Bioinformatician I 40 Hours Days Bwh - Path Bioinformatics

Brigham and Womens Hospital is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race sex color religion national origin sexual orientation protected veteran status or on the basis of disability.

GENERAL SUMMARY/OVERVIEW STATEMENT:

The Center for Advanced Molecular Diagnostics (CAMD) is the clinical molecular diagnostics laboratory for three Harvard Medical School hospitals: Brigham and Womens Hospital DanaFarber Cancer Institute and for the pediatric cancer patients of Boston Childrens Hospital. Our mission is to provide innovative molecular and cytogenetic diagnostic services to assist with the clinical care of patients in our hospitals and affiliated clinics with a primary focus on cancer care. This is exemplified by the PROFILE program which is a collaborative effort to advance translational and personalized cancer medicine by implementing tumor genomic profiling for all cancer patients who receive care at one of the collaborating hospitals. PROFILE employs stateofthe art genomics technology to generate a detailed report of medically actionable genetic alterations in a CLIAcertified and realtime process to facilitate rapid clinical application. These cancer genomic profiles are being used to guide patient treatment and/or stratification for clinical trials of novel anticancer agents.

Working under very general supervision the Computational Bioinformatician I will have demonstrated competency is one of more of the following areas of specialization: algorithm development data analysis quality assurance/testing pipeline software/computing development user interface design & report development webbased application development Laboratory Information Management System (LIMS) development or report development as described below.

PRINCIPAL DUTIES AND RESPONSIBILITIES:

Algorithm Development:

1.Design and apply bioinformatics algorithms using tumor sequencing data building data models and databases using various software and statistical tools to aid in the analysis and interpretation of genetic data.

Quality Assurance/ System Testing:

2.Analyze data quality and integrity of data output from existing algorithms as part of the complex multistep specimen tracking and reporting process across multiple systems and webbased interfaces

Data Analysis:

3.Analyze large molecular datasets of tumor sequencing data to help critically review and analyze the results of specimen testing working closely with faculty and staff to troubleshoot problems recommend technologybased solutions or determine computational strategies.

Pipeline:

4.Design maintain and troubleshoot data processing/software pipelines and data architecture using various computational tools.

User Interface/Report Development:

5.Modify and develop new data visualization tools using datasets and webbased bioinformatics tools with emphasis on integrating various data types identifying opportunities and needs for innovative solutions for the analysis and management of biological data in relevant databases.

6.Collaborate with other PROFILE IS group staff and Center leadership on the development of software and custom scripts to automate data retrieval improve user interfaces create new statistical tools and reports etc.

7.Modify existing website content and develop new content and user tools

LIMS Maintenance & Development:

8.Maintain troubleshoot and modify existing webbased Laboratory Information Management System (LIMS) which is a locally developed application that tracks specimens throughout the sequencing and data analysis process involving complex instrument/software interfaces.

9.Manage interfaces between LIMS and other clinical software systems which use LIMS data. The major example is PowerPath which is the software platform through which interpretative case reports are generated and released to clinicians and investigators.

General:

10.Work with CAMD/PROFILE leadership on other research collaborations for DFCI/BWH or outside investigators

11.Collaborate with other faculty and staff on the communication of research results through conference presentations scientific publications or project reports.

12.Provide direct technical and scientific customer support for Profile investigators and staff.

13.Train technical and other staff on new applications processes hardware etc.

14.Performs all other duties and responsibilities as directed.

BIOINFORMATICS SOFTWARE ENGINEER

The Bioinformatics Software Engineer will join the current bioinformatics group to design build and test the analysis workflow infrastructure for genomic data generated by nextgeneration sequencing (NGS).

The Bioinformatics Software Engineer will report to the Group Leader of Bioinformatics and will have the following responsibilities:

Develop test and deploy productionquality highperformance software and highlyscalable algorithms to work with nextgeneration sequence data

Take a lead role in designing and implementing the next iteration of our NGS sequencing pipeline.

Work collaboratively with other bioinformaticians and lab members to define requirements and specifications for the pipeline and analysis tools

Additional tasks including but not limited to: Rapidly learn code base and tools. Automate and implement additional functionality to current pipeline. Provide input on functional design of future projects. Work closely with end users to debug problems in production environments.

QUALIFICATIONS:

1.Minimum of 2 years of relevant experience in bioinformatics computational biology or programming/analysis working in a research and/or clinical environment working with large research datasets. Experience working in a large cancer genetics research or clinical program highly desirable.

2.Bachelors degree in bioinformatics systems or computational biology computer science or equivalent required. Advanced degree preferred.

3.Proven strong programming skills and experience in algorithm development in both Windows and Linux environments.

SKILLS/ABILITIES/COMPETENCIES REQUIRED:

1.Excellent attention to detail

2.Excellent organizational and problem solving skills

3.Strong communication skills to be able to work effectively with multidisciplinary staff interacting with individuals at many levels of multiple institutions.

BS/MS in Computer Science Bioinformatics Engineering or related discipline with 3 years experience is required.

Demonstrated experience building largescale software systems is essential

Expert level of objectoriented design in Java/Python in a UNIX/Linux environment utilizing agile development methodologies is required.

Prior experience using pipeline frameworks (bpipe or similar) is preferred

Experience using short read alignment algorithms for both DNA and RNA

Experience with unit testing best practices for version control and source code management systems (svn/git) is required.

Must be familiar with cluster based computing. Prior experience with SGE is a plus.

Excellent communication and effective problemsolving skills; and ability to interact with multidisciplinary staff in a fastpaced environment. The successful candidate should be able to work independently prioritize and manage a variety of tasks and shift priorities rapidly.

WORKING CONDITIONS:

Fast paced laboratory environment with large workload and frequent deadlines