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Software Engineer I/II

2 months ago

Dallas, United States SPECTRAFORCE Full time

Job Role: Software Engineer II (Computational pipeline automation)

Location: Cambridge, MA, (2-3 days onsite)

Duration: 23 Months Contract

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

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

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.

Education for Level II:

  • 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.


Education for Level I:

  • 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
  • Master’s Degree in A bachelor’s degree in Engineering/ IT/Computer Engineering/Computer Science/Bioinformatics or related discipline with a minimum of 3 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 1 years of experience in software development and pipeline automation in the pharmaceutical and/or biotech industry


Notes from HM:

  • Typical day: Computational pipeline automation. 2 major pipelines. Build CRISPR pipeline. Meeting with wet lab scientist. Meeting Bioinformatician. 20% of time in meetings. Implement pipelines in the automation system. Build the pipeline. Data coming in and processing the data. Working with IT engineers to help figure out cloud.
  • Key Skills: Nextflow expertise. Cloud computing expertise. Rewrite codes


About Us: Established in 2004, SPECTRAFORCE® is one of the largest and fastest-growing diversity-owned staffing firms in the US. The growth of our company is a direct result of our global client service delivery model that is powered by our state-of-the-art A.I. proprietary talent acquisition platform, robust ISO 9001:2015/ISO 27001 certified processes, and strong and passionate client engaged teams. We have built our business by providing talent and project-based solutions, including Contingent, Permanent, and Statement of Work (SOW) services to over 140 clients in the US, Canada, Puerto Rico, Costa Rica, and India. Key industries that we service include Technology, Financial Services, Life Sciences, Healthcare, Telecom, Retail, Utilities and Transportation. SPECTRAFORCE is built on a concept of “human connection,” defined by our branding attitude of NEWJOBPHORIA®, which is the excitement of bringing joy and freedom to the work lifestyle so our people and clients can reach their highest potential. Learn more at:

Benefits: SPECTRAFORCE offers ACA compliant health benefits as well as dental, vision, accident, critical illness, voluntary life, and hospital indemnity insurances to eligible employees. Additional benefits offered to eligible employees include commuter benefits, 401K plan with matching, and a referral bonus program. SPECTRAFORCE provides unpaid leave as well as paid sick leave when required by law.


Equal Opportunity Employer: SPECTRAFORCE is an equal opportunity employer and does not discriminate against any employee or applicant for employment because of race, religion, color, sex, national origin, age, sexual orientation, gender identity, genetic information, disability or veteran status, or any other category protected by applicable federal, state, or local laws. Please contact Human Resources at LOA@spectraforce.com if you require reasonable accommodation.

At SPECTRAFORCE, we are committed to maintaining a workplace that ensures fair compensation and wage transparency in adherence with all applicable state and local laws.