ecerami.com

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cBio @ MSKCC

O'Reilly.com

Springer Online

Cytoscape.org

JDAS

Carla Cerami Hand (My sister!)

Welcome to ecerami.com. My name is Ethan Cerami, and I am a Senior Software Engineer at the Computational Biology Center at Memorial Sloan Kettering Cancer Center. Thanks for stopping by!

• Cytoscape: I am an active contributor to Cytoscape. Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks.
• cPath: cPath is an open resource for storing biological pathways, created at cBio.

By Ethan Cerami, Springer-Verlag

XML for Bioinformatics aims to provide biologists, software engineers, and bioinformatics professionals with a comprehensive introduction to XML and current XML applications in bioinformatics. The book assumes no background in XML, and take readers from basic to intermediate XML concepts. Core topics include: fundamentals of XML, creating XML grammars, web services via SOAP, and parsing XML documents in Perl and Java.

Companion Book Web Site (with all examples)

Order from Amazon.com

 

By Ethan Cerami, O'Reilly & Associates

Book Description from O'Reilly: This concise book gives programmers both a concrete introduction and handy reference to XML web services. It explains the foundations of this new breed of distributed services, demonstrates quick ways to create services with open-source Java tools, and explores four key emerging technologies: XML-RPC, SOAP, UDDI, and WSDL. If you want to break through the Web Services hype and find useful information on these evolving technologies, look no further.

Book Web Site

Book Examples

Free sample Chapter 6: WSDL Essentials.

By Ethan Cerami and Simon St.Laurent, McGraw-Hill.

Book Description from McGraw-Hill: Building XML Applications provides developers with a solid introduction to XML and key programming tools for building robust, scalable XML applications in Java. After a thorough introduction to XML's place in the developer's toolkit and its syntax, Building XML Applications presents detailed coverage of parsers, a key tool for developers. Focusing on Java development, the sample applications use the Simple API for XML (SAX) to create parser-independent solutions that can fit in a wide variety of situations. Other XML tools, like style sheets, namespaces, linking, and the Document Object Model (DOM) are also explored, giving developers a friendly but approachable introduction to these revolutionary technologies.

 

RESTful Error Handling
Unlike SOAP, REST-based web services do not have a well-defined convention for returning error messages. What's a developer to do?  December 1, 2003

Back to the Memex
In 1945, Vannever Bush described the Memex, a machine which closely resembles the World Wide Web of today. We have come a long way, but we still fall short of Bush's vision. Sep. 25, 2003

Web Services for Bioinformatics
Ethan Cerami explores two bioinformatic Web Services you can try out today -- XEMBL and BQS -- and shows code examples of how the interfaces work.  May. 14, 2002

Top Ten FAQs for Web Services
Ethan Cerami, author of Web Services Essentials answers ten of the most frequently asked questions about Web services, from what one is to how you can get started.  Feb. 12, 2002