Lead Application Engineer - LIMS

Job Locations US-VA-Manassas
Role Type
Information Systems
Job ID
Scientific Background
Bioinformatics, Biology, Genomics / Genetics


The Lead Application Engineer is a subject matter expert who coordinates and leads activities for using informatics tools to process, analyze, and interpret digital laboratory data. They are responsible for analyzing, programming, and configuring end-user applications and/or systems used to capture and analyze life-science laboratory data and instrument results. They support, troubleshoot, document, and maintain cloud or on-premise enterprise and open-source software applications supporting digital laboratory systems. They carry out complex, domain-specific data analysis and reporting in support of the ongoing needs of scientific staff needs. Systems include, but are not limited to, Laboratory Information Management Systems (LIMS), Electronic Laboratory Notebooks (ELN), Manufacturing Execution Systems (MES), open-source domain-specific analysis pipelines, and other workflow management systems. They also support scientific staff and management by managing, processing, and analyzing digital laboratory data, including genomic and molecular biology data.


The Lead Application Engineer is responsible for overseeing the life cycle planning of strategizing, architecting, deploying, operating, evolving, and retiring internal scientific applications and configuring both open-source and commercial software products intended for capturing, warehousing, and analyzing scientific data. They oversee and manage the daily activities of other Bioinformatician and Software Engineers to support the needs of the organization. Lead Bioinformatician also will work directly with Product Owners, Business Analysts, and End-Users to implement solutions that meet specified requirements.



• Lead writing of code using current programming language and technology, complete programming, and perform testing and debugging of internally developed applications and configure commercial applications.
• Process, analyze, and interpret high volumes of digital biological data (e.g., genomic, Next-Generation Sequencing (NGS), proteomic, transcriptomic data) as well as process data obtained during workflow execution.
• Develop, test, and deploy modules, functionalities, and configurations of L7 Informatics’ ESP platform to meet the needs of different laboratories and stakeholders.
• Develop ESP product plug-ins (Python and JavaScript) to meet End-User requirements.
• Develop configurations for cloud-based deployments, preferably Microsoft Azure.
• Support staff with writing, maintaining, and improving production scripts which automate processes and analyses related to NGS.
• Support application testing, deployment, maintenance, and evolutions activities by correcting program errors, responding to changes and enhancements.
• Analyze detailed business, functional, technical requirements, and specifications for applications.
• Act independently to analyze data, solve, and correct issues in real time, providing problem solving resolution.
• Oversee the daily activities of application engineering staff and develop their skills to meet the needs of the organization. Identify skill gaps and communicate staffing needs to Senior Management.
• Compose documentation and procedures for installation and maintenance of applications.
• Partner with Bioinformatics, IT and Data Science teams to ensure organizational process includes the full utilization of available technology to enhance productivity and improve work process.
• Develop and facilitate end-user training programs, and work with staff to create customized reporting for better system utilization.
• Plan and support regular audits with the cybersecurity team.
• Use independent judgement to develop methods and techniques to support the achievement of organizational goals and objectives.
• Maintain software updates, ensure compatibility, communicate feature changes, outages, and updates to end users.
• Utilize professional concepts to serve as a subject matter expert to staff and Senior Management on how applications can contribute to objectives.


Education and Experience:

• Bachelor's degree and 8 or more years' experience, including 0-2 years' supervisory experience or equivalent experience.
• Five or more years’ experience and demonstrated subject matter expertise in Bioinformatics, Computational Biology, Genomics, and/or Data Science.
• Five years of experience working with digital laboratory systems and workflow management platforms.
• Minimum of five years of experience working with scientific database management systems (SDMS) or similar SQL based relational database systems. Experience in SQL queries preferred.
• Experience with integrating digital systems (i.e. LIMS) with physical lab equipment other devices and/or third-party applications.
• Five plus years of experience with two or more: Python, PostgreSQL, JavaScript, HTML, CSS.
• Five plus years of experience configuring and administering Linux systems.
• Experience setting up networking, shared file systems, and Kubernetes preferred.
• Experience with IT systems, technologies, and programming languages, including Python, JavaScript, Postgres, and Docker/Kubernetes.
• Experience with computational modeling of real-world processes preferred.
• Experience with L7 Informatics’ ESP platform is preferred.


Other Duties:

  • Perform other duties as assigned.

Founded in 1925, ATCC is a non-profit organization with a mission to acquire, authenticate, preserve, develop, standardize, and distribute biological materials and information for the advancement and application of scientific knowledge. 


ATCC is an Equal Opportunity Employer and does not discriminate against any employee or applicant for employment because of race, color, sex, age, national origin, religion, sexual orientation, gender identity, status as a veteran, and basis of disability or any other federal, state or local protected class.




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