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.
Willing to defend and enforce the discipline of software engineering: We're passionate about what we are doing. The successful candidate will be someone who will help keep us honest and to make sure that what we produce is a quality product that is well documented, usable, extensible and (most importantly) reproducible.
A successful candidate will be expected to perform the following tasks:
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, including typing, the dataclasses library and functional idioms including realizations, maps, generators, and the like. Candidate will be asked to create, document, publish, distribute and maintain software libraries using GitHub, Markdown, HTML, Jupyter, TDD or BDD, etc.
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, visualization of the results and applying a combination of RDF and OWL ontologies in an OWL reasoner such as Protégé.
RESTful Web Services - Candidate must have (or develop) a solid understanding of the principles that underlie Resource Oriented Architecture (ROA) and be able to consume, create, document and deploy RESTful Web Services paradigm.
Docker – Candidate must be(come) familiar with the principles behind docker and be able to consume, create and deploy docker containers and compositions.
FHIR – A significant portion of the candidate's work will directly or indirectly involve HL7 FHIR. Candidate should be comfortable with both the FHIR technology and the FHIR community. Candidate should be able to work with various FHIR standards group to create and implement
Java 8 or later – while we attempt to avoid Java as much as possible, we still find ourselves in a position where we have to create Java based tools for data transformation, integration or other publishing tasks. Candidate may periodically be given a working Java library or toolkit (e.g. the contents of https://github.com/HL7/fhir or https://github.com/jamesagnew/hapi-fhir) and modify, extend and deploy services based on those libraries. This will involve Maven / Ivy / ant and other related tools.
Bachelor's degree. 6 years related experience. Additional education may substitute for required experience and additional related experience may substitute for required education, to the extent permitted by the JHU equivalency formula.
JHU Equivalency Formula: 30 undergraduate degree credits (semester hours) or 18 graduate degree credits may substitute for one year of experience. For jobs where equivalency is permitted, up to two years of non-related college course work may be applied towards the total minimum education/experience required for the respective job.
YAML and JSON – ability to read, consume and produce data using these formats
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.)
XML – ability to read and consume XML and XML schema
RDF and SPARQL – ability to read, consume and create RDF in Turtle and other formats. Experience with SPARQL gets extra points.
Jupyter Notebooks – experience with Pandas and other environments a plus. Ability to create Jupyter magic would get several extra points.
OWL, Reasoners and Ontologies – any experience in the use of, reasoning about, creation of ontologies. Extra points for BFO, OBO and/or SNOMED CT.
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.
Compiler and DSL development – we are working with and enhancing various tools that all fall under this rubric
'R' and statistics in general – we will be modeling and working with statistical tools and content
Knowledge Graphs – GraphQL and Neo4J have crossed our horizon.
Classified Title: Sr. Software Engineer Working Title: Sr. Software Engineer Role/Level/Range: ATP/04/PF Starting Salary Range: $79,864 - $109,781 Employee Group: Full Time Schedule:M-F; 8:30am - 5:00 pm Exempt Status: Exempt Location:2024 E. Monument Street Department Name: 10003311-SOM ICTR Inst Clin Translational Resrch Personnel Area: School of Medicine
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