DDTS, Rational ClearQuest, CM Syn- ergy, and Razor. CM Synergy provides good support for processes through a task-based process model and auto- mated operations for the change process. ClearQuest and Razor stress workflow management, with the option of cus- tomizing standard processes. Commer- cial issue-tracking systems such as TrackStudio let users define workflows for each type of issue. Figure 1. Part of an advanced bug search in Mozilla using Bugzilla. Figure 2. Bugzilla screen view of a specific issue (a bug, enhancement, feature, task, or patch).

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