Database Solutions for Biological Systems

Abstract

Abstract - Database Solutions for Biological Systems

My thesis is about Database Solutions for Biological Systems. I present some background information about di erent technologies like XML, languages de ned in XML, databases and architecture types. I also present several solutions for a model repository. The last part of my thesis is the actual implementation of a model repository which I have called the Biological Model Repository (BMR). Only one solution is implemented.

Part I - Languages The essential part of my thesis are the languages de ned in XML that are used as the basis of storage in my application. The languages are MathML and SBML. MathML is a mathematical markup language that is de ned in XML, while SBML (Systems Biology Markup Language) is a biological markup language that is also de ned in XML. SBML use a subset of MathML operators to express mathematical functions, and is mainly used as a tool to facilitate the rAbstract - Database Solutions for Biological Systems My thesis is about Database Solutions for Biological Systems. I present some background information about di erent technologies like XML, languages de ned in XML, databases and architecture types. I also present several solutions for a model repository. The last part of my thesis is the actual implementation of a model repository which I have called the Biological Model Repository (BMR). Only one solution is implemented. Part I - Languages The essential part of my thesis are the languages de ned in XML that are used as the basis of storage in my application. The languages are MathML and SBML. MathML is a mathematical markup language that is de ned in XML, while SBML (Systems Biology Markup Language) is a biological markup language that is also de ned in XML. SBML use a subset of MathML operators to express mathematical functions, and is mainly used as a tool to facilitate the research in Systems Biology.

Part II - Implementation The second part of my thesis is about the implementation of a model repository that can store SBML models. The BMR is implemented using J2EE speci cations and a backend database. I have used EJB to de ne both the model (database) and the bussines logic. As a GUI I have used a combination of Java Servlets, JSP and pure HTML. The code needs a jboss server with a integrated Tomcat container in order to work. The result is a web based model repository with the possibilities to store and view models. A beta version if the BMR is available for downlaod at the following adress http://folk.uio.no/michalst/bmr-dist/. 1esearch in Systems Biology. Part II - Implementation The second part of my thesis is about the implementation of a model repository that can store SBML models. The BMR is implemented using J2EE speci cations and a backend database. I have used EJB to de ne both the model (database) and the bussines logic. As a GUI I have used a combination of Java Servlets, JSP and pure HTML. The code needs a jboss server with a integrated Tomcat container in order to work. The result is a web based model repository with the possibilities to store and view models. A beta version if the BMR is available for downlaod at the following adress http://folk.uio.no/michalst/bmr-dist/.