Bioinformatics / bioinformatics
Molecular Biology
| Position ID: | Cornell-Institute of Biotechnology-EPIBIOINFO [#22011, WDR-00032175] |
| Position Title: | Research Software Engineer, Cornell Epigenomics Facility |
| Position Type: | Non tenure-track faculty |
| Position Location: | Ithaca, New York 14853, United States [map] |
| Subject Areas: | Genomics / Bioinformatics Bioinformatics / bioinformatics Molecular Biology |
| Appl Deadline: | finished (2022/06/30, finished 2023/07/01) |
| Position Description: | |
The Biotechnology Resource Center Epigenomics Facility at the Cornell Institute of Biotechnology is seeking a Research Software Engineer. This position will work proactively with
our team of scientists, faculty and technicians and is responsible for designing
and identifying the requirements for newly engineered software and database
applications. This position provides support for the development and
maintenance of IT research systems, supporting scientific discoveries for
research facility. The work in this lab mainly provides support for DNA
sequencing using a patented ChiP-exo assay performed on the Illumina NextSeq
platform. Serving as team lead for other
programmers and contributing to detailed project documentation are also
critical duties for this position.
Responsibilities Include: Programming and running analysis on the high performance computing clusters. Maintaining and extending the scripting capabilities of the lab members on the HPC clusters for specific experimental design needs and analysis. Responsible for quality assurance review and evaluation of new and existing software products. Writing software and scripting novel solutions to solve computational biology problems. Provide documentation and support for new research methods, including publication with faculty and researchers when applicable. At a minimum, work developed for the lab is required to be published in appropriate Open Source scientific communities and prior experience developing software for distribution is very important.
Maintaining and extending the existing relational database systems that provide data curation of next generation sequencing data collected about experiments run in the lab. Engineer and write the specifications and code in support of a new APIs to enable scripts to work interactively with the new database system. Provide support to the researchers to specify requirements for developing collaborative software frameworks for internal and external use. Design, code, test, debug, and document applications dealing with the overall operating system, such as sophisticated file maintenance routines, large telecommunications networks, and advanced mathematical/scientific software packages.
Developing an interface for data collection, dissemination and further analysis as needed. Develop the design and programming of a new user interface available through a web browser for accessing the lab's experimental data and the new database system. Ensure the design supports a robust technology solution, taking into account the user requirements, technical requirements, etc. (e.g., solution architecture); ensure technology requirements allow modeling and address performance and security. Implement existing quality control pipelines on various types of genomic and sequencing data in order to prepare files and meta-data for data curation in the database system for the lab.
Recommendations for languages to use, propose libraries to install and packages to be supported for the lab's infrastructure to curate and maintain the database systems and online interface. This position will also provide a team leadership role for other students and research programmers, assisting them with bioinformatics and statistics- based analysis.
This position is a two-year term appointment with the possibility of extension contingent on continued funding and successful performance. A hybrid remote work arrangement is possible.
Qualifications
Ph.D. in bioinformatics or a related field is required.
Programming skills are required. Specific skillsets include but are not limited to: High Performance Computing software development and support; relational and NoSQL database programming development, and API creation; and web-based programming using languages such as Python, JavaScript and Java.
Working knowledge of concepts and terminology in molecular biology, genomics, and related sciences.
Interest in working on multiple interdisciplinary research projects.
Excellent oral and written communication skills. Benefits and rewards include:
Department Mission and Background Information
The Cornell Institute of Biotechnology is a dynamic hub for life sciences research at Cornell University. The Institute (http://www.biotech.cornell.edu) offers cutting edge biotechnologies, expertise in applications, technology testing and development and consultation for life sciences researchers at Cornell University and outside institutions. The Institute houses the Biotechnology Resource Center (BRC), which offers shared core facilities services to catalyze and promote life sciences research, and is involved with many intercampus initiatives and multi-institutional collaborations. In addition to Epigenomics, the BRC includes core facility operations in Genomics, Bioinformatics, Imaging, Flow Cytometry, Proteomics and Metabolomics, and Biotechnology Development. The Institute also administers the Center for Advanced Technology (CAT) in the Life Sciences to assist life science researchers in the development of biotechnologies with commercial potential in partnership with New York State industries, and the Center for Life Sciences Ventures, a state-of- the-art business incubator for emerging biotechnology companies. With its extensive network of academic, federal, not‐for‐profit enterprises and commercial partners, the BRC serves as a vital partner in life sciences research and innovation.
Cornell Institute of Biotechnology staff enjoy working in a collaborative and innovative organization within Cornell University, an award-winning employer recognized for supporting employee health, workplace diversity, work-life fit, and environmental sustainability. Cornell University offers competitive compensation and benefits. The Institute is located on the main Ithaca campus, in the heart of the Finger Lakes of central New York State. Ithaca and the surrounding area is noted for high quality of living surrounded by natural beauty and a vibrant community.
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