The Staff Scientist 1 will serve as the Technical Lead for NCBI RefSeq bioinformatics pipelines, including Foreign Contamination Screening pipelines and the Eukaryotic Genome Annotation Pipeline (EGAP). NCBI’s bioinformatics pipelines serve the research and clinical community and drive new life sciences discoveries, with ongoing development on making the data more useful and easily accessible, taking full advantage of new technologies such as Cloud computing and embracing FAIR principles (Findable, Accessible, Interoperable, Reusable). The contamination screening activities include developing, maintaining, and operating the databases and screening processes that provide contamination screening for GenBank submissions, as well as European Nucleotide Archive (ENA) and DNA Database of Japan (DDBJ) assemblies obtained through the International Nucleotide Sequence Data Consortium (INSDC) exchange. Screening includes the detection of cloning vector contamination and cross-contamination between organisms in sequences submitted to GenBank (genomes and transcriptome sequence archive (TSA) sequences).

The eukaryotic annotation process is an automated pipeline producing annotation of coding and non-coding genes, transcripts, and proteins on finished and unfinished public genome assemblies. It provides content for various NCBI resources including Nucleotide, Protein, BLAST, Gene, Datasets, and Sequence Viewer. Annotation tasks extend from the fetching of raw and curated data from public repositories (sequence and assembly databases) through the alignment of sequences and the prediction of genes, to the submission of the accessioned and named annotation products to public databases. The current production EGAP is an annotation service running at NCBI and relying on internal-only resources, with the annotation products published and made available to the scientific community.

As part of NCBI’s efforts in Comparative Genome Resources, a portable version of EGAP is in development, making use of modern technologies including containerization and Cloud computation, to allow the research community to annotate genomes with their compute resources. This product aims to improve access to high quality, easy to run annotation tools and to meet the challenges of the high volume of genomes that need to be annotated. The portable annotation tool will satisfy researcher needs to iterate more quickly with the scientific method and the cycle of science, by having annotation as early as possible and prior to publication or submission.

The Staff Scientist 1 will have extensive experience in sequence data curation, analysis, delivery, and management, and will act as primary program operational contact for technical activities related to bioinformatics and sequence analysis for the relevant products. The role requires communication and collaboration with SeqPlus and IEB leadership to discuss product priorities and activities and provide strategic recommendations for product development and engagement; provides strategic recommendations to SeqPlus leadership for development and engagement opportunities so that researchers may take maximal advantage of NCBI’s sequence content as relevant to their research and/or sequence data analysis needs; collaborates with the Product Owner to provides a product vision and plan with appropriate prioritizing of feature development for informatics applications supporting the creation, refinement, and delivery of NCBI sequence and metadata; coordinates work priorities for a multi-disciplinary team comprised of software developers, data curators, and data analysts; serves as a product ambassador internally and externally, keeping customers and stakeholders informed of product status, sharing knowledge, and answering questions related to the product; connects with, and engages in, collaborations with external entities and institutions informing the development of tools delivering sequence data and metadata; supports SeqPlus operational goals by collaborating with members of other program product teams, including managers, subject matter experts (SMEs), product owners, project managers, developers, and others; represents NCBI’s products, standards, and values externally, through participation in working groups, committees, presenting at conferences, webinars or publications; and works in an Agile Framework for product development.

Additional responsibilities include:

• Working with a diverse group of scientists, bioinformaticians and other developers across the center to implement efficient bioinformatics algorithms. • Managing the efforts of the program's software development team in an Agile framework. • Assuming responsibility for the development, implementation, testing, and continued maintenance of NCBI bioinformatics pipelines, including FCS, EGAP, and future pipelines which may be developed. • Acting as a liaison between the development team and program leadership. • Facilitating the development of cloud-ready tools and pipelines to support sustainable scalability and enable use by collaborators and scientists in the field. • Ensuring on-schedule delivery of software solutions for the product line and organization. • Managing the development lifecycle of software for assigned products, directing, and coordinating the actions of the development team. • Providing technical leadership and guidance to the development team. • Providing work estimates for development tasks. • Learning new technologies, keeping up with internal systems, and sharing knowledge with the team. • Researching new techniques and bioinformatics tools and practices in pursuit of advancing the goals of the program and product line. • Creating and maintaining technical documentation related to the product line. • Ensuring high code quality for software development tasks.

