Boyce Thompson Institute for Plant Research - Senior Bioinformatics Analyst bei Boyce Thompson Institute for Plant Research

Summary

The position will focus on analysis of large-scale biological datasets, and maintenance and development of existing and novel databases or informatic infrastructures. 

Conduct analyses as directed by a supervisor, including:

§ Foundational knowledge in most relevant programming languages, bioinformatic software, and pipeline development tools

§ Ongoing training in new software’s required for bioinformatic projects

§ Assisting with the preparation of reports, manuscripts and presentations

§ Operates with complete oversight by the PI, research scientists, and/or specialists in the lab

§ Extensive knowledge in all relevant programming languages, bioinformatic software, and pipeline development tools

§ Has the capacity to operate semi-autonomously with moderate oversight by the PI, research scientists, and/or specialists in the lab

§ Design analyses to support questions/hypotheses from PI/supervisors

§ Collaborate with principal investigators (PIs) in formulating research questions and hypotheses

§ Has the capacity to operate completely autonomously with minimal oversight by the PI, research scientists, and/or specialists in the lab

§ Has the capacity to train others on bioinformatic software and analyses

Participate in professional development activities, which may include:

§ Regular meetings regarding the progress and direction of research with the supervisor or in group meetings

§ Participating in Institute seminars and events

§ Participating in activities to develop communication, management and other soft skills

§ Participating in BTI committees/societies

§ Attending conferences

Essential Job Functions

Working independently and only under very general supervision of the Principal Investigators (PI’s), interact with the users of The Triticeae Toolbox (T3) to identify and document new user needs, and develop plans to engineer these into software features of T3. Organize and improve the overall software engineering / development system that we use at T3. Maintain reliable systems administration of the T3 servers. Respond to requests from the Jannink Lab for specific data searches and document the queries that enabled those searches. Assure that the program achieves the project outcomes by facilitating communication and accountability among collaborators, managing project work plans, timelines and tasks, developing semi-annual reports, develop and update content for project web pages, aiding in program communication with collaborators. Work with PI on the overall evaluation of the project activities and outcomes to implement surveys, and collaborate with the PI in analyzing and summarizing the survey data to help the collaborators use this information to modify work plans and tasks. On a more local level, perform similar upload tasks for data from the Cornell small grains breeding program in conjunction with Dr. Mark Sorrells. Advocate for T3/oat among North American oat geneticists and breeders. This advocacy will involve acquiring a detailed knowledge of the T3 database and an ability to demonstrate its features and interpret their value for breeding. Will need to travel to visit with researchers across North America for this purpose.

Small grains breeding program data upload: Data Entry (15%):

Prioritize interaction with members of the Wheat Coordinated Agricultural Project to upload their data when issues arise. Maintain a “Contact Us” link to enable data upload of small grains breeding data from other programs world wide, as the demand arises. Maintain contact with coordinators of small grains cooperative nurseries led by the USDA to streamline their operations for data upload. Do the same for groups of small grains breeders operating nurseries independently of USDA.

Improve T3 useability and communicate with users (20%):

Assist in developing feature concepts and work project through to delivery and support. Discuss with T3 users features that may be useful for them. Write requirement documents that describe the needs and how they would be implemented. Estimate the complexity and time that it may take to implement these features. Provide brief presentations and prepare discussions of these issues. Design, develop, support, training and enhancements to T3. Create and document workflows that will be useful for T3 users. Describe these workflows in documents with exercises that can be used for training. When a new feature or workflow is only partially complete, create presentations of the current state of these developments to present to T3 users for their guidance to prioritize next steps.

Development of new features and performance improvement (35%):

Find ways to efficiently and effectively manage T3 in development, test and production tasks. Create unit tests for any features that we develop. Run tests prior to deployment of new database frontends or patches. Respond to and resolve database access and performance issues. Assess where bottlenecks occur when there are query or data transfer performance issues. If these issues are resolvable within our group do so. If the issues require coordination with the main Breedbase development group, initiate that coordination. Create ticketing and tracking systems for coordinated development. Work with developers to design and implement applications. Work with other Breedbase and surrounding digital ecosystem teams to conceive and develop BrAPPs. These are small modular applications that use the BrAPI application program interface specification to extract data from T3 and analyze or visualize it in ways that are useful for T3 users and users of other BrAPI compliant databases. Work with team members to develop overall priority of feature development and implementation. Create ticketing and organizing systems to track and discuss progress. In some cases, coordinate developments with the main Breedbase development team and / or with the Android Field Book development team. If other developers are relevant (e.g., BrAPP developers) communicate with them and create coordination. Conduct research and make recommendations on database products. Given discussion of database needs and / or user experience needs, find external services (typically web services) that might fulfill those needs, create descriptions of those services useful to team members and lead discussions on the purchase and use of those services. Create models for new database development and/or changes to existing ones. Plan and coordinate data migrations between systems. Determine best practices for moving data between Production public databases, Sandbox databases used for initial data upload, and Password-protected databases with embargoed data.

