University of Delaware Bioinformatics Software Engineer in Newark, Delaware

University of Delaware

Job Title: Bioinformatics Software Engineer
Job ID: 104179
Location: Newark, DE

Bioinformatics Software Engineer, Center for Bioinformatics & Computational Biology- Computer & Information Sciences, College of Engineering

DEADLINE: December 5, 2016

Pay Grade: 31S


Under the limited direction of the Edward G. Jefferson Chair Professor and Director of the Center, the Bioinformatics Software Engineer will assume responsibilities for leading and developing bioinformatics systems and software tools supporting a number of grant-funded projects (listed below), as well as several collaborative projects being established.

  • NIH/2R01GM080646-10: PRO: A Protein Ontology in OBO Foundry for Scalable Integration of Biomedical Knowledge
  • NIH/1U01GM120953-01: Semantic Literature Annotation and Integrative Panomics Analysis for PTM-Disease Knowledge Network Discovery
  • NIH/1U01HG008390-01: MACE2K-Molecular and Clinical Extraction: A Natural Language Processing Tool for Personalized Medicine
  • NIH/1U54HL127624-01: BD2K-LINCS DCIC eDSR: Collaborative Resource for LINCS Panomics PTM Knowledge Network

The candidate will be expected to work in a team environment, working closely with collaborating investigators across partner institutions, as well as informatics and scientific team members and student trainees at the Center for Bioinformatics & Computational Biology to achieve goals. The candidate will be responsible for the development of computational framework, software tools, databases and web portals, from system design and implementation to integrative testing and dissemination. The resources developed will support research activities at the Center for Bioinformatics & Computational Biology and its broad research and user community.

  • Coordinate closely with the bioinformatics team to further develop the PRO protein ontology resource, iPTMnet post-translational modification network resource, iProLINK text mining systems, as well as new collaborative bioinformatics resources being established.
  • Drive development of bioinformatics databases, data analytics and text mining tools, as well as web interfaces for searching, browsing and visualization.
  • Drive development of system workflows to incorporate new software modules, analysis tools, functional features and new data types and data sources, and to improve system performance, integrity, accessibility, scalability and interoperability.
  • Provide technical guidance and leadership to project team members and student trainees, oversee detailed documentation of all development and analysis activities, including standard operating procedures for analysis pipelines developed.
  • Work with multidisciplinary collaborating investigators to determine and specify new bioinformatics analysis needs, develop new functional requirements, and prototype and document these needs.
  • Maintain a broad knowledge of state-of-the-art technology, software, and systems relevant to job duties. Make recommendations as to potential technological improvements.
  • Perform miscellaneous job-related duties as assigned.

  • Master's degree in Computer Sciences or Bioinformatics.
  • Minimum of seven years of working experience in software engineering, with specialization in software development, data management, bioinformatics and machine learning.
  • Minimum of four years of working experience in bioinformatics database and software analysis pipeline development.
  • Knowledge and familiarity with major bioinformatics resources and analysis tools, biomedical ontologies, and statistical packages for functional interpretation of genomics, transcriptomic and proteomic data and construction of systems biology networks.
  • Broad experience with all phases of software development life cycle.
  • Proficiency in relational databases, including MySQL/MariaDB and Oracle.
  • Proficiency in programming languages Java, Python, Perl, R, PHP, JSP, Javascript, HTML/CSS.
  • Experience with bioinformatics programming and software development in various systems environments: Unix/Linux, OSX, Windows, HPC Cluster, AWS.
  • Proven ability to work independently and collaboratively in a team research environment, coordinating computing activities with the faculty, students and staff users, particularly with multidisciplinary audiences.
  • Ability to make procedural decisions and judgments, analyze and solve problems, and prioritize, plan and organize work.
  • Excellent oral and written communication skills.
  • Knowledge and familiarity with the operation and structure of University standard word processing, presentation, database, electronic mail, and spreadsheet software packages; networking, server hardware and software; and knowledge of current technological developments.

How To Apply

When applying please submit a one-page cover letter and your resume as one document. Also, please remember to provide names, addresses and telephone number of at least three references in the online application.

Equal Employment Opportunity

The University of Delaware is an Equal Opportunity Employer which encourages applications from Minority Group Members, Women, Individuals with Disabilities and Veterans. The University's Notice of Non-Discrimination can be found at