Senior Development Engineer - Bioinformatics

Organization
University of Massachusetts Medical School
Job Location
Worcester, MA 01605
Salary
Yearly Salary
Job Description

Overview:

 

Located in Worcester, the University of Massachusetts Medical School (UMMS) is one of the fastest-growing academic health centers in the country and is home to the School of Medicine, the Graduate School of Biomedical Sciences and the Graduate School of Nursing. During the past four decades UMMS researchers have made advances in a broad range of disease families, from HIV and infectious diseases to cancer, genetic disorders, diabetes and immune disease. UMMS faculty discovered the link between the immune system and type-1 diabetes, found the genetic cause underlying the third-most-common form of the muscular dystrophies, established the fundamental difference between HIV and other retroviruses and co-discovered RNA interference (a gene-silencing process which has become a tool in research focused on such areas as diabetes, HIV/AIDS and cancer).

 

The last years has seen an explosion of large sequencing datasets. It is now common for a single experiment to generate hundreds of gigabytes of data. Sequencing has become the readout of choice for many assays ranging from transcriptional profiling (RNA-Seq), protein-nucleic acid interactions (ChIP and CLIP sequencing) and genotyping through exome or whole genome sequencing. Processing of these large datasets has become the challenge of genomics. The Bioinformatics Core brings “Big Data” analysis to the masses by:

 

1) Implementing state-of-the-art pipelines that can be run on a web interface while executing on a large high performance cluster.

 

2) Conducting a set of training sessions ranging from statistics, basic programming and data analysis “data-tons”.

 

Work in the bioinformatics core involves interacting with researches across campus to understand new informatics challenges, develop, implement or evaluate novel informatics tools and to teach informatics and statistics to non-technical audiences.

 MAJOR RESPONSIBILITIES:

  • Provides mentoring and knowledge transfer to Application Engineers including providing input to code reviews, training and developing staff Supports business process, problem analysis and consultation.
  • Excellent analytical and organizational skills with the ability to handle multiple project and timelines required.
  • Ability to work independently within guidelines, provide technical consulting on complex projects considering equipment capacity, limitations, operating time and desired results required.
  • Experience in formal Quality Review process, including but not limited to, instructing, directing, mentoring and reviewing other team members required.
  • Ability to ensure SDLC methodology is followed, including conducting inspections and post implementation reviews required.
  • Ability to create detailed technical design, code, test, debugs, document, and maintain applications required.
  • Knowledge of FTP and HIPAA compliant ANSI formatted EDI transactions required.
  • Work directly with the user and/or vendors to articulate and document user application needs.
  • Lead in the development of functional specifications, which articulate clearly and completely all project deliverables consistent with user expectations and vendor/third party needs.
  • Supervise the design, development, implementation, integration, production support, and continuous enhancement of applications to ensure reliable, integrated and stable information repositories.
  • Manage the development and maintenance of proper technical and user documentation for each system in a consistent and structured manner.
  • Ensure quality control through testing and debugging software for accuracy, completeness, and system integrity.
  • Interact effectively (verbally, written, etc.) with users, vendors and management to ensure delivery and use of application is consistent with agreed upon project goals.
  • Supervise and direct staff as assigned. Participate in recruiting and staff performance reviews as assigned.
  • Continue development of skills and expertise in present and emerging technologies by participating in formal training when possible and by independent self-teaching and tutorials.
  • Perform other duties as required.

REQUIRED QUALIFICATIONS:

  • Bachelor's Degree in Information Systems, Computer Science, a related field, or equivalent experience
  • 6 years of related experience
    • One or more of the following application development languages:
    • Strong object-oriented analysis, design and programming skills
    • Rapid Application Development experience
    • Demonstrated experience working Agile/Scrum framework
  • Solid interpersonal skills, with ability to work well with people of all levels of information technology expertise and comfort in varied organizational relationships.
  • Windows Services in managed code
  • Understanding of Windows Communication Foundation
  • Experience with WPF
  • Experience with SQL Serve 2008 databases
  • Experience writing multithreaded programs
  • Experience with cloud technologies and services
  • Experience using modern development processes/tools and developing through the complete Software Development Life Cycle
  • Experience converting functional requirements into technical requirements
  • Experience with Visual Studio 2010/2012 Team System is a plus
  • Excellent verbal and written communication skills
  • Excellent problem solving skills
  • C, C++
  • SQL

PREFERRED QUALIFICATIONS:

  • Java/Python/Perl/Awk application development languages
  • Extensive Linux knowledge
  • Web/Application servers: Apache, nginx
  • Web technologies: Javascript, JQuery, Ajax etc.
  • PHP5 or a web development knowledge with MySQL
  • Strong interest in Biology
  • Restful Web Service design and implementation
  • Amazon Web Services and Amazon
  • Docker
  • Pipeline, workflow design principles
  • PostgreSQL, Oracle and other open source database platforms
  • Familiarity with Sequencing Data analysis (RNA-Seq, ChIP-Seq, etc)
  • Familiarity with the Galaxy application
  • Understanding of Bowtie, BWA, Tophat, RSEM, STAR, third party analysis tools
  • Bioperl
  • Tomcat and other web servers

 

 Additional Information:

Why Join UMass Medical School?

The University of Massachusetts Medical School (UMMS) offers a very competitive compensation and benefits package including four weeks paid vacation, free tuition at any Massachusetts state school, a robust and affordable variety of health and dental plans, participation in the state retirement plan, and a rewarding environment driven by distinctive work in progressive education and research.

 

If challenging and competitive work in a fast paced environment appeal to you, consider sharing your talents with one of the fastest growing academic health centers in the country.

 

Ranked 5th in primary-care education and 48th in research among the United States' 125 medical schools in the 2014 U.S. News & World Report annual guide, "America’s Best Graduate Schools,” UMMS is also a world recognized research center. Beyond its core mission of distinction in health sciences education, UMMS has exploded onto the national and international scene as a major center for research with UMMS researchers making pivotal advances in HIV, cancer, diabetes, genetic disorders, infectious disease and in understanding the molecular basis of disease.

UMass Medical School is committed to being an equal opportunity and affirmative action employer and recognizes the power of a diverse community. We encourage applications from protected veterans, individuals with disabilities and those with varied experiences, perspectives and backgrounds to consider UMass Medical School as their employer of choice.
Review of applications will begin immediately and the position will remain open until filled.

 

Apply Here

How to Apply

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