We propose to develop a novel user interface to interact with biological applications. If successful, this will open new ways of interacting with biological entities such as genes, molecules, proteins and biological networks. Initially we would like to develop a systems biology prototype application which would allow drawing biological networks on smooth surfaces using an infrared pen. Based on infrared pen movements on the surface, the system will determine what entities and connections the user would like to draw or edit in the application. The user would also be able to select notations from the palette and drop it in the drawing area. These entities and diagrams would be stored in standard formats such as Extended Systems Biology Mark-up Language (SBML) in order to be exported and used in other biological applications. One of the major problems in the network design field is that often biological networks are very big and are difficult to visualise on a small screen. Our proposed application would be useful for projecting diagrams on a whiteboard and for editing them interactively. Our main focus in this project would be to employ algorithms to correctly identify infrared pen movements and to build a user friendly interface. We would also investigate the limitation and constraints of our proposed approach. For our prototype application we would implement a limited number of actions/gestures which could be performed through infrared pen and could be translated into biological notations. These biological notations would be displayed in our application on a computer screen. The main challenge would be to make sure that the system accurately understands infrared device movements and differentiates between different notations. Our proposed hardware for our application is very cost effective and easily available. For our application we will use the following hardware components:
1. Projector for displaying editor on a smooth surface.
2. Desktop or laptop computer for processing.
3. Infrared pen for interacting with the editor on a smooth surface. The infrared pen will emit infrared light which would be captured by the infrared sensor.
4. Wiimote for sensing the infrared light produced by the infrared pen.
This hardware approach was first proposed by Johnny Lee (http://johnnylee.net/projects/wii/Wiimote) in 2007. He used a wiimote infrared sensor to develop an inexpensive interactive whiteboard and finger tracking applications.
Who am I?:
Igor Goryanin, Shakir Ali, Hongwu Ma
How is it novel? What is exciting about it?:
Currently most bioinformatics and systems biology applications are confined to standard user interface actions such as keyboard and mouse clicks. These are not ideal solutions considering the fact that most biological entities are 3-dimensional. It is more natural to use a touch interface than a mouse or keyboard. The recent introduction of new gaming devices such as the Nintendo Wii, the Xbox and the PS3 have sparked renewed interest in new computing interfaces. Microsoft is planning to release Project Natal this year in which users would be able to interact with the system with their hands and body movements. We believe that in a few years time there will be a demand both in industry and research to employ similar technologies in all applications. The novelty of our system is to apply the latest human computer interaction techniques in the field of bioinformatics and systems biology. We believe that we will be the first group to introduce this kind of application in this area.
What will I do next? What opportunities will it open up?:
The next step would be to make our system compliant with Systems Biology Graphical Notation (SBGN) and to provide standard APIs. This will make it accessible to a wider community and allow other developers to integrate this interface with their applications and editors. We would also integrate this into widely used systems biology editors as a plug-in. It will also open up opportunities for further research and development.
What constitutes success? How risky is it?:
This project will be considered successful if we can build an application which can draw biological notations on a computer screen based on user input on a flat surface through an infrared pen. There are inherent risks which are associated with any research project. However, based on our strong experience in systems biology application development we are confident that the risk associated with this project is limited.
What resources do I bring to the project?:
Prof. Igor Goryanin is an expert in the Systems Biology field and an author of DBSolve, a software package for mathematical stimulation and analysis of cellular metabolism and regulation. He has also supervised the development of Edinburgh Pathway Editor, a visual editor for Systems Biology. His group brings knowledge of systems biology notation design, systems biology network modelling and systems biology software development. Dr. Hongwu Ma is a postdoc and has 9 years of experience in biological network analysis and modelling. He will be involved in analysis, design and testing of this application.
What resources and expertise do I need?:
We require a Research Assistant for 5 months to develop this project. We have already identified a suitable candidate for our project. Shakir Ali has worked for 4 years at the Edinburgh Centre for Bioinformatics. He has experience in management and development of bioinformatics and systems biology applications. He has also worked for more than 6 years in the software industry. Shakir will take part in analysis, design, implementation and testing of this product. The product will be developed in Java. We are asking for funding of 5 man-months for this Research Assistant to develop this project.
What shared resources, if any, will the project create?:
This will be an open source project and will be freely available to the research community. We plan to build standard APIs so that it could easily be integrated with other applications and editors.
What is the timescale?:
We propose a time scale of five months. This system would be developed in several stages:
1. Prepare hardware. Build and test driver for Wiimote infrared sensor connected to PC (1 month).
2. Develop program to infer different biological notations based on input signals. (1.5 month)
3. Develop an editor to display diagrams determined in step 2. (1 month).
4. Test system on different surfaces and environment. (1 month)
5. Fix bugs and release final product. (0.5 month).
