Bioinformatics Engineer

Windber, PA; Windber (PA); On-site; USD 90,000 - 130,000; Full time

Job summary

CSSIMMW is seeking a highly skilled Bioinformatics Software Engineer to join the cross-functional team between the Biomedical Informatics Infrastructure and Bioinformatics departments in Windber, PA. The role focuses on developing, deploying, and integrating experimental data into software for visualization and analysis of large cancer datasets.

The ideal candidate brings a Master's degree in a related field and at least four years of experience with genomic data, open-source visualization

Qualifications

• Master's degree in Bioinformatics, Computational Biology, Computer Science, Life Sciences/Molecular Biology or related field.
• Four years minimum experience working with genomic and related data.
• Experience with open-source web-based applications for visualization (e.g., cBioPortal).
• Four years minimum experience developing software tools with C#, Python, R, JavaScript and SQL.
• Experience with cloud technologies such as AWS.
• Proficient in Windows and Linux environments.
• Strong communication, problem-solving, and collaboration skills.
• Ability to manage deadlines and multi-task in a dynamic environment.

Responsibilities

• Evaluate and implement new bioinformatic systems and data visualization solutions (e.g., cBioPortal).
• Lead data operations to visualize large cancer-related datasets and integrate results into open-source web-based frameworks.
• Provide application support and data query/analysis support to researchers.
• Contribute to QA/QC during development, upgrades, and deployment of systems.
• Write reports and present research results to leadership and in publications.

Skills

Bioinformatics

cBioPortal

Software development

Cloud (AWS)

Windows/Linux

Communication

Project management

Teamwork

Education

Master's degree in Bioinformatics

Tools

C#

Python

R

JavaScript

SQL

AWS

Job description

Job Details Job Location: Windber, PA 15963 Position Type: Full Time Education Level: Graduate Degree Travel Percentage: Negligible Job Shift: Day Job Category: Biotech

PURPOSE OF JOB:

The Bioinformatics Department at CSSIMMW is responsible for providing bioinformatic and analytical support to the daily operations of the institute and conducting translational research in both technological and scientific fields. And the Biomedical Informatics Infrastructure Department is responsible for providing informatics support for the daily operations of the institute, including support for biomedical informatics research in both technological and scientific fields. This is a cross-functional position between the two departments that is responsible for development, deployment and integration of experimental data and results into software used for visualization and analysis of large-scale cancer data sets. A strong understanding of bioinformatics and software application development is critical to develop and maintain applications and data operations. This position requires extensive communications with supervisors, peers, and end users.

ESSENTIAL FUNCTIONS OF JOB: (other duties may be assigned)

• Evaluate and implement new bioinformatic systems.
  • Evaluate and test both internal and external systems, with emphasis for data visualization and interpretation (ex. cBioPortal).
  • Make recommendations to leadership on the selection of new systems.
  • Collaborate with IT admins and development teams on software installation, upgrade, and deployment.
  • Contribute to QA/QC of the new system and on each upgrade.
• Lead data operation to visualize large complex cancer related data sets
  • Integrate project results data into open-sourced web-based software framework for visualization and interpretation of large data sets (ex. cBioPortal)
  • Evaluate new data types and formats, for integration to our system, and create necessary parsers.
  • Configure the system interface for new data types and analyses
  • Responsible for all QA/QC of the data and display before releasing to the users
• Provide user support
  • Provide application support to users
  • Provide data query and analysis support to internal and external researchers
  • Gather user feedback for improvement
  • Support the integration with other databases and software systems.
• Contribute to the improvement of bioinformatics and software systems within the institute
  • Keep up to date with advancements in bioinformatics and software engineering for the continuous improvement of our systems.
  • Participate in requirement gathering, design, and development of new applications and modifications to existing applications
  • Contribute to QA/QC of the applications in close collaboration with the development team.
• Write reports and abstracts
  • Provide summary reports to leadership
  • Present research and development results in peer-reviewed journals and conferences
  • Support grant applications

OTHER DUTIES OF THIS POSITION:

• Handle all confidential and proprietary information in accordance with policies and procedures.
• Assist other staff as needed and assigned.
• Maintain a clean and safe working environment
• Adhere to safety standards and regulations of the Institute.
• Perform preventative maintenance, troubleshooting, and operation of scientific equipment interfacing with technical support and sales staff as needed.
• Provide training to employees and interns as needed
• Participate in CSSIMMW’s community involvement activities.
• Attend meetings, training sessions, and presentations as necessary.
• Perform other related duties as required.

SUPERVISION RECEIVED:

This position is under the supervision of the Director of Bioinformatics.

SUPERVISION GIVEN:

None.

MENTAL/PHYSICAL REQUIREMENTS OF JOB:

• CONSTANTLY (75 - 100%)
• Ability to sit, reach, communicate orally and hear conversation; Repetitive finger movement; Use of depth perception and color vision; Ability to use both hands and both legs
• FREQUENTLY (25 - 75%)
• Ability to stand, walk; Ability to lift and carry: Light (Max 10 - 15 lbs.)
• OCCASIONALLY (0 - 25%)
• Ability to lift: Mod (Max 25 lbs.); Ability to push/pull (est. weight: 10 - 15 lbs.)
• Ability to manage multiple projects/tasks, pay close attention to details, work in a constantly changing environment. work with high pressure for results, meet frequent deadlines, have a high level of decision making, ability to establish own goals, have a predictable work schedule, work closely with others, be creative, maintain adequate record keeping and routine paperwork.

WORK ENVIRONMENT:

This position occasionally requires: General laboratory environment.

PERSONAL PROTECTIVE EQUIPMENT:

This position requires standard lab PPE including lab coat and gloves when in the lab setting.

QUALIFICATIONS:

Education/Training/License/Certification:

Master's degree in Bioinformatics, Computational Biology, Computer Science, Life Sciences/Molecular Biology or a related field.

Work Experience:

• Four years minimum experience of working of different genomic and experience data.
• Advanced experience working with open-source web-based applications used to visualize large data such as cBioPortal
• Four years minimum experience developing software tools using programming languages, such as C#, Python, R, JavaScript, and SQL
• Experience with cloud technologies such as AWS
• Experience interfacing with both scientific and engineering teams
• Proficiency working in Windows and Linux environments
• Pragmatic self-starter who is proactive, self-motivated, team-oriented, and customer-focused with a strong work ethic
• Ability to meet deadlines within a dynamic environment and able to handle multiple tasks simultaneously while adapting to changing priorities
• Proactively learns products and new projects and stays abreast of Bioinformatics, computational or industry trends
• Excellent verbal and written communication and strong problem-solving skills
• Demonstrated skills in project management and formal continuous process improvement techniques
• Ability to work effectively in collaboration with diverse groups of people
• Ability to use Windows OS and Microsoft Office applications

KNOWLEDGE, SKILLS, AND ABILITIES REQUIRED:

• Capability to work independently and as a team player
• Strong understanding of software design and architecture.
• Strong understanding of Bioinformatics
• Advanced skills integrating data into open-source web-based applications for visualizing large data sets (cBioPortal experience would be a plus)
• Experience implementing modern web-based user interface designs
• Excellent oral and written communication skills, including an ability to deal with people at various levels.
• Ability to work well under pressure, facilitate solutions, and meet deadlines and milestones for projects assigned.
• Ability to present experimental results in an appropriate format.

OTHER:

• Work is performed entirely in support of grant funded programs and is therefore dependent solely on the availability of funds.
• New Incumbents incur six months probationary periods.