The Bioinformatics Research Laboratory (BRL) resides within the department of Molecular and Human Genetics at Baylor College of Medicine, and participates in several national and international genomic, transcriptomic, and precision medicine projects. BRL leads data coordination and resource development for the Extracellular RNA Communication Consortium (ERCC): ( https://exrna.org /), an NIH consortium focused on understanding the role of extracellular RNA (exRNA) and exosomes, and their potential use as biomarkers. Following completion of ERCC Stage I (2013-2019) NIH has provided additional funding for ERCC Stage II (2019-2023), which will focus on developing advanced methods for exRNA and exRNA carrier identification and characterization. The Senior Programmer Analyst will act as a Product Owner/Manager for the tools and services developed by BRL for the ERCC.
A key part of the ERCC mission is to develop advanced software methods for exRNA and exRNA carrier identification and characterization. Example applications to be supported and further enhanced include the exRNA Atlas, exceRpt analytical pipeline, and data submission pipeline. The Senior Programmer/Analyst will evaluate requirements and perform feasibility studies for new analysis applications using a variety of 'omic' data, implement improvements to exceRpt, data submission pipelines and the exRNA Atlas, evaluate resource requirements for conducting computational analyses using these applications, and implement and test solutions while working closely with consortium members to obtain user feedback. These activities will be carried out as part of the ERCC data coordination center (DCC).
A 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 ERCC collaborators and stakeholders.
- Work with BRL software development team to design, code, implement, test, and debug ERCC programs and tools, and manage timelines.
- Ensure that ERCC 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 data processing pipelines; and
work with BRL staff to integrate new tools for data analysis and
- 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.
- Four years of relevant experience.
Candidates must have a solid understanding and experience in programming, preferably in scripting languages, and must be familiar with existing bioinformatics tools and data archives. The successful candidate will be able 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. In addition, candidates must have excellent English-language communication skills, interpersonal skills, and be capable of working within a team of biologists and programmers. Candidates who can contribute to system administration of in-house virtualized and non-virtualized IT assets as a minor duty will also be viewed favorably.
Applicants must have strong knowledge and experience with development, compilation, and deployment in a GNU/Linux environment. Additional requirements include:
- 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 is a plus.
Baylor College of Medicine is an Equal Opportunity/Affirmative Action/Equal Access Employer.
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