Software Engineer(Computational pipeline automation)

2 months ago

Cambridge, Massachusetts, United States INTELLISWIFT INC Full time

Job ID: Qualifications:

Actual Job title: Software Engineer(Computational pipeline automation)

Education:
• A bachelor's degree in Engineering/ IT/Computer Engineering/Computer Science/Bioinformatics or related discipline with a minimum of 7 years of experience in software development and pipeline automation in the pharmaceutical and/or biotech industry
• Master's Degree in A bachelor's degree in Engineering/ IT/Computer Engineering/Computer Science/Bioinformatics or related discipline with a minimum of 5 years of experience in software development and pipeline automation in the pharmaceutical and/or biotech industry.
• PHD candidates in Engineering/ IT/Computer Engineering/Computer Science/Bioinformatics or related discipline with relevant with a minimum of 3 years of experience in software development and pipeline automation in the pharmaceutical and/or biotech industry

Required Skills
• Engineering skills to be able to optimize data analysis workflows for speed and usability
• Proficiency in programming languages such as Python and R, with experience in data analysis and machine learning libraries.
• Practical experience with deep learning frameworks, such as TensorFlow or PyTorch
• Serve as subject matter expert to Nextflow pipelines.
• Strong knowledge of cloud-based infrastructure such as AWS and batch computing services like AWS Batch.
• Demonstrated experience in developing and implementing standardized analytical workflows and processes.
• Familiarity with Github and code documentation best practices
• Software engineer with significant experience and knowledge of the industry best practices.
• Deep understanding of the entire software development life cycle and common life science tools.
• Experienced in pipeline design and implementation, results validation, and visualization.
• Capable of designing and building complete solutions. Has a proven track record of successful projects.
• Experience in developing bioinformatics pipelines for analysis of complex genomic or phenotypic data
• Experience with image analysis, specifically analysis of fluorescence microscopy images is preferred
• Excellent communication skills and interpersonal skills with the ability to work collaboratively in a multi-disciplinary team

Note:
• Role is based is Cambridge,MA.
• Hybrid role(2-3 days/week onsite)

Responsibilities:

We are seeking a passionate Software Engineer who can help with the computational pipeline automation.

Primary Responsibilities:
• Collaborate with cross-functional teams to understand project goals and data analysis requirements.
• Develop advanced Nextflow pipelines designed to enhance the efficiency of processing large Spatial Omics (spatial transcriptomics, multiplex immunofluorescence, optical pooled CRISPR screens) datasets at scale.
• Streamline computational workflow, leveraging parallelization, CPU (Central Processing Unit) and GPU (Graphic processing Unit) capabilities to optimize processing time and resource utilization.
• Lead the development of automated computational pipelines and Nextflow conversion.
• Collaborate closely with product and engineering teams to design and implement automated data analysis workflows and pipelines effectively.
• Process data through existing pipelines while optimizing and modifying pipelines as wet lab technologies and computational toolbox evolve.
• Iteratively improve and streamline pipelines, with the ultimate goal of getting pipeline to production phase where non-experts can readily run it at scale.
• Work with different data producers and owners to implement framework and processes effectively.

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