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Associate Bioinformatician


Apply now Job no: 502756
Position Type: Staff
Location: Boston Main Campus
Categories: Information Technology Services

About Northeastern:

Founded in 1898, Northeastern is a global research university and a world leader in experiential learning. The same commitment to connecting with the world drives our use-inspired research enterprise. The university offers a comprehensive range of undergraduate and graduate programs leading to degrees through the doctorate in nine colleges and schools. Our campuses in Charlotte, N.C., San Francisco, Seattle, and Toronto are regional platforms for undergraduate and graduate learning and collaborative research. Northeastern pursues advanced research in security and materials at the Innovation Campus in Burlington, Massachusetts, and in coastal sustainability at the Marine Science Center in Nahant, Massachusetts.

 

About the Opportunity:

The Research Computing (RC) team at Northeastern University (NU) seeks a motivated, self-starting individual to be a member of our dynamic team as an Associate Bioinformatician. The successful candidate will be a key link between the RC team and the research community at NU, including faculty and students across a broad range of departments, as well as outside users and partners, in order to help them understand and utilize RC resources for their research and teaching.

As an Associate Bioinformatician at NU, your primary objective will be to support and enhance the research enterprise through direct interaction with faculty and students.  You will assist research groups in taking full advantage of Discovery, NU’s 1,700+ node HPC cluster installed at the Massachusetts Green High Performance Computing Center.  You will help with optimization of code and leveraging of scheduler features to maximize throughput of jobs.   In addition, you will work with research groups to help identify, implement and improve their computational and data workflow, as well as assist in facilitating computing and data infrastructure solutions specific to Northeastern University researchers.  As a PhD level scientist, you will also participate in grant funding opportunities, and author research papers and presentations, with faculty members at Northeastern University.

 

Responsibilities:

Software and Infrastructure Support

  • Partner with scientist and research staff to efficiently and effectively use NU HPC clusters at MGHPCC, to be expanded to over 10,000 cores with high bandwidth, low latency interconnects, and 3+ petabytes of data storage
  • Work with research groups to help identify, implement, and improve their computational and data workflows; assist in facilitating computing and data infrastructure solutions specific to NU researchers
  • Participate in the research and deployment of new technologies such as GPUs, Big Data and ML technologies (Hadoop, Tensorflow, etc), and cloud computing resources (AWS, Azure, GCP)
  • Develop effective pipelines for high throughput analysis, maximizing the utilization of computational resources
  • Troubleshoot, isolate, and resolve application errors, and other technical issues
  • Benchmark application codes, develop regression tests, and deploy application performance tools
  • Assist biologically focused faculty in the development of appropriate software stacks for analysis of sequencing and biological samples
  • Assist in developing and writing proposals to enhance the research enterprise at NU
  • Work with scientists and researchers to effectively use complementary national resources, including at national laboratories and other user facilities (TACC, NCSA, SDSC, MSI, ALCF, OLCF, etc)

Data Management and Workflow Development

  • Help define and deploy a comprehensive computational and data vision for NU researchers
  • Participate in the development and implementation of backup policies
  • Participate in the integration of HPC and storage resources with research equipment such as sequencers, microscopes, etc.

Internal and External Documentation

  • Attend scientific, RC, or HPC centric conferences to explore technologies relevant to the mission of RC at NU
  • Interface with senior management to develop a documentation strategy (e.g. user manuals, interface documentation, etc.)
  • Communicate progress and participate in reviews with technical staff and senior management

Community Engagement

  • Develop new and creative ways to engage the user community through both documentation, as well as through in-person workshops and community events
  • Develop, present, and maintain training sessions and workshops, both online and in-person, relevant to RC services and resources

Qualifications:

  • Ph.D. in biology, molecular biology, biostatistics, bioinformatics, computational biology, or other related discipline.
  • Strong scientific background in biology (molecular biology, genetics, developmental biology, biochemistry, etc)
  • High proficiency in Python
  • Knowledge in biostatistics packages (R or Matlab) and SQL queries
  • Proficiency working in Unix/Linux environments
  • Proficiency in commonly used command-line tools (Bedtools, Blast+, SAMTools, Bowtie2, Picard, GATK, etc)
  • Experience in a batch HPC environment with a parallel file system using Slurm
  • Experience in an academic or research community environment
  • Experience with scientific workflows
  • Excellent interpersonal communication skills
  • Ability to understand and communicate statistical measures for interrogating the quality of data manipulation
  • Ability and willingness to learn new technologies and remain current in developing trends in the scientific computing community
  • Ability to communicate and document clearly
  • Demonstrated strong individual writing skills
  • Desire for continuous self-improvement and maintenance of skills through training
  • Curious by nature and unafraid of asking questions until you understand well-enough to teach someone else
  • Self-starter, with a proven track record for creativity and initiative
  • Able to prioritize multiple projects and work streams in a fast-paced environment

 


Preferred Qualifications:

  •  Postdoctoral work at a computing facility or biologically focused industry research environment
  • Strong publication record consistent with a history of collaborative research in computational science
  • High proficiency in R
  • Experience with parallel programming paradigms, including but not limited to; MPI, OpenMP, and CUDA
  • Proficiency with pipelines for handling reads from different platforms (Illumina, IonTorrent, PacBio, etc)
  • Knowledge of different mapping algorithms for next gen sequencing reads to published genomes
  • Knowledge of de novo genome assembly tools and algorithms
  • Knowledge of sources of error in library preparation and bioinformatics analysis of next gen sequencing data

 

Salary Grade:

 12

Additional Information:

A criminal background check is required for this position.

Northeastern University is an equal opportunity employer, seeking to recruit and support a broadly diverse community of faculty and staff.  Northeastern values and celebrates diversity in all its forms and strives to foster an inclusive culture built on respect that affirms inter-group relations and builds cohesion. 

All qualified applicants are encouraged to apply and will receive consideration for employment without regard to race, religion, color, national origin, age, sex, sexual orientation, disability status, or any other  characteristic protected by applicable law.

To learn more about Northeastern University’s commitment and support of diversity and inclusion, please see www.northeastern.edu/diversity.

 

 

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