Research Software Developer

Oregon Health & Science University
Department of Medical Informatics and Clinical Epidemiology
United States Oregon Portland
www.ohsu.edu/xd/education/schools/school-of-medicine/departments/clinical-departments/dmice/

Description

Our group is a part of an NIH supported, internationally collaborated Reactome project, the most comprehensive, open source biological pathway knowledgebase, widely used in the community for Systems Biology data analysis and visualization. We have an immediate opening for a software programmer with strong Java programming experience. As a research programmer, you will be working on a newly NIH funded project to develop a Reactome portal for the NIH Illuminating the Druggable Genome (IDG) Program by integrating Reactome web-based widgets with large data sets covering understudied proteins in the context of biological pathways and networks in a cloud computing environment. Extensive and solid Java programming experience is required.

Responsibilities:
• Develop new features to existing Reactome GWT widgets to display a variety of data sources to support visualization of understudied proteins in the context of pathways and networks
• Develop a server-side application to integrate multiple data sources to support prediction of functional interactions among proteins
• Maintain the code using GitHub and document the source code by following standard procedures in software development
• Work with a global team to expand the reach of Reactome into the community
• Assist in preparing progress reports, scientific manuscripts, and new grant applications


Qualifications

Required Qualifications:
• Bachelor’s degree with courses in computer science and biology and at least 3 years of experience in the field
• Or Master’s degree in Bioinformatics or Computer Science with at least 1 year of working experience in the field
• Solid and strong experience in Java and object-oriented programming by following standard programming conventions and best practice
• Working experience in Linux, apache tomcat, SQL database and/or no-SQL database
• Experience of working in a team environment with a distributed source code management system (e.g. GitHub) and daily communication
• Self-motivated, willing to learn new things, and enjoy working in a globally distributed team environment

Preferred Qualifications:
• Working experience with GWT
• Working experience in MySQL and Neo4j databases
• Experience with Spring and Hibernate
• Programming with Java Swing and JavaScript
• Experience with Amazon AWS
• Some experience with machine learning and R is a plus


Start date

As soon as possible

Start date

To be determined

How to Apply

Please send your application cover letter, CV, and three reference letters to wug@ohsu.edu.