Suggestion for a new JSBML Beginners Guide

Using the existing JSBML documentation material (http://sbml.org/Software/JSBML/docs; the JSBML User Guide, the JSBML Tutorial, and JSBM`s Java API documentation) in a software development project for bachelor students we tried to evaluate how suitable this material is for students that start to learn how to use JSBML.

This evaluation reveals that the existing material is only of limited use for teaching beginners. The JSBML User Guide was described as to extensive and difficult for a beginner. The students preferred the structure of the JSBML Tutorial which combined explanatory text with small examples and exercises. But the limited number of topics in this tutorial was criticized. This underlines the need for new teaching material that is suitable for beginners.

Based on our experience from the software development project we suggest to write a new JSBML Beginners Guide. This Guide should provide an Eclipse-based introduction to reading, creating, manipulating and writing SBML files with JSBML. The structure of this new JSBML Beginners Guide will be similar to the one of the JSBML Tutorial i.e. combining explanatory text with small examples and exercises.

The new JSBML Beginners Guide should cover the following topics:

1. installing Java; obtaining JSBML; installing and setting up Eclipse
2. where to find information about JSBML packages, classes, methods … -> JSBML's Java API documentation; SBML.org
3. a quick introduction to SBML
4. reading an SBML document; get and isSet methods
5. creating, manipulating and writing an SBML document; set and unset methods; TidySBMLWriter
6. math elements in JSBML
7. validating an SBML document
8. how to use the ModelBuilder
9. advanced features of JSBML: how to annotate a model, the filter method, ...
10. SBML Level 3 packages: which packages exist and how to use them
11. using JSBML in other programming languages than Java
12. Frequently Asked Questions