System Administration of T3 (15%): 

Assist with designing and implementing systems, policies, procedures for T3 backups and data archiving to ensure effective protection and integrity of data assets. Create plans and implementation for regular backups and recovery in the case it’s needed. These plans are needed both for the database and for front end user-facing interfaces. Install and configure relevant network components to ensure database access, database consistency and integrity. Administer Docker images of the database. Track versioning of the three species specific databases (wheat, barley, oat), the “sandbox” databases that parallel them that are used for data upload, as well as password-protected databases with embargoed data. Install, upgrade and maintain relational databases, middleware and related tools. When PostgreSQL updates occur, determine if the update is needed by T3 and if so, develop plans to update the underlying engine without disruption to the site. Create administration scripts to monitor memory use of the system and analyze system logs to identify potential problems. 

Provide data and functional analysis for the lab group (10%):

Create, review and tune SQL and PL/SQL code for Jannink Lab members. Given specifications by team members, develop database search functions and queries that enable the identification and extraction from the database of datasets that have characteristics useful for plant breeding analysis. For all specific searches and queries, document these for other current and future data curators.

Participate in projects or other duties as assigned with occasional work responsibility falling above or below current classification. 

Completion of any university required compliance trainings. 

Pursue individual professional development as determined jointly with supervisor.

Attend training and expansion of skills through participation in job related courses, seminars and workshops.

Continuously maintain all required educational and position qualifications to fulfill job requirements.

Education and Certification

· A Master’s degree in Bioinformatics, Computer Science or related fields, or a Bachelor’s degree with significant relevant experience.

· Experience in and/or demonstrated commitment to supporting diversity, equity, access, inclusion, and wellbeing. 

· Passionate about working in an organization that values and promotes diversity, equity, inclusion, anti-racism, and wellbeing. 

· Ability to serve as an advocate for individuals of all ethnicities, genders, ages, and backgrounds. 

· Ability to cultivate and develop inclusive and equitable working relationships with students, faculty, staff, and community members.

Experience and Knowledge

· Experience with Linux

· Proficiency in at least one programing language such as Perl, Python or R

· Experience with analyzing next-generation sequencing data, and genomic and genetic data

· Experience with web-based bioinformatics database development

· Ability to work effectively in a team environment;

· Good communication and analytical skills.

· Understanding of the design and conduct of plant breeding field trials. Experience collecting data in such trials. Attention to detail. Strong interpersonal skills and ability to work as part of a diverse team, while contributing to a high-quality and respectful work environment. Excellent oral and written communication skills, with the ability to communicate effectively with colleagues and staff across multi-disciplinary areas. Ability to help establish realistic goals and deliver work on schedule. Ability to work independently and solve problems as they arise. Ability to communicate with tact and diplomacy with a wide range of people. Ability to handle sensitive/confidential material. Travel as needed for project both locally and internationally. Must have and maintain a valid driver license. Driver check will be conducted.

· Bachelor’s in plant breeding or in some area of Plant Science and two years experience in plant breeding / or Master’s in some area of Plant Science involving research. Experience with small grains agronomy or genetics and/or experience working with databases. Experience with careful listening and interpretation in discussions with plant breeders.

· Five or more years formal or informal experience in software engineering.

Supervisory Responsibilities

No direct supervisory responsibilities. May provide mentoring to undergraduate and graduate student workers.

Communication Skills

Effective written and verbal communication, as well as interpersonal skills, are required. Ability to maintain accurate lab notebooks and electronic records in English. Ability to draft publications and sections of grant proposals. Ability to speak effectively one-on-one or in small groups, and to present information to groups internal and external to the Institute.

Computer Skills

The position requires the proficiency in basic business applications, and may require use of scientific programs.

Travel

Occasional travel to off-site meetings or conferences. Occasional fieldwork may be required.

Physical Demands and Working Conditions

Some physical exertion may be required such as long periods of standing, recurring bending and occasional lifting when participating in field work. May require occasional early morning, evening or weekend work.