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Software Engineer Trainee Jobs in Boston, MA (NOW HIRING)

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Senior Systems Engineer

Boston, MA · On-site

$113K - $155K/yr

We are building the enterprise software infrastructure to capture, catalog, refine, enrich, and ... trainees. * Knowledge of virtualization, high-performance networking and enterprise security.

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$69K

$160.3K

$223.3K

How much do software engineer trainee jobs pay per year?

As of Aug 10, 2026, the average yearly pay for software engineer trainee in Boston, MA is $160,270.00, according to ZipRecruiter salary data. Most workers in this role earn between $130,400.00 and $187,900.00 per year, depending on experience, location, and employer.

What is a software engineer trainee?

A Software Engineer Trainee is an entry-level position where individuals gain hands-on experience in software development. They typically work under the guidance of senior engineers, learning programming languages, software development methodologies, and debugging techniques. Their responsibilities may include coding, testing, and assisting in the design of applications. This role helps bridge the gap between academic knowledge and real-world software development practices. It is an opportunity to develop technical skills and gain industry exposure before advancing to a full-time software engineering role.

What kind of mentorship or training can I expect as a software engineer trainee?

As a Software Engineer Trainee, you can typically expect to receive structured onboarding, ongoing mentorship from experienced engineers, and participation in regular training sessions. Most teams pair trainees with more senior developers for code reviews, guidance on best practices, and support in understanding project workflows. You may also be encouraged to work on small projects or contribute to larger initiatives to apply your learning in real-world situations. This hands-on, supportive environment is designed to accelerate your growth and help you build the skills needed for a successful software engineering career.

What are the key skills and qualifications needed to thrive as a software engineer trainee, and why are they important?

To thrive as a Software Engineer Trainee, you need a solid understanding of programming fundamentals, problem-solving abilities, and