pathFinder: A web-based tool for identifying possible Signal Transduction Pathways

Over the past several years the research of signal transduction pathways has received much attention from the fields of bioinformatics and biology alike. These pathways have been found to be key factors in many major cell processes and also have been discovered to play an important role in the function of numerous lethal diseases. In general, signal transduction pathways are processes in an organism where a cell converts one kind of signal or stimulus into another in order to transmit information. It is without a doubt the most common and effective way of transferring signals between distant cells in the body, and thus these processes play a huge role in our every day activities.

To aid in the research of these pathways, a web based tool 'pathFinder' was developed to identify all possible signal transduction pathways between given target and activator messengers. This process is done by referencing a list of known pairs to determine whether a path can be made. Each pair in the list is supported by references of research pertaining to their interaction, thus providing an advantage over other current tools in that each pair is somewhat validated, making the tool highly accurate. A baseline version of such tool has been developed and is currently being used, and certain improvements were implemented to make the tool more user friendly and efficient. These upgrades included making the system database driven as well as adapting the underlying structure of the system to the Struts MVC framework to make the system much easier to manage. Also, the ability for researchers to submit new dyds with available references for inclusion in the database was also added to make the program more interactive. Finally, a redesign of the layout of the website was done to further enhance ease and usability. Technologies used to complete these additions included an Oracle database managed through Toad software, implementation of the Struts MVC framework in J2EE software environment, web design including Tiles framework with Java Server Pages, validation framework, JavaScript, and algorithm development using the Java programming language.