• Ph.D. in Bioinformatics, Computer Science, Engineering, or a related field. • Software engineering and maintenance, feature/algorithm design from initial concept to implementation and large-scale testing and analysis, pipeline automation engineering and execution. • 10+ years of relevant bioinformatics engineering experience in areas such as sequence assembly, nucleotide and protein alignment, and both structural and functional annotation. • 5+ years of experience handling large amounts of data or working in a distributed computing environment. • Experience with bioinformatics tools such as BEDTools, SAM Tools, BLAST, DIAMOND, STAR, and SRA Toolkit. • Experience with bioinformatics workflow management systems (e.g., Nextflow, Galaxy, CWL). • Experience with programming in a Linux environment and modern software containerization technologies (Docker, Singularity). • Cloud experience with both Amazon Web Services (AWS EC2, S3, Lambda) and Google Cloud Platform (GCP GKE, Google Cloud Storage, Cloud functions). • Proficiency in at least one of programming languages: Java, C, C++. • Fluency in some scripting languages such as BASH, csh, Perl, or Python. • Ability to work with common structured documents (at least one of XML, JSON). • Experience with open-source projects. • Experience with CI/CD pipelines, unit tests, integration, and regression testing. Desired Competencies: • 15+ years of working with genetic and biological data. • Familiarity with NGS computational tools and formats (BWA, GATK, etc.) • Demonstrated active involvement into open- source communities (github, etc.) • Working knowledge of?modern software development tools;?including version control (e.g., Git), build management and continuous integration (e.g., TeamCity, GitLab), and issue tracking (e.g., JIRA). • Experience with Application Security (AppSec) best practices for software development, including defensive coding and an understanding of attack surface mitigation in the context of software containers (Docker, Singularity).

The successful applicant must have demonstrated the necessary skills and abilities to lead, direct, organize, and coordinate complex research and development projects and will have exceptional technical competence. Candidates must be able to work independently, have excellent communication skills and a proven ability to successfully engage with others to create useful resources to achieve shared objectives.

The IEB is responsible for designing and building NCBI's production software and databases. They: (1) perform applied research in the area of data representation and analysis for molecular biology data, including development of computer based systems for the storage, management, and retrieval of knowledge concerning molecular biology, genetics, and biochemistry; (2) design schema and specifications for representation of sequence genetic and structural information in databases which will serve as national resources; (3) design and develop distributed software systems from the prototype to operational phases which provide researchers with both local and remote computational services; (4) coordinate access to sequence, genetic, structural, and bibliographic databases; (5) establish collaborative informatics research projects with NIH Intramural laboratories as well as extramural academic groups; (6) consult and advise other government agencies and research laboratories on advanced methods of software and database design; and (7) develop and promote standards for databases, data exchange, and biological nomenclature. NCBI programs and activities supported by this position are highly complex, mission- critical, and have national and international impact, as they directly support dissemination of biomedical information in service to NIH and the broader biomedical community through NCBI, an organization with a budget of more than $150 million and a staff of more than 700 Federal and contract staff.

Commitment to Diversity and Equal Employment Opportunity

NIH/NLM encourages the application and nomination of qualified women, minorities, and individuals with disabilities. The U.S. government does not discriminate in employment based on race, color, religion, sex (including sexual orientation, pregnancy, and gender identity), national origin, political affiliation, marital status, disability, genetic information, age, membership in an employee organization, retaliation, parental status, military service, or other non-merit factors. NIH/NLM will provide reasonable accommodations to applicants with disabilities as appropriate. If you require reasonable accommodation during any part of the application and hiring process, please notify us.

Reasonable Accommodation

You can request a reasonable accommodation at any time during the application or hiring process or while on the job. Requests are considered on a case-by-case basis.