Full-Time Bioinformatics: scientific programmer/data scientist
We are seeking a talented and driven programmer to join the laboratory of Jake Michaelson, PhD in the department of psychiatry at the University of Iowa.
This person will work in a research laboratory that uses a combination of genomic and computational approaches to study the molecular basis of neuropsychiatric conditions, including autism spectrum disorders. This person will be responsible for the development and maintenance of the backend of a web interface for a bioinformatics resource, as well as other data science tasks.
CHARACTERISTIC DUTIES AND RESPONSIBILITIES
- coordinate with researchers to translate proof-of-concept code into production-ready, public-facing web resources
- acquire and perform quality control of large data sets from public and controlled-access sources
- transform, clean, and reshape large data sets, e.g., using common Linux/UNIX command line utilities
- develop and maintain SQL databases, as well as APIs to interface with the databases
- use and maintain the lab’s revision control software
- general system administration and maintenance of computational infrastructure (10-20% time)
- interface with UI IT entities (HCIS, ITS, etc.) to ensure the lab’s compliance with security and privacy requirements
- participate in the lab’s scientific mission by keeping up with developments in computer science and software engineering, and summarizing/sharing findings (e.g., in lab meetings)
- train lab staff in computational methods as needed
- other duties as assigned
A Bachelor’s degree in Computer Science, Engineering, Bioinformatics or a related field, or an equivalent combination of education and experience is required.
- Minimum of 3 years post-baccalaureate, or Master’s degree level experience in computer science, software engineering, bioinformatics, or related field
- Relevant experience in scientific discipline plus the ability to translate, adapt, and apply this knowledge
- Experience with SQL databases including schema and query design, performance optimization, and security
- Demonstrated experience with the Linux/UNIX environment, including the use of standard command line utilities such as sed, awk, grep, etc. as well as shell scripting
- Demonstrated experience with at least one scripting language such as Python
- Demonstrated experience with at least one compiled language such as C or FORTRAN
- Demonstrated experience with revision control software such as git
- Excellent communication and customer relations skills, including the ability to communicate effectively, both orally and in writing, with technical and non-technical staff.
- Master’s degree in a quantitative discipline
- In-depth knowledge of regular expressions
- Experience with R
- Demonstrated experience with XML, including XPath and Xquery
- Experience with node.js
- Experience with web scraping
- Experience with text mining
- Experience with high performance computing (e.g. SGE)
- Experience in bioinformatics, especially sequence analysis or gene expression analysis
- Experience creating and deploying virtual machines
- Experience in applied statistics or machine learning
The University of Iowa combines a fantastic scientific environment with a healthy work-life balance. Faculty and staff living in Iowa City enjoy the affordability and friendliness of small town life while also benefiting from the cultural engagement and activities that come from being the home to a major university.