Bioinformatics Engineer (LIMS)
Location
Waltham, MA | United States
Job description
Job Description: Bioinformatics Engineer (LIMS)
We are seeking a skilled and motivated Bioinformatics Engineer to join our team. In this role, you will play a critical role in developing and maintaining our Laboratory Information Management System (LIMS), optimizing bioinformatics workflows, managing databases, and implementing data analysis pipelines. You will work closely with interdisciplinary teams to support various research and development projects and ensure efficient data management and analysis processes.
Responsibilities:
LIMS Development:
- Design, develop, and maintain a robust Laboratory Information Management System (LIMS) tailored to the specific needs of our research projects.
- Customize and configure LIMS functionalities to streamline sample tracking, data integration, and reporting.
- Collaborate with stakeholders to gather requirements and implement user-friendly interfaces for data entry and retrieval.
Bioinformatics Workflows:
- Develop and optimize bioinformatics workflows for primary and secondary data analysis.
- Implement best practices and standards for reproducible research and data quality control, including data ingestion workflows and FAIR principles.
- Stay updated with latest bioinformatics tools, algorithms, and methodologies to continuously improve and automate data analysis capabilities.
- Automate routine tasks and processes to increase efficiency and scalability.
Database Management:
- Design and maintain databases to efficiently store and manage large-scale genomic, transcriptomic, and other omics data.
- Ensure data integrity, security, and accessibility, following industry standards and regulations.
- Develop and maintain data pipelines for data ingestion, transformation, and integration from various sources.
Documentation and Training:
- Document software code, algorithms, and workflows to ensure reproducibility and facilitate knowledge sharing.
- Provide training and support to researchers and laboratory staff on using bioinformatics tools, databases, and analysis pipelines.
Qualifications:
- Excellent analytical and problem-solving skills, with the ability to work independently and collaboratively in a multidisciplinary team.
- Effective communication skills with the ability to convey complex technical concepts to diverse audiences.
- Bachelor’s or Master’s degree in Computer Science, Bioinformatics, Computational Biology, or a related field.
- Strong programming skills with experience in software development and version control systems (e.g., Git).
- Familiarity with high-performance computing (HPC) environments and parallel computing techniques and/or experience with cloud computing platforms (e.g., AWS) and containerization technologies (e.g., Docker, Singularity).
- Expertise in database design, management, and querying using SQL and NoSQL databases (e.g., MySQL, MongoDB).
Preferred Qualifications:
- Programming experience in at least one of Python, R, or JavaScript.
- Experience with Web API design, specifically REST interfaces.
- Proficiency in bioinformatics tools and software packages for sequence analysis, genomics, and statistical analysis (e.g., BLAST, SAMtools, GATK, Bioconductor).
- Experience in developing and maintaining Laboratory Information Management Systems (LIMS).
- Knowledge of bioinformatics workflow management systems (e.g., Nextflow, Snakemake) and workflow languages (e.g., CWL, WDL).
- Understanding of molecular biology and genomics concepts, including omics technologies and data analysis pipelines.
- Experience in bioinformatics consulting or working in a research environment is a plus.
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