Job Req ID:  112351

Sr. Software Engineer

The Biomedical Informatics and Data Science section of General Internal Medicine is seeking a highly skilled Sr. Software Engineer to design and implement an integrated suite of tools to integrate knowledge from multiple domains to discover new causes of, and treatments for, disease. The position has several responsibilities. While the primary focus will be on software and software engineering, this position will play a critical role in the design and direction of the overall projects, determining how to turn leadership vision into practical implementation while utilizing a team of software engineers.


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, including typing, the data classes 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 Protg.
  • 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.
  • JavaScript – an ideal candidate would be fluent in JavaScript, CSS and client-side development tools.

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. Must 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: Able to set own schedule and goals but, at the same time, is willing and able to ask for guidance and assistance when uncertainty arises.
  • Must be able to take leadership vision and design and implement solutions.
  • 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.


Minimum Qualifications
  • Bachelor's Degree.
  • Six years of related experience with solid background in software engineering.
  • 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.
  • High level of proficiency with Python 3.
  • Able to work with Java, Javascript and occasionally C++, Go, etc. as needed.
  • Demonstrated ability to work in an open source, community-based development environment.


Preferred Qualifications
  • 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,
  • Bioinformatics – genes, genotypes, phenotypes, chromosomes, chemicals.
  • Knowledge Graphs – GraphQL and Neo4J have crossed our horizon.

 


 

Classified Title: Sr. Software Engineer 
Role/Level/Range: ATP/04/PF  
Starting Salary Range: Min $84,700 - Max $148,300 Annually ($116,500 targeted; Commensurate with experience) 
Employee group: Full Time 
Schedule: M-F; 8:30-5:00 
Exempt Status: Exempt 
Location: Remote 
Department name: SOM DOM GIM BIDS 
Personnel area: School of Medicine 

 

Total Rewards
The referenced salary range is based on Johns Hopkins University’s good faith belief at the time of posting. Actual compensation may vary based on factors such as geographic location, work experience, market conditions, education/training and skill level. Johns Hopkins offers a total rewards package that supports our employees' health, life, career and retirement. More information can be found here: https://hr.jhu.edu/benefits-worklife/

 

Please refer to the job description above to see which forms of equivalency are permitted for this position. If permitted, equivalencies will follow these guidelines:
JHU Equivalency Formula: 30 undergraduate degree credits (semester hours) or 18 graduate degree credits may substitute for one year of experience. Additional related experience may substitute for required education on the same basis. 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.

**Applicants who do not meet the posted requirements but are completing their final academic semester/quarter will be considered eligible for employment and may be asked to provide additional information confirming their academic completion date.


The successful candidate(s) for this position will be subject to a pre-employment background check. Johns Hopkins is committed to hiring individuals with a justice-involved background, consistent with applicable policies and current practice. A prior criminal history does not automatically preclude candidates from employment at Johns Hopkins University. In accordance with applicable law, the university will review, on an individual basis, the date of a candidate’s conviction, the nature of the conviction and how the conviction relates to an essential job-related qualification or function.

 

The Johns Hopkins University values diversity, equity and inclusion and advances these through our key strategic framework, the JHU Roadmap on Diversity and Inclusion.

 

Accommodation Information

If you are interested in applying for employment with The Johns Hopkins University and require special assistance or accommodation during any part of the pre-employment process, please contact the Talent Acquisition Office at jhurecruitment@jhu.edu. For TTY users, call via Maryland Relay or dial 711. For more information about workplace accommodations or accessibility at Johns Hopkins University, please visit accessibility.jhu.edu.

 

Johns Hopkins has mandated COVID-19 and influenza vaccines, as applicable. The COVID-19 vaccine does not apply to positions located in the State of Florida. Exceptions to the COVID and flu vaccine requirements may be provided to individuals for religious beliefs or medical reasons. Requests for an exception must be submitted to the JHU vaccination registry. For additional information, applicants for SOM positions should visit https://www.hopkinsmedicine.org/coronavirus/covid-19-vaccine/ and all other JHU applicants should visit https://covidinfo.jhu.edu/health-safety/covid-vaccination-information/.

 

The following additional provisions may apply, depending on campus. Your recruiter will advise accordingly.

The pre-employment physical for positions in clinical areas, laboratories, working with research subjects, or involving community contact requires documentation of immune status against Rubella (German measles), Rubeola (Measles), Mumps, Varicella (chickenpox), Hepatitis B and documentation of having received the Tdap (Tetanus, diphtheria, pertussis) vaccination. This may include documentation of having two (2) MMR vaccines; two (2) Varicella vaccines; or antibody status to these diseases from laboratory testing. Blood tests for immunities to these diseases are ordinarily included in the pre-employment physical exam except for those employees who provide results of blood tests or immunization documentation from their own health care providers. Any vaccinations required for these diseases will be given at no cost in our Occupational Health office.

 

Note: Job Postings are updated daily and remain online until filled.

 

 

Total Rewards
The referenced salary range is based on Johns Hopkins University’s good faith belief at the time of posting. Actual compensation may vary based on factors such as geographic location, work experience, market conditions, education/training and skill level. Johns Hopkins offers a total rewards package that supports our employees' health, life, career and retirement. More information can be found here: https://hr.jhu.edu/benefits-worklife/.

Accommodation Information
If you are interested in applying for employment with The Johns Hopkins University and require special assistance or accommodation during any part of the pre-employment process, please contact the Talent Acquisition Office at jhurecruitment@jhu.edu. For TTY users, call via Maryland Relay or dial 711. For more information about workplace accommodations or accessibility at Johns Hopkins University, please visit https://accessibility.jhu.edu/.

Equal Opportunity Employer
All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, or status as a protected veteran.

EEO is the Law:
https://www.eeoc.gov/sites/default/files/2023-06/22-088_EEOC_KnowYourRights6.12ScreenRdr.pdf

Remote