ERIS HPC Support Specialist

Go to the Partners careers page to apply online. Job ID is 3014876

About Us

As a not-for-profit organization, Partners HealthCare is committed to supporting patient care, research, teaching, and service to the community by leading innovation across our system. Founded by Brigham and Women’s Hospital and Massachusetts General Hospital, Partners HealthCare supports a complete continuum of care including community and specialty hospitals, a managed care organization, a physician network, community health centers, home care and other health-related entities. Several of our hospitals are teaching affiliates of Harvard Medical School, and our system is a national leader in biomedical research. 

We’re focused on a people-first culture for our system’s patients and our professional family. That’s why we provide our employees with more ways to achieve their potential. Partners HealthCare is committed to aligning our employees’ personal aspirations with projects that match their capabilities and creating a culture that empowers our managers to become trusted mentors. We support each member of our team to own their personal development—and we recognize success at every step. 

Our employees use the Partners HealthCare values to govern decisions, actions and behaviors. These values guide how we get our work done: Patients, Affordability, Accountability & Service Commitment, Decisiveness, Innovation & Thoughtful Risk; and how we treat each other: Diversity & Inclusion, Integrity & Respect, Learning, Continuous Improvement & Personal Growth, Teamwork & Collaboration. 

General Overview 

Do you thrive on variety and innovation in your daily work? On interaction with world-leading investigators? On working at the interface of *Omics and scientific computing? For information/inquiries: hpcsupport(at)partners(dot)org. 
The Division of Enterprise Research IS (ERIS is seeking a Scientific Computing Project Specialist to work within our High Performance Computing (HPC) and Big Data group to support the bioinformatics and analytics needs of Massachusetts General Hospital (MGH), Brigham and Women’s Hospital (BWH), McLean and their affiliates of the research/teaching hospitals of Harvard Medical School. This position will have a broad range of responsibilities including: innovation of the overall Informatics/Application Services including expansion of current and new application services and training; working within and improving large HPC systems; interaction with internationally recognized scientists and researchers in consulting and integrating their applications/algorithms into the HPC environment. Scientific areas include genetic analysis, next-gen sequencing (RNA-seq, Chip-seq, exome and microbial sequencing and analysis), with emergent fields of functional neuro-imaging, cryo-EM, etc; and troubleshooting and tuning informatics pipelines with investigators for their efficient. Platforms and tech installed within the Linux (predominately) and Windows clusters include Galaxy Servers, Matlab, many biological databases (NCBI, GoldenPath, Ensembl…), GP-GPU clusters, sequence analysis algs, and SMP environments. Typical applications include large-scale genetic/genomic sequencing analysis (Microbiome, Cancer Genome, Clinical Sequencing), biomedical image analysis and visualization using various in-house developed or commercial parallel computing applications. 

The unifying characteristics of the position are an eagerness to quickly learn, apply and integrate new technologies and techniques of High-Performance and Parallel Computing with Bio/Chem/Neuro/Path-informatics to support ERIS in its mission to enable world-leading research discovery by renowned leaders in their scientific fields. ERIS has recently launched the IDEA (Integrated Data Environment of Analytics) Platform for Data Science. Versatility and breadth in computationally intense scientific and informatics skills, ability to work independently, outstanding customer service and training skills, and the ability to help teams and projects successfully accomplish their research objectives will be your successful qualities in this role. Candidates are not expected to be deeply knowledgeable in all areas, but must demonstrate the ability and motivation to learn. Ideal candidates thrive on variety and innovation in their daily work, on interaction with leading investigators, adept communicators, and on working with a wide range of technologies in an academic environment. 


  • Work within a focused team to support users in all aspects of their scientific computing needs, techniques and software for biomedical research. 
  • Working with the team: project management of departmental and enterprise projects; participate in architecting and designing systems and services. 
  • Own and manage scientific computing software suites: Matlab, galaxy, cluster-installed apps/algs/libraries/data. 
  • Work directly with faculty, physician-scientists and application/informaticians in designing, prototyping/testing, tuning for parallelization, problem analysis, and documenting analytical pipelines. 
  • Liaise as scientific/informatics solutions subject matter expert for Harvard Medical School, Massachusetts General Hospital, Brigham and Women’s Hospital, McLean and Dana Farber Cancer Institute researchers, faculty and technical staff. 
  • Respond to user’s request for direct support of applications troubleshooting by use of collaborative and traditional technologies (CRM-tools, phone, in-lab, web-conferencing, etc). 
  • Develop relationship with and work closely with industry in delivering solutions and fostering partnership opportunities for enabling the HPC-informatics ecosystem, including applications, algorithms and tools. 
  • Transferring knowledge and promoting new technologies within user community through seminars, one-on-one help sessions and wiki documentation: good presentation, training and documentation skills, essential. 
  • Assist users to install, configure and/or script informatics tools and applications, understanding and guiding work and data flows for their analysis. 
  • Linux, UNIX administration and Windows administration or other responsibilities as appropriate. 
  • Uses the Partners HealthCare values to govern decisions, actions and behaviors. These values guide how we get our work done: Patients, Affordability, Accountability & Service Commitment, Decisiveness, Innovation & Thoughtful Risk; and how we treat each other: Diversity & Inclusion, Integrity & Respect, Learning, Continuous Improvement & Personal Growth, Teamwork & Collaboration. 


