Institute for Immunology and Informatics - Bioinformatics Programmer

Title: Bioinformatics Programmer

Job Description

The Institute for Immunology and Informatics (I’Cubed) is a dynamic research institute pioneering vaccine discovery and development. The mission of I’Cubed is to apply the use of cutting- edge informatics tools to design new therapeutics and vaccines to treat and cure human diseases. Located on the Providence campus of the University of Rhode Island, the institute is expanding its science and technology based work force. I’Cubed currently seeks a candidate excited about contributing to cutting edge research projects in Computational Biology. This is a grant-funded, one year contract position.

The successful candidate will be an Bioinformatics IT Programmer/Website support developer who has a recent degree in CS and who will be responsible for implementing the vaccine design tools made available by EpiVax, Inc. on the URI interface. The EpiMatrix system, a set of tools to predict vaccine candidates, has been developed as an application of the Oracle database. The various EpiMatrix algorithms have been developed in Oracle’s PL/SQL and present a collection of application programming interfaces (APIs) to the application developer. The Bioinformatics programmer would continue the work begun on the iVAX project (a website to access the informatics tools): 1. Design and develop web portal infrastructure, including interface, registration and feedback applications; 2. Upload to, or link with, genome databases for neglected tropical diseases, where the tools may call up genome sequences. Make this interface seamless and user-friendly; 3. Design, develop, and deploy portlets (small applications designed to interact with the EpiMatrix APIs) for each of the vaccine design algorithms; 4. Release the completed website to a selected set of vaccine researchers for beta testing; 5. Survey beta testers to identify shortcomings within the portal including technical flaws (e.g., programming bugs), design flaws (e.g. cumbersome or restricted navigation and/or workflow restrictions), and shortfalls in content (e.g., missing but important capabilities, weakness or poor usability of report outputs, or insufficiently detailed or accessible documentation); 6. Upload genomes to the website (Malaria, Schisotsomiasis, Dengue) and debug the interface.

Applicants should value collaboration and teamwork while also being able to work individually and prioritize multiple projects. A high degree of professionalism, customer focus, and organizational skills is required.

Primary Responsibilities

· Enhancement of existing iVax web based applications in an HTML/JavaScript/Apache/Oracle PL/SQL environment.
· Application development, testing, documentation, and maintenance of new applications and application modules using HTML, JavaScript and PL/SQL or Java.
· Development and application of single use programs related to the summarization, analysis and presentation of project specific datasets.
· Construction, curation, and maintenance of data libraries related to the field of Computational Immunology.
Qualifications

I. Education: An undergraduate degree in computer science, engineering, math, or related discipline is required. Previous exposure to biology and/or bioinformatics is a required.
II. Experience: Experience in HTML based application development with some scripting language such as JavaScript, Java, Basic, PHP, or Python required. Experience with SQL and or Oracle PL/SQL a strong plus. Some knowledge of basic statistics or statistical packages such as SAS or SPSS is a plus. Experience with network administration in a mixed environment (Linux, Windows, OSX) is a plus.
III. General: Strong reading and writing skills, detail orientation, and strong work ethic are essential.
Other

This position offers a unique opportunity to the right candidate. A successful applicant can expect to benefit from many training and growth opportunities presented in a fast paced environment.
Please Contact: annied@uri.edu or Denice.Spero@gmail.com