Bioinformatics Analyst III (Data Management), Laboratory of Dr. Todd Michael

The Salk Institute's Harnessing Plants Initiative (HPI) is an innovative and bold approach to fight climate change by optimizing a plant's natural ability to capture and store carbon and adapt to diverse climate conditions.

HPI is comprised of two programs: CRoPS (CO2 Removal on a Planetary Scale), which aims to develop crops called Salk Ideal Plants that can store more carbon in the ground for longer; and CPR (Coastal Plant Restoration), which is working toward genetically informed restoration and preservation of the world's wetlands, which act as signicant carbon sinks. In addition, more ground carbon means farmers benefit from improved soil health.

To accomplish this end, the Salk's HPI aims to understand which genes and molecular processes determine root traits that potentially increase carbon sequestration growth, as well as to test plant lines with such traits in lab, greenhouse and field environments and assess their effect on soil carbon accumulation and permanence. This research is directly leveraged in the pioneering CRoPS project that aims to develop crop plants that sequester more carbon via extensive root systems containing recalcitrant carbon polymers to fight climate change. For this we are working to enhance the carbon sequestration capacity in several important crop species throughout different soil types and geographies.

We are currently seeking a highly motivated and independent Software Engineer (full stack developer) to contribute to the system architecture (including design patterns, reliability, and scaling) of new and current systems for lab, greenhouse, and field trials data management. As such, the Software Engineer will interface with several Salk scientists and collaborating plant biology and soil scientists to contribute and develop and scale such systems.

Ideal candidates should be passionate about mitigating climate change, intellectually curious, highly productive, and enjoy working in a committed and diverse team driven to uncover new and impactful solutions with application to the larger problem of climate change. The Software Engineer will join a vibrant group of molecular biologists, plant geneticists, computational biologists, and soils scientists to work in a team that is determined to address a global problem with the power of plant biology and soil science.

(75%) Data Management and Organization

• Apply full stack development expertise in both front end and back-end systems.
• Translate Excel data to structured cloud database storage.
• Merge server to lab equipment via telemetry.
• Develop HPI-wide data naming and structuring conventions for additional data pooling and analyses.
• Provide consultation to HPI PI's and scientists on various topics related to research computing, including (but not limited to) the use of existing services, service policies, and research requirements.
• Ensure protocols and applications used to conduct research are in compliance with data agreements.

(5%) Research Data Design and Presentation

• Contribute and assist with project inception, experimental design, analysis, and result presentation.
• Assist with the preparation of data for: manuscripts, publications, grant applications, posters, and other presentations.
• Present results verbally and with visual aids in one-on-one meetings, group meetings, or conferences.
• Maintain digital and analog lab notebook, including experimental design, time, methods, materials, and results.

• Work closely with researchers from multiple laboratories and scientific backgrounds simultaneously.
• Work independently or with limited supervision on informatics research projects under direction from senior core staff or with research collaborators.
• Use published pipelines, scripts, and tools to prepare and process large datasets.
• Work in a cloud computing environment.
• Keep informed of new developments and technical advances in the data science and machine learning fields by reading primary literature and vendor websites.

• Keep abreast of new scientific advances in bioinformatics, data science, artificial intelligence, machine learning and biological fields related to current projects.
• Research, implement, and test, and present on new tools and pipelines for high- throughput data analysis.
• Participate in the design and coding of analysis pipelines and cutting-edge data analysis algorithms.
• Participate in the design, coding, and presentation of novel analysis tools for cutting- edge data analysis.
• Present advanced analysis results, tools, and pipelines at group meetings, scientific conferences, and scientific journals under the supervision of senior core personnel.

• Provide assistance and training to researchers on how to analyze and interpret data.
• Help educate and advise researchers on the pros and cons of available analysis tools, and approaches, in one-on-one training sessions, or larger group workshops.
• Ensure users are aware of the limitations of analyses and approaches to help ensure high standard of scientific research.
• Provide training to graduate students, less experienced bio informaticists, and/or research assistants as needed.

• Help maintain scripts, software, website, tools, wiki, and pipelines.
• Help ensure that servers, hardware, and cloud instances relevant to data analyses are operating properly and report all possible problems.
• Bridge the data management gap between satellite sites, collaborators, and main campus.
• Bolster network connectivity between Salk / HPI satellite sites.
• Liaise with IT department and manufacturers with regard to hardware or software maintenance, data security, and implementation of regular data back-ups.
• Upload genomic data to SRA/NCBI for long term retention.

Required:

• A minimum of 6 years of related experience or equivalent combination of education and experience. If PhD, experience acquired through PhD program may be considered in lieu of professional experience.
• Intermediate to expert programming experience (Perl, Bash, Python, C/C++, Java, R or equivalent).
• Strong presentation and communication skills.
• Experience working in a Linux/UNIX operating system in a high-performance computing environment.
• Familiarity with cloud computing and containerization.
• Postgres database, AWS cloud development, Lambda, EC2 and Docker; and
• Knowledge of React and/or Retool development tools.

Preferred:

• Experience with analyzing plant field, lab and genome data.
• Familiarity with next-generation sequencing technologies and assays.
• Background and/or experience with machine-learning algorithms and/or computational modeling.

Required:

• Bachelor's degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics, related discipline or equivalent.

Preferred:

• MS degree or PhD degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics, or related discipline.

Required:

• Proven organizational and time management skills to successfully set priorities, meet established deadlines, and recognize new problems with constantly changing priorities and frequent interruptions.
• Strong communication skills (both verbal and written) needed to interact professionally and effectively in the work environment. Ability to read, comprehend, and discuss research materials. Proven ability to write, edit and proofread research results. Skill at explaining difficult concepts and training users and students.
• Ability to interact diplomatically and professionally with all levels of Institute staff and external contacts.
• Ability to identify, download, install, troubleshoot, and assess new analysis tools.
• Experience with standard business office equipment and commonly used software and tools, such as Microsoft Office, electronic mail, and the internet.

Preferred:

• Experience applying machine learning approaches for data integration and data mining.
• High proficiency in a scientific programming language (Perl, Python, C/C++, Java, R or Web applications).
• Demonstrated knowledge and experience with MAC or Linux/UNIX operating systems.
• Theoretical and practical knowledge of biological sciences (particularly clinical and molecular biology).

The salary range for this position is $100,000 - $131,000 annually.

• Must be willing to work a flexible schedule to support research needs.
• Successful completion of the Institute's background investigation.
• Must be willing to sign a confidentiality agreement.
• Must be willing to work in an animal-related research environment.

This position will be constantly adjusting focus, seeing, sitting, touching/feeling.