Senior Computational Scientist - Scientific Computing & Data

Key Skills

Cryo, Data science techniques, GPUs, HIPAA, Jupyter Notebook, MATLAB Programming, MongoDB, MySQL, Optimization, Python Programming, PyTorch, R Programming, R-Shiny, RStudio, TensorFlow

Job Description

The Scientific Computing and Data group at the Icahn School of Medicine at Mount Sinai partners with scientists to accelerate scientific discovery. To achieve these aims, we support a cutting-edge high-performance computing and data ecosystem along with MD/PhD-level support for researchers. The group is composed of a high-performance computing team, the research clinical data warehouse team and a research data services team.

As a member of the MSSM Scientific Computing Group, the Senior Computational Scientist partners and leads projects with other scientists and researchers to plan joint scientific projects that will effectively use MSSM HPC (high performance computing) clusters, data science tools and other modern computational and data science techniques. This individual researches scientific approaches and decides on the path forward for new applications and technologies. The incumbent is a customer-focused leader who sets a positive, productive and courteous tone for the Scientific Computing group and operates under little to no supervision. This position reports to the Director for Computational & Data Ecosystem in Scientific Computing. 

Responsibilities

• Partners directly with scientific and research staff to lead projects to efficiently and effectively use MSSM HPC clusters and other modern data science tools and infrastructure. Improves researcher productivity through highly optimized computational and data workflows.
• Leads the research, analysis and deployment of new applications and other technologies such as GPU’s, Hadoop, container and cloud computing. Troubleshoots, isolates and resolves technical issues as the most senior level of support.
• Coordinates and leads software and environment benchmarking efforts. 
• Develop and implement automated regression tests for the HPC environment. Evaluates and approves application programming environments. 
• Oversees the installation infrastructure and management of numerical libraries and application performance tools.
• Leads effort to develop a needs requirements and define and deploy a comprehensive computational and data vision for MSSM researchers.
• Provides the highest level of courteous, productive and team-based interaction with not only the HPC team but also with the partner scientists. 
• Trains Associate Computational Scientists, Computational Scientists,bioinformatician, HPC Users, etc.
• Manage the Mount Sinai Data Commons - Data Ark server space and all data sets, creating and maintaining an efficient file structure and providing user-access according to the specific restrictions of the different data sets and user support needed. 
• Conducts user surveys and leads the allocations process. Participates in chargeback/fee recovery analysis and provides suggestions to make operations sustainable. 
• Researches, deploys and optimizes resource management and scheduling software and policies and actively monitoring. 
• Provides recommendations for innovative technology periodically and customer service approaches that are science/research driven to improve the effectiveness, efficiency, and customer satisfaction of the resources; Communicates with clinicians, researchers and other team members to understand and develop use cases and jointly develop plans, proposals and provide effective technological solutions.
• Collect usage metrics in all aspects and develop reports.
• Works as a strong team player within the group, within Mount Sinai, and externally. Provide after hours support in case of a critical issue.
• Writes, publishes and presents papers at national and international conferences.
• Assists in developing and writing proposals and reports. Creates and provides clear documentation on all items.
• Other relevant duties as assigned.

Qualifications

• Ph.D. in a scientific domain required.
• 7+ years (higher preferred) in a scientific/academic computing environment
• Strong experience installing and supporting bio, genomics, chemistry codes and AI programs such as GATK, CryoSPARC, R, Python, Shiny, Jupyter, Rstudio, NAMD, AMBER, Matlab, Gromacs, Schrödinger, pytorch, tensorflow, etc
• Strong experience with MPI, OpenMP and numerical libraries
• Strong experience with GPUs
• Strong programming experience in any applicable language
• Experience with scientific workflows
• Experience with Job scheduler such as LSF or Slurm
• Experience with data transfer tools such as globus and cloud CLI
• Experience with data science, containers and cloud environments
• Experience with instrumenting and optimizing application codes
• Experience in an academic or research community environment
• Experience with Open OnDemand is preferred
• Experience with web applications such as python flask, Shiny, R Markdown, etc, and database such as MySQL or MongoDB is preferred
• Experience with HIPAA compliance is preferred

Employer Description

Strength Through Diversity

The Mount Sinai Health System believes that diversity, equity, and inclusion are key drivers for excellence. We share a common devotion to delivering exceptional patient care. When you join us, you become a part of Mount Sinai’s unrivaled record of achievement, education, and advancement as we revolutionize medicine together. We invite you to participate actively as a part of the Mount Sinai Health System team by:

• Using a lens of equity in all aspects of patient care delivery, education, and research to promote policies and practices to allow opportunities for all to thrive and reach their potential.
• Serving as a role model confronting racist, sexist, or other inappropriate actions by speaking up, challenging exclusionary organizational practices, and standing side-by-side in support of colleagues who experience discrimination.
• Inspiring and fostering an environment of anti-racist behaviors among and between departments and co-workers.

We work hard to acquire and retain the best people and to create an inclusive, welcoming and nurturing work environment where all feel they are valued, belong and are able to professional advance. We share the belief that all employees, regardless of job title or expertise contribute to the patient experience and quality of patient care.

 Explore more about this opportunity and how you can help us write a new chapter in our history!