Our team is looking for a skilled software developer/engineer to help us create an integrated suite of tools that can be used to integrate knowledge from multiple domains in order to discover new causes of and treatments for disease. While a successful candidate’s primary focus will be on software and software engineering, they will play an active role in the design and direction of the overall project.
We are looking for an individual who is:
Motivated and excited to learn: Our group often finds itself on the leading (bleeding) edge of software tools and methodology. A successful candidate should be able to adapt to new environments, approaches, tools and, when necessary to be able to extend an existing tool for a new purpose or, if necessary, develop an entirely new approach to solve a problem.
Self-directed: A successful candidate needs to be able to set their own schedule and goals but, at the same time, is willing and able to ask for guidance and assistance when uncertainty arises.
Able to thrive in a loosely structured research-oriented environment.
Specific Duties & Responsibilities
Python Software Development – A significant portion of this project will involve developing and enhancing software in the Python 3 environment. Candidate should have solid Python 3 skills and be comfortable with the latest Python 3 libraries and tools. Candidate will create, document, publish, distribute and maintain software libraries.
Working with RDF, OWL and Knowledge Graphs – Most of the data we are working is either already in RDF or is being transformed to it. Candidate will need a strong understanding of RDF, OWL, Linked Open Data and (ideally) knowledge graphs. Project tasks will include the transformation of information into standardized RDF, and storing RDF triples in a triple store or a graph database.
RESTful Web Services - Candidate must have (or develop) a solid understanding of the principles of RESTful web services and be able to consume, create, document and deploy RESTful APIs.
Docker – Candidate must be(come) familiar with the principles behind docker and be able to consume, create and deploy docker containers and compositions.
Java 8 or later – Candidate is familiar with the Java programming language and tools to develop software for data transformation, integration or other publishing tasks. Candidate may periodically need to modify, extend and deploy services based on working Java libraries or toolkits.
Bachelor’s degree required. Additional experience may be substituted for education.
Three years of related work experience with computer systems and applications. Additional education may substitute for experience:
Equivalency Formula: 30 undergraduate degree credits or 18 graduate degree credits = 1 year of experience. For jobs where equivalency is permitted, up to two years of non-related college coursework may be applied towards the total minimum education/experience required for the respective job.
Additional consideration will be given to skills in:
YAML and JSON – ability to read, consume and produce data using these formats
RDF and SPARQL – ability to read, consume and create RDF in Turtle and other formats. Experience with SPARQL preferred.
OWL, Reasoners and Ontologies – any experience in the use of, reasoning about, creation of ontologies. Extra points for BFO, OBO and/or SNOMED CT.
JSON-LD – ability to create JSON-LD contexts and use them to transform JSON into RDF. (Working knowledge of the JSON-LD 1.1 specification a plus.)
Jupyter notebooks and related libraries
Github, github actions, markdown
Terminologies and terminology services – With the expectation that we will need to build one of these, experience with terminology services and terminology service standards would be a plus.
HL7 FHIR – we are using FHIR, transforming FHIR and helping create new FHIR standards. Much of the work will be involved in various aspects of this environment, so familiarity would be beneficial.
Bioinformatics – knowledge in genes, genotypes, phenotypes, chromosomes, chemicals, …
Knowledge Graphs – Experiences with Graph databases such as Neo4J is a plus.
Databases – Familiar with common relational databases and SQL.
Special Knowledge, Skills, and Abilities
Ability to move about or sit for an extended period of time
Reaching by extending hand(s) or arm(s) in any direction
Finger dexterity required to manipulate objects with fingers for example, using a keyboard
Communication skills using the spoken word
Possible exposure to communicable diseases
Classified Title: Sr. Programmer Analyst Working Title: Sr. Programmer Analyst Role/Level/Range: ATP/04/PD Starting Salary Range: $59,280 - $81,430; Commensurate with experience Employee group: Full Time Schedule: Monday-Friday, 8:30am-5:00p, Up to 37.5 hours/week Exempt Status: Exempt Location: 04-MD:School of Medicine Campus Department name: 10002809-SOM DOM General Internal Medicine Personnel area: School of Medicine
The successful candidate(s) for this position will be subject to a pre-employment background check.
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