Cloud Computing Engineer

  • Salk Institute for Biological Studies
  • La Jolla, CA 920371002, USA
  • Jul 11, 2022
Full time Computer & Web Services, Info Technology

Job Description


The Salk Cloud Initiative represents a new matrix organization within the Institute with a mission to develop new capabilities and resources to facilitate interaction with large and complex data sets across multiple disciplines. This position will design, manage and support the Institute's framework for cloud data and software engineers, working collaboratively with scientists to migrate their pipelines to the cloud, providing training needed for long-term sustainable cloud-based compute and data storage in support of basic research at the Institute. The cloud initiative serves as a nexus within the Institute for data-centered partnerships with technology companies and academic organizations.

The Institute's IT department is looking for a Cloud Computing Engineer to join our team. Your work will assist hundreds of investigators and core facilities to accelerate and achieve their research goals using new platforms, technologies, and approaches to high-performance and big-data computing.

Reporting to the Sr. Director of IT, you will join a small team that designs, deploys and supports research focused, IT cloud platforms for use by the Salk community. You will provide support for Salk researchers and core personnel looking to transition computational pipelines and tools into cloud-based solutions. As a domain knowledge expert, you will help architect the transition to a hybrid cloud compute and storage infrastructure at the institute, accelerating the pace of data-driven research at the Institute, while providing training needed for researchers to utilize the hybrid infrastructure efficiently.  You will develop a strategy for a sustainable hybrid cloud infrastructure at the institute that will enable Salk scientists to properly utilize cloud computing and storage for scientific discovery, while serving as a knowledge leader and facilitator.  This position has a hybrid schedule with considerable flexibility.


  • Cloud Architecture Design and Management (20%)
    1. Architect a cloud-based platform, including network design, security, redundancy, account management and role-based permissions framework for use by cloud research computing specialists to containerize existing workflows and build cloud-native solutions to emergent research needs.
    2. Work with cloud research teams to ensure that we get maximum computational and storage value by intelligently using cloud options such as AWS spot market and preemptable VMs in GCP, and Amazon Deep Glacier archival storage.
    3. Facilitate the benefits of modern Object Storage systems and migrate workflows away from Posix file system dependencies to cloud-native using docker based workflows and object storage
    4. Develop and maintain tools to track cloud usage patterns, including tools for alerting on and/or interrupting anomalous workloads.
    5. Manage vendor relationships and cloud contractual agreements and billing tools with cloud providers; provide best value and efficiency in proposals
  • Cloud Research and Infrastructure Project Support (35%)
    1. Working directly with computational biologists and core staff, help implement custom computational pipelines in the cloud, utilizing the most appropriate cloud-based solutions for each project.
    2. Maintain an ecosystem of existing solutions which can be adapted to solve similar biological problems.
    3. Help researchers set up transfer of data to/from the cloud, navigating the balance between cost and ease-of-use.
    4. Support administrative cloud computing efforts including IaaS and PaaS projects from the IT/IS team and other admin units.
    5. Recommend and evangelize new cloud-based platform services that increase computational productivity or enable new capabilities.
    6. Contribute documentation using Github or Confluence to a consolidated knowledgebase that covers cloud-based research computing and best practices for operational configuration of cloud resources
  • Cloud Technical Training (20%)
    1. Provide architectural input to a cross-functional cloud architecture team and build relationships with other IT professionals and core bioinformatics staff at Salk and educate them about cloud based scientific computing.
    2. Working with the Sr. Bioinformatics Core Director and Cloud Infrastructure Architect, develop training resources in the form of a central website/wiki designed to inform Salk scientists about cloud computing solutions at the Salk.
    3. Participate in the design/presentation of cloud compute informational seminars and workshops.
  • Cloud Infrastructure Technical Support and Consulting (20%)
    1. Provide technical support and troubleshooting to resolve cloud-based computational and storage technical issues.
    2. Troubleshoot end-to-end data transfer and performance issues (including streaming of on-prem data sources into cloud-based analysis pipelines).
    3. Provide architectural input to a cross-functional cloud architecture team and build relationships with other IT professionals at Salk and educate them about cloud based scientific computing.
    4. Review Cloud architectures proposed by other teams for consistency with Institute guidelines on infrastructure design and security.
  • Other Duties As Assigned (5%)



