This position will remain open until a successful candidate has been identified.
The NDEx Senior Developer will be one of the primary software engineers for the NDEx project, an open-source bioinformatics software project.
The mission of the NDEx project is to create infrastructure and applications to support the effective use of biological networks by the research, pharmaceutical, and clinical communities. The NDEx project has the potential to impact many aspects of biological research and drug development and is already being incorporated in projects in academia and industry.
The NDEx team has developed a web-service platform and associated interfaces and utilities. It creates applications based on those services and helps other researches build their own applications using NDEx services. The NDEx platform enables sharing, storing, accessing, and publishing biological knowledge as computable networks. The project manages a public website using the NDEx platform, providing a global resource for scientists and organizations (see www.ndexbio.org for more details).
The NDEx Senior Developer will be a key technical expert for the NDEx development team, solving problems that are both technically and scientifically challenging for a large and varied community of users.
This role requires an individual who can take initiative and provide leadership in both the design and implementation of project software and in understanding the needs and use cases of the users of the NDEx platform. The NDEx project uses diverse technologies to deliver high-performance access to the stored networks and to implement front-end integration with web-based interfaces and visualization.
The position requires the flexibility to work with the core NDEx large-scale bioinformatics database, the web services that access that database, and the interfaces, applications and utilities using those web services. The NDEx Senior Developer will work with front-end interface, and back-end service and database technologies and must be able to rapidly acquire skills in new programming languages, packages, and databases.
The NDEx Senior developer will work closely with other members of the development team and will interact with scientists using NDEx to gather requirements for system extensions and applications.
The NDEx Senior Developer will design, implement, and extend software including:
- Core NDEx server and database software, including database schemas and REST web service APIs.
- Metrics, measurement systems, and logging utilities to assess and monitor system performance.
- Web client applications using NDEx, including the primary NDEx user interface deployed on the public website
- NDEx-related applications software, such as Cytoscape Apps, example applications, NDEx utilities.
- System administration utilities and procedures for public and internal servers of the project.
- Utilities for software testing, deployment and distribution.
- Utilities for database management, backup, migration, and recovery.
The NDEx Senior Developer will interface with colleagues from project sponsors, and with collaborators both within the UCSD community and worldwide.
The NDEx Senior Developer will work in a fast-paced environment and will be responsible for meeting deadlines, working both independently and with the NDEx team. The developer must be able to communicate clearly in a team environment, to solve complex problems in a timely manner, and to share technical knowledge with other members of the team.
The target audience of the NDEx project will be biologists and developers creating applications for biologists, and so the NDEx Senior Developer will need to understand the modeling of complex biological concepts in the course of requirements gathering, example application development, and test development.
Undergraduate or Graduate Degree in computer science or related area, plus 10 (ten+) or more years of work or research experience in software development.
Demonstrated two (2) years of experience in at least one of the following scripting languages: Python, R, Matlab.
In-depth knowledge of bioin