The Bioinformatics Research Laboratory (BRL) in the department of Molecular and Human Genetics at Baylor College of Medicine, Houston, TX, participates in national and international genomic, transcriptomic, and precision medicine projects, in addition to numerous collaborations within the Texas Medical Center. The purpose of this Programmer/Analyst II position is to support the Clinical Genome Resource (Clingen) ( https://clinicalgenome.org/ ), an NIH-funded effort dedicated to developing resources for defining the clinical relevance of genes and variants for use in research and precision medicine. As a member of ClinGen, BRL is developing key resources in support of this mission. An illustrative list of recent and active BRL Clingen contributions includes: The ClinGen Allele Registry ( http://reg.clinicalgenome.org ), the ClinGen Actionability Curation Interface ( https://actionability.clinicalgenome.org/ac/ ), and the ClinGen Evidence Repository ( https://erepo.genome.network ). Several new Clingen services are planned or in early stages of implementation. This position will evaluate requirements and perform feasibility studies for new Clingen resources using a variety of genetic data, implement improvements to existing Clingen resources, evaluate resource requirements for conducting new types of analyses using these resources, and implement and test solutions while working closely with consortium members to obtain user feedback. A key goal for the software created by programmers will be their application to important biological questions for publication in high impact journals. Recent articles include: Murillo et al. (Cell, 2019), Carrero et al. (Oncogene, 2019), Pawliczek et al. (Human Mutation, 2018), Onuchic et al. (Science, 2018), and Patel et al. (Genome Medicine, 2017).
- Attend web conference calls to gather, evaluate, and prioritize requirements with Clingen collaborators and stakeholders.
- Work with BRL software development team to design, code, implement, test, and debug Clingen programs and tools, and manage timelines.
- Ensure that Clingen programs and tools are developed, tested and delivered on time. Prepare program documentation and educate users on the new functionalities.
- Develop use cases to guide user adoption.
- Participate in the integration of high-volume data sets.
- Design, implement, and execute Clingen resources; and work with BRL staff to integrate new tools for genetic data analysis and visualization.
- Bachelor’s degree in Computer Science, Management Information Systems, Information Technology, or a related field. Four years of related experience may substitute for degree requirement.
- Two years of relevant experience.
- Master's degree in a related field.
- Must have a solid understanding and experience in programming, preferably in scripting languages, and must be familiar with existing bioinformatics tools and data archives.
- Ability to design, code, test, and debug generic software solutions with an emphasis on reusability, and which extend an existing system. Successful applicants will present and discuss requirements, specifications, backend and UI designs, create necessary test data, test software, and prepare documentation.
- Knowledge and experience with development, compilation, and deployment in a GNU/Linux environment.
- Working understanding of mutexes, threads, guards, and conditional and atomic variables.
- Ability to contribute to and use shared object-oriented code libraries.
- Functional familiarity with one or more modern 3rd generation languages such as Python, Ruby, Perl, and/or EcmaScript 5/6, as well as standard web technologies such as Ajax, CSS, HTML, REST APIs, JSON-LD. Typical data processing pipelines will operate in a GNU/Linux environment and be implemented using programming languages such as Python, Ruby, and NodeJS.
- Experience with document, graph, and relational databases.
- Experience with good software engineering practices, designing and developing software solutions to specifications and according to local standards and practices, and with the use of version control systems.
- Must have excellent English-language communication skills, interpersonal skills, and be capable of working within a team.
- Ability to contribute to system administration of in-house virtualized and non-virtualized IT assets as a minor duty.
Baylor College of Medicine is an Equal Opportunity/Affirmative Action/Equal Access Employer.