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Staff Software Developer

Lawrence Berkeley National Laboratory
Berkeley, California
This is a full-time career appointment, exempt (monthly paid) from overtime pay.
Closing date
Dec 30, 2021

View more

Field of specialization
Information Science
Work Function
Job Type
Full time
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Staff Software Developer - 94092

Organization: JG-Joint Genome Institute


Lawrence Berkeley National Lab’s (LBNL, Joint Genome Institute Division ( has an opening for a Software Developer to join the team.


In this exciting role, you will lead the design and development of software in support of synthetic biology projects.  Acting as a key contributor, will utilize in-depth and advanced knowledge in bioengineering, genomics, and computational biology to develop computational tools and approaches for the design, assembly, and sequence QC of synthetic DNA constructs and combinatorial libraries, and may coordinate activities of other personnel. Duties and responsibilities include working closely with the DNA Synthesis Platform to build and implement computational tools enabling streamlined deployment of cutting-edge molecular approaches at scale, with an approximately 80/20 split between tool development and team lead.  Will provide feedback to end users on both technical and biological interpretation of the data. Will collaborate with various JGI groups on data analysis and facilitate transfer of knowledge of technologies and applications to JGI staff as needed. You will report to the DNA Synthesis Platform Lead.


What You Will Do:

Software developer 

• Lead and/or participate in the development of computational approaches to aid in the design, assembly and analysis of DNA constructs, oligonucleotide pools and synthetic libraries. 

• Work closely with the platform group to provide interpretation of downstream data output and iteratively improve design software accordingly.

• Maintain an accurate and detailed documentation of tools developed.

• Ensure that developed tools have biologist-appropriate user interfaces and functionality. 

• Present technical and analytical status updates in weekly meetings. 

• Contribute to scientific research papers, reports and presentations. 

• Follow standard practices for executing version control, testing, and release.

• Implement data-specific user interfaces and data retrieval reports.

• Assist users to resolve tool malfunction or data entry errors.

• Survey and provide feedback on existing and new third-party software that can be incorporated into our workflows.

• Provide updates of progress in regular meetings.

• Promote a culture that reflects JGI core values of work/life balance, respect, teamwork, collaboration, diversity & inclusion, team-building, employee development, communication, and first-rate science. 


Team lead of the DNA Synthesis Bioinformatics group 

• Strategize for and develop future informatic applications. 

• May coordinate activities of other team members.

• May manage collaborative projects with other teams. 


What is Required:

• A minimum of 8 years of experience programming in Python, Java or R in a UNIX environment with a Bachelor's degree; or 6 years and a Master's degree.

• Experience successfully managing and leading a team of software developers in a research science setting. 

• Extensive experience leading all stages of independent scientific software development projects through publication in peer reviewed journals and presentation at scientific meetings.

• Knowledge of synthetic biology/bioengineering/computational biology/genome science.

• Proficiency with scripted programming languages (Python preferable) in a Unix environment.

• Proficiency with object-orientated languages (JAVA preferable).

• Experience with web application frameworks (Tomcat/Django/Flask).

• Experience with relational database design, query language, and administration (SQL, Postgres, MySQL).

• Experience with HPC environments.

• Experience with containers (Docker). 

• Experience with web development and related technologies (Javascript, ORMs, REST APIs).

• Familiarity with full stack software development and deployment.

• Analytical skills sufficient to troubleshoot discrepancies in data results and make improvement recommendations.

• Strong organizational and record-keeping skills.

• Experience with and adherence to software development best practices (version control, code review).

• Effective oral and written communication skills as well as interpersonal skills.

• Ability to work independently and as a team member in a diverse team environment.

• Ability to handle multiple tasks in parallel while working on a large number of projects.

• Effective problem-solving, decision-making, organizational and analytical skills.


Desired Qualifications:

• Ph.D. degree in computational biology, bioinformatics, synthetic biology, or a similar field.

• Experience performing computational analysis of complex biological datasets, focused on biological design.

• Familiarity with commercial laboratory software (e.g. Benchling, LabKey etc). 

• Experience in writing software for analysis of DNA sequence or experimental data.

• Proficiency in utilizing assembled genomes, various alignment tools, visualization tools, and other genome interrogation and analysis software.

• Familiarity with statistical tools and interpretation of data. 

• Proficiency with compiled programming languages (C/C++, Java or others) in a Unix environment.

• Experienced with Data Exchange Standards in synthetic biology such as SBOL.

• Experience with workflow managers (Cromwell preferable).



• This is a full-time career appointment, exempt (monthly paid) from overtime pay.

• This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.

• Work will be primarily performed at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.


How To Apply

Apply directly online at and follow the on-line instructions to complete the application process.


Equal Employment Opportunity:

Based on University of California Policy - SARS-CoV-2 (COVID-19) Vaccination Program and U.S Federal Government requirements, Berkeley Lab requires that all members of our community obtain the COVID-19 vaccine as soon as they are eligible. As a condition of employment at Berkeley Lab, all Covered Individuals must Participate in the COVID-19 Vaccination Program by providing proof of Full Vaccination or submitting a request for Exception or Deferral. Visit for more information.


Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA, and strives to continue building community with these shared values and commitments. Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab's mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status.


Equal Opportunity and IDEA Information Links:

Know your rights, click here ( for the supplement: Equal Employment Opportunity is the Law and the Pay Transparency Nondiscrimination Provision ( under 41 CFR 60-1.4.

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