Dina Research School

Workshop: XML technologies for storing and exchanging data

Tunekærgård Landboskole, 29-30 April 2004

Introduction

XML, or Extensible Markup Language, is a recent standard for representing data and exchanging data between people and between programs.

At first you may find it hard to think of a more boring topic for a workshop. But then you realize that the central innovation that brought the World Wide Web into existence ten years ago was HTML. And HTML is nothing but a standard for representing data and exchanging data between Web servers, Web browsers and people.

XML is related to HTML but much more widely useful. Some example uses of XML technologies include:

• storing, documenting and exchanging any kind of experimental data;
• representing the structure of molecules (Chemical Markup Language), including biomolecules;
• representing Bayesian networks and decision diagrams (XBN);
• representing biosequences such as DNA and proteins (NCBI Genbank);
• representing the result of biosequence database searches (NCBI Blast);
• representing gene expression experiments based on microarrays (Microarray Markup Language);
• storing text documents and spreadsheets (OpenOffice, and future versions of Microsoft Word and Excel);
• ... plus thousands of other uses.

The advantage of XML for storing experimental data is that the format is self-describing, text-based, and not proprietary. Today, experimental data are often stored as SAS datasets or in spreadsheets, but after some years it may be difficult to remember whether 1130 means 1130 minutes, or 11 hours and 30 minutes, or whether it is a code indicating something else altogether. Also, how would you read data from a 1988 Supercalc spreadsheet today? Experimental data that were expensive to collect get lost over the years because they were poorly documented or stored in proprietary binary formats.

XML and related technologies such as are open standards, maintained by the World Wide Web consortium (W3C).

This workshop will introduce XML and related technologies from the ground up and show how they can be used in relation to agricultural and biological research and practice.

The speakers include Anders Møller and Michael Schwartzbach from Aarhus University, widely recognized experts on XML technologies and developers; see http://www.brics.dk/~amoeller/XML/.

The workshop is aiming at

• Ph.D.-students in the agricultural and biological sciences whose work involves dataseries of some form and who are interested in learning about modern approaches to modelling and computation for dataseries.

• Ph.D.-students with a background in mathematics, computer science, or engineering who are interested in learning more about the applications in the biological sciences.

The DINA Research School is part of a Nordic cooperation. The workshop language will be English unless all participants have Danish as the first language.

We are looking forward to seeing you at Tune Landboskole!

Author: phd@dina.kvl.dk. Updated: 23 marts 2004