Data Processing Specialist - Thoracic Surgery

Job title: Data Processing Specialist - Thoracic Surgery

Site: The Brigham and Women's Hospital, Inc.

Mass General Brigham relies on a wide range of professionals, including doctors, nurses, business people, tech experts, researchers, and systems analysts to advance our mission. As a not-for-profit, we support patient care, research, teaching, and community service, striving to provide exceptional care. We believe that high-performing teams drive groundbreaking medical discoveries and invite all applicants to join us and experience what it means to be part of Mass General Brigham.

Job Summary

Responsible for acquiring data from primary or secondary data sources and maintaining databases/data systems. Also responsible for identifying, analyzing, and interpreting trends or patterns in complex data sets and cleaning data to correct problems.

Qualifications

Education

• Bachelor's Degree Management Information Systems required or Bachelor's Degree Related Field of Study required Master's Degree Related Field of Study preferred

• Can this role accept experience in lieu of a degree? No

Experience

• Data Analysis

• 2-3 years required

• Essential Functions (Key Roles & Responsibilities)

• Cloud storage and large transfers (core for the migration)

• Hands-on AWS S3: storage classes (Standard, Glacier, Deep Archive), restore requests and their timing, lifecycle rules, IAM credentials, AWS CLI or boto3.

• Cost planning before moving data: storage, retrieval and egress fees

• Bulk transfer tools: Globus, rclone, aws s3 sync, and FTPS/Aspera pulls from sequencing vendors; resumable, parallel transfers; bandwidth planning

• Verification at scale: md5/sha256 manifests, file-count and byte reconciliation between source and destination, and a written sign-off before anything is deleted at the source.

• Cluster and storage administration

• Slurm batch jobs and job arrays; shared filesystems (Lustre, GPFS, NFS), quotas, Unix groups and permissions.

• Institutional research computing (MGB ERIS or similar): requesting storage, organising it into fast, bulk and archive tiers.

• Archive hygiene: packing millions of small files into tar archives before archiving, and determining storage requirements

• Sequencing and lab data formats beyond FASTQ/BAM

• CRAM and its dependence on the exact reference genome; VCF; long-read data (Oxford Nanopore POD5/FAST5, PacBio HiFi BAM).

• Single-cell and spatial outputs (10x Genomics, Xenium bundles) and whole-slide images (SVS, NDPI, TIFF).

• Vendor deliverables: sample sheets, QC reports, demultiplexing, and run, lane and library IDs.

• Sample database, biobank and compliance

• REDCap (widely used at MGB) and/or a biobank LIMS such as OpenSpecimen or FreezerPro; barcoding, freezer inventory, chain of custody.

• Data modelling of the chain patient → specimen/block → section/aliquot → library → sequencing run → file, with a data dictionary and controlled vocabularies.

• Handling patient data: HIPAA, IRB protocols, coded (de-identified) sample IDs, access control, data use agreements and MGB data-security policy.

• Public data submission: has deposited data in SRA, dbGaP, GEO or EGA for publications, or is willing to learn.

• Working practices

• Git and re-runnable, logged scripts; clear READMEs and runbooks someone else can follow.

• Running a multi-month migration: inventory first, agreed priorities, a tracking sheet, regular status updates.

• Supporting wet-lab staff; working with sequencing vendors and cores.

• Performs other duties as assigned by PI

• Complies with all policies and standards as assigned by Research Manager

• Additional Job Details (if applicable)

• Remote Type

• Onsite

• Work Location

• 20 Shattuck Street

• Scheduled Weekly Hours

• 0

• Employee Type

• Per Diem

• Work Shift

• Day (United States of America)

• Pay Range

• $17.71 - $24.28/Hourly

• Grade

• 2

• Mass General Brigham Competency Framework

• At Mass General Brigham, our competency framework defines what effective leadership “looks like” by specifying which behaviors are most critical for successful performance at each job level. The framework is comprised of ten competencies (half People-Focused, half Performance-Focused) and are defined by observable and measurable skills and behaviors that contribute to workplace effectiveness and career success. These competencies are used to evaluate performance, make hiring decisions, identify development needs, mobilize employees across our system, and establish a strong talent pipeline.