Expanding genomic data management to transform breeding across crops and institutes
The Genomic Open-source Breeding Informatics Initiative (GOBii) was created to combat the issue of barely increasing yields in developing countries within the last 10 years. Specifically this project was created to improve the breeding process of staple crops such as maize, rice, wheat, sorghum and chickpea. The main service GOBii provides is a large, fast database and multiple data analysis tools. However as the deployment and maintenance of the database is complex, smaller institutions without dedicated support systems often cannot use GOBii’s tools.
To overcome this problem I designed and implemented a configuration interface which allows easy modification of and expansion to a running GOBii instance, as well as simplifying the deployment process. The configuration tool is built into the existing user management tool Timescope and uses ZK for the user interface and Java for the programming logic.
The project is roughly split into three categories. Firstly we had the modification of user details, secondly the addition and deletion of crops and thirdly various backend operations. Modifying user details included changing credentials, as well as configuring associated email accounts and analysis tools. The second part of the project focused around crop operations, specifically adding the ability to easily add and remove crop information, as well as making sure that all the associated backend processes were created or deleted correctly. In the final stage of the project I implemented additional functionalities to ensure an overall more robust and operational program. This step included adding the ability to import and export settings, configuring automated data backups, increasing password security and providing detailed log reporting.
The configuration tool will help all current and future clients to function in a more autonomous manner as operations that used to take a dedicated tech support can now fully be performed locally. Furthermore as the program is highly modular and configurable it is easily expandable to future functionalities that might be requested by customers.
As somebody coming from a nearly exclusively computer science background I viewed this experience as a fantastic way of branching out into a new field. Through talking to my fellow interns and the weekly seminars I feel like I was able to learn about so many new topics, concepts and ideas within the wider scope of biology. These interactions enabled me to gain a better understanding of how much even such a relatively small field such as plant biology has to offer. As somebody who’s prior experience had mostly been limited to school projects I appreciated being granted this opportunity to see how to incorporate my computer science knowledge within the field of biology. I am especially thankful for the time my mentor and everyone in the GOBii lab took to make me feel comfortable and respected. Over the whole project I felt trusted and treated as a peer and not just an intern which allowed me to be able to perform to my best ability and grow from the experience. Being an intern here gave me insights and first hand experience in a real software development process, the wide spectrum of bioinformatics and the computational side of research. Overall I am incredibly grateful to GOBii and BTI for granting me this opportunity and I hope to continue being involved with (plant) biology in some shape during my masters degree.