  • A minimum of 10 years administering and working with Linux systems of various flavors (Centos/Redhat preferred)
  • 5+ years experience and deep knowledge of AWS and Google cloud services and their APIs, including popular storage, networking, security and automated provisioning tools
  • Experience with various forms of infrastructure and application virtualization such as VMware, Docker, Singularity, Amazon Lambda (serverless computing)
  • 5 years working with Python or other modern scripting language
  • Extensive knowledge of cloud technologies required - including but not limited to S3, EC2, ECS, RDS, Glacier, and EBS
  • Development and implementation of Cloud & Hybrid Cloud Strategies leveraging AWS or Google Cloud
  • Current hands-on experience providing modernization to a platform utilizing AWS or Google Cloud.
  • Hands-on Cloud Architecture, Design, and Development experience
  • Demonstrated experience moving data to and from the cloud in a cost-effective way at high speed
  • Well-rounded knowledge of systems, network, security, storage, cloud products and technologies in Linux environments
  • Advanced experience working with automated tools, scripting and working with batch-processing environments
  • Familiarity with infrastructure as code concepts and infrastructure automation tools (terraform, cloud formation)
  • Experience troubleshooting performance issues with Linux based computing environments, storage platforms and cloud-based networking infrastructure
  • Knowledge of application, network and infrastructure security best practices
  • Knowledge of tools and platforms to provide cloud application and security monitoring


  • Research IT application experience that includes hands-on software development, DevOps engineering, systems administration, and/or systems architecture
  • Experience in at least one additional scripting language (Bash, Javascript/node, etc)
  • Demonstrated experience with cloud-native technologies such as MapReduce, Cloudformation, Container as a Service offerings, and various storage platforms and automated data tiering capabilities
  • Experience with high-speed networking and data migration to/from cloud infrastructure with high throughput
  • Relevant cloud administration certifications such as GCP Cloud Architect or AWS Professional Solutions Architect
  • Experience building and managing a multi-tentant cloud platform for organizational use
  • Experience using configuration management and/or automation systems such as Chef, Puppet, Ansible, cfengine, or Salt
  • Experience with GPU-based systems
  • Experience in writing web based tools used to manage operations. (e.g. Flask)
  • Knowledge of R, Matlab, and Galaxy experience is a plus
  • Experience working within the software development or scientific computing/research environment a big plus.
  • Experience in a research or educational environment a big plus
  • Experience working in matrix-based or cross-functional/multidisciplinary teams
  • Experience in a research or educational environment



  • Strong communications skills with ability to communicate effectively to a broad variety of constituencies including executive administration, department heads, principal investigators and senior researchers
  • Ability to work independently or as part of a project team to analyze requirements and determine appropriate design approaches
  • Ability to work with the software development and scientific computing/research communities
  • Ability to train peers on cloud technologies and infrastructure management
  • Ability to train scientists on cloud technologies and infrastructure management
  • Work with department leadership on establishing and managing priorities
  • Assist in developing budgets and track expenses for cloud-based infrastructure projects
  • Ability to manage multiple projects with varying priorities at the same time
  • Ability to quickly adapt to new technologies and learn independently


  • Ability to produce high quality written materials including training and infrastructure documentation (e.g., maintain a wiki)
  • Constantly curious about new developments and technologies
  • Ability to train peers on cloud technologies and infrastructure management



  • Bachelor's degree in computer science, IT, or related scientific discipline, or an equivalent amount of demonstrated experience in lieu of a degree


  • Advanced degree in computer science, IT, bioinformatics or related scientific discipline


  • Must be willing to work in an animal-related research environment.
  • Satisfactory completion of the Institute's background investigation.
  • Willing to sign a confidentiality agreement


The incumbent in this position will be constantly adjusting focus, grasping, hearing, keying, seeing, sitting, talking, analyzing, calculating, communicating, reading, reasoning, writing, and working indoors.


Application Details

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