Bioinformatics Software Developer (Prokaryotic Superprogram)

Lawrence Berkeley National Laboratory
Job Location
Walnut Creek, CA
Job Description

Bioinformatics Software Developer (Prokaryotic Superprogram) - 80319

Organization:  GN-Genomics


The Department of Energy (DOE) Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an immediate opportunity for a skilled and creative bioinformatics software developer to develop models and algorithms to mine large-scale genomics data for novel secondary metabolite gene clusters. 


The ideal candidate will be comfortable working with very large datasets in an interdisciplinary scientific group and regularly presenting technical results to a scientific audience. Must be familiar with basic structural and functional annotation of prokaryotic genomes. A few years of experience with software development in JAVA/ Perl/ Python plus experience with relational databases are required. A background in algorithms and machine learning algorithms and/or experience with web-based development are highly preferred. 



• Collaborate successful with team members that develop algorithms and models for discovering novel biosynthetic gene clusters. 

• Gather feedback and requirements to design and develop software for the above and take ownership of the software. 

• Design effective solutions compatible with existing systems, namely, the (Integrated Microbial Genomes) IMG family of systems. 

• Interface with biologists and biochemists to gather feedback and requirements. 

• Develop production quality software/pipelines for data loading in IMG. 

• Participate in formal and informal design and code reviews. 

• Apply analytical skills and creativity to troubleshoot problems. 

• Contribute to the growth and maintenance of IMG ABC (IMG-ABC, Atlas of Biosynthetic gene Clusters). 

• May create documentation and training materials. 


In addition to the above, the following are responsibilities for a higher-level software developer: 

• Work at a higher level of independence and responsibilities in carrying out assignments. 

• Work closely with the systems administration group to optimize hardware and configuration for maximal portal performance and stability. 

• Troubleshoot more complex systems and data analysis problems. 



• Degree in Computer Science, Engineering, Bioinformatics, or related field plus typically a minimum of two years of relevant work experience 

• Experience with genomics data, analytical tools, and methods 

• Demonstrated success designing, implementing, and supporting large systems and software in a scientific or technical environment 

• Good working knowledge of basic genomic concepts, data types, and data analysis methods, and their representation in software systems 

• Demonstrated experience coding and debugging Java and Perl 

• Demonstrated experience with database systems 

• Expertise with web development: HTML, CSS and Java script 

• Proficient SQL skills, with good knowledge of database performance optimization related to schema design 

• Proficient analytical, problem-solving and decision-making skills to independently make sound judgments and creative solutions to moderately complex problems 

• Effective time management, organization and planning skills; ability to work effectively in team environment 

• Good software development practices (e.g., self-documenting code, source control, bug tracking) 

• Preferred - Experience with SGE or other HPC environments 

• Preferred - Experience with large MySQL-based data sets 


In addition to the above, the following are qualifications for consideration as a higher-level software developer: 

• Overall equivalent of education and relevant work experience as a relevant degree plus typically five years of work experience; advanced degree is preferred. 

• Extensive genomic analysis software experience, and substantial knowledge of various bioinformatics algorithms related to sequence analysis 

• Previous experience as a key developer on a genomics project 

• Demonstrated knowledge and proficient technical ability in full life-cycle software development, database design and access, web user interface design, development and deployment. 

• Ability to troubleshoot complex web component and database systems issues 


Notes: A single 1-year term appointment will be hired at the job classification level appropriate for the successful candidate’s breadth and depth of relevant experience. The appointment may be renewed and/or convert to career based upon successful performance, continued funding and ongoing need. A background check is required. 


Working schedule: Due to the research project objectives and related challenges, working on evenings and weekends is very common. (This is an exempt level position with no overtime pay.) This role collaborates closely with dedicated research staff who are successful within this high-pressure environment. As an ongoing component of this impactful work, success in this role is high profile and may lead to first author in related publications. 


How To Apply

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


About Us 

Rapid technological advances in genomics have transformed modern biology. From its inception, the Department of Energy Joint Genome Institute has been at the forefront of large-scale sequence-based science. Learn more about JGI happenings at and about opportunities at 


Research in the OMICs Analysis group is focused on: 1) Unraveling the depths of biological phenomena in microbes and metagenome communities using large-scale analysis of –omics data; 2) Developing forward-looking strategies for the deployment of computational workflows at peta- and exa- scales on multicore and manycore architectures with the ultimate objective of facilitating omics-based scientific investigations. Learn more about the OMICs Group at the JGI ( 


Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Berkeley Lab’s science is a global enterprise. Our scientists work at the frontiers of knowledge to better understand our universe and to address the challenges facing our nation and our planet. Read about our excellent benefits ( 


Berkeley Lab is an Equal Opportunity/Affirmative Action Employer.  All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status.

How to Apply

How To Apply

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

NIH's Michael Lauer looks at the number of grants, their amount, and funding success rates at the agency for last year.

At Nature, Johns Hopkins' Gundula Bosch describes her graduate program that aims to get doctoral students thinking about the big picture.

Patricia Fara writes about childcare funding, and women in science and science history at NPR.

National Institute of Environmental Health Sciences researchers have visualized the career paths of former postdocs.