  • Bachelor’s Degree in Computer Science or related field required. MS in a Computational Science, Bioinformatics or equivalent experience in biomedical research highly desirable. 
  • A combination of education and experience may be substituted for requirements. 
  • 5+ years mix of development or management of informatics applications and web services on Unix/Linux systems. 
  • 3+ years of strong scripting or programming experience in at least three of the following: R, Python, Perl, C/C++/C#, Matlab, Java, Ruby, SQL. 
  • Strong knowledge of Linux/UNIX systems, Windows (HPC) Server also desirable. 
  • 3+ years of demonstrated experience using computational clusters, HPC and/or grid computing environments. 
  • Strong Knowledge of one of the following scheduling systems, LSF, Sun Grid Engine or PBS. LSF preferred. 
  • 3+ years experience supporting/developing informatics systems in higher education, academic medical center, or healthcare-related company preferred. 
  • Experience supporting related components of 3rd-party and open-source applications (including Galaxy, cufflinks/bowtie/tophat, Matlab, GenePattern) 
  • Bioinformatics, RHEL certifications a plus. 

Skills, Abilities, Competencies 

  • Ability to work independently and demonstrate excellent project management and communication skills with a strong demonstration of commitment to customer service. 
  • Comfortable working in a dynamic environment and developing flexible solutions to meet evolving requirements--ability to multitask and prioritize work requirements with minimal supervision. 
  • Demonstrated ability to work seamlessly within a team, while exhibiting a high level of initiative and professionalism. 
  • Demonstrated willingness to learn new technologies. 
  • Ability to multitask and prioritize work requirements and projects, working in support of a distributed workforce. 
  • Exceptional problem solving and negotiation skills. 
  • Excellent interpersonal skills, including written and verbal, to effectively and professionally communicate with cross functional teams including staff at all levels of the organization including both technical and non-technical personnel. Ability to successfully negotiate and collaborate with others of different skill sets, backgrounds an levels within and external to the organization.  
  • Expert knowledge of HPC environments and computational techniques (MPI/OpenMP/GPGPU/CUDA). 
  • Advanced knowledge of two of the following fields; computational biology/chemistry, bioinformatics, cheminformatics, neuroinformatics, medical informatics or related areas 
  • Advanced knowledge of tools such as Galaxy, GenePattern, Accelrys, BioConductor, and NCBI/GoldenPath/Ensemble repositories and tools, Chipster, etc. 
  • Advanced knowledge or use of Analytical software platforms used in scientific investigation: Matlab, eHits, SAS. 
  • Knowledge of Next Generation Sequencing (NGS) pipelines is desired 

Working Conditions 
Standard office environment with possible local travel to Partners sites. 
As projects and priorities dictate, may be required to work occasional non-standard hours to support major projects. 
Ability to lift computer-related equipment up to 25 pounds. 

Supervisory Responsibility 

No direct reports; may indirectly provide leadership and guidance to less seasoned and new staff 
EEO Statement Partners HealthCare is an Equal Opportunity Employer & by embracing diverse skills, perspectives and ideas, we choose to lead. All qualified applicants will receive consideration for employment without regard to race, color, religious creed, national origin, sex, age, gender identity, disability, sexual orientation, military service, genetic information, and/or other status protected under law. 

Primary Location: MA-Charlestown-OCC-PHS
Work Locations: OCC-PHS One Constitution Center  Charlestown 02129
Job: IT Project Management
Organization: Partners HealthCare(PHS)
Schedule: Full-time
Standard Hours: 40
Shift: Day Job
Employee Status: Regular
Recruiting Department: PHS Information Systems
Job Posting: Apr 26, 2016

Go to the Partners careers page to apply online. Job ID is 3014876