Developer II (Computer Science)

Johns Hopkins University•Baltimore, MD

1d•$53,800 - $94,400•Hybrid

About The Position

Whiting School of Engineering’s Computer Science Department is seeking a Developer II to assist the Phillippy lab in the development of bioinformatics methods for the analysis of long-read DNA sequencing data and personalized genomes. Assigned projects may include methods development for DNA sequencing, comparative genomics, genome assembly, and genome interpretation. The candidate will work closely with other members of the team, including students, postdocs, and senior staff, to advance the lab’s research mission. The Developer II participates in the creation, implementation, maintenance, performance, production support and documentation of various departmental and enterprise-wide application systems. This includes but is not limited to the installation, modification, and testing of new and/or upgraded applications (packages or homegrown), operating systems, file structures, hardware, communication devices, and productivity tools. Applies analysis techniques and procedures to gather and then translate business requirements into functional/technical specifications and designs. Using functional specifications and designs, produces all or part of the deliverables. Maintains databases and application system code.

Requirements

Bachelor’s Degree.
One year of related experience with computer systems and applications.
Additional education may substitute for required experience and additional related experience may substitute for required education beyond a high school diploma/graduation equivalent, to the extent permitted by the JHU equivalency formula.

Nice To Haves

Knowledge in the assigned application as well as the platform on which it runs.
Bachelor’s Degree in computer science or related field, with a breadth of coursework covering the sciences and math; advanced computing topics such as algorithms, graph theory, machine learning, and ethics; and specialized topics in computational biology
Strong practical computational skills, particularly in Python, R, and shell scripting (as well as C, Java, JS, Go, React, SQL)
Experience in a research computing environment, including with version control, pipeline development, and high-performance computing systems
Two plus years of experience working with genomic data, including knowledge and use of common, file formats: sam/bam, fastq, vcf, paf, bed.
software: samtools, bedtools, deepvariant, modkit, minimap.
pipelines / skills: alignment, variant calling, methylation data analysis.
Effective written and verbal communication skills and the ability to read and interpret scientific literature.
Interest in developing and/or applying computational methods for genome assembly, sequence alignment, variant detection, variant annotation, and information visualization.
Agile Methodology - Developing
Code Review - Developing
Debugging - Developing
JIRA - Developing
Microservices - Developing
Model View Controller - Developing
Product Life Cycle Management - Developing
Restful API - Developing
Secure Coding - Developing
Software Design Patterns - Developing
Software Development Life Cycle - Developing
Unit Testing - Developing

Responsibilities

Under guidance define business/clinical/education problems by meeting with clients to observe and understand current processes and the issues related to those processes.
Gather system requirements by meeting with clients and researching existing technology to understand the business requirements for new applications.
Develop detailed tasks by analyzing project scope and milestones for projects to ensure product is delivered quickly according to software lifecycle standards.
Write functional/technical specifications by taking the provided system requirements, putting them into functional and technical descriptions for use by programmers and business analysts to develop technical solutions.
Develop/change data input, files/database structures, data transformation, algorithms, and data output by using appropriate computer language/tools to provide technical solution for application development tasks.
Document code and associated processes by adhering to development methodologies, adding code comments and appropriate documentation to various knowledge-based system(s) to simplify code maintenance and to improve the support.
Create and document test scenarios using the appropriate testing tools to validate and verify application functionality.
Test all changes by using the appropriate test scenarios to ensure all delivered solutions work as expected and errors are handled in a meaningful way.
Author and maintain documentation by writing audience-appropriate materials to serve as technical and/or end-user references.
Implement changes by adhering to the change management policies and procedures for any given project to communicate to all parties the nature, significance, and risk factors of the solution.
Monitor changes and resolve problems by responding to problems as they occur, by reviewing all processing and output of the newly implemented solution, and by proactively ensuring the solution works successfully to satisfy the customer requirements and to provide a smooth transition to the new solution.
Provide support by triaging and resolving issues to ensure prompt, effective service.
Develop robust computational methods to advance comparative and personalized genomics.
Analyze data to contribute to biological discovery about previously inaccessible regions of the genome.
Maintain software engineering best practices and disseminate results and software.
Read scientific literature for background and to stay up to date in the field.
Meet frequently with supervisor to report on progress.
Present at internal lab meetings as well as to collaborators, and engage in all other lab activities.
Author scientific publications reporting on results and methods.
Support teaching activities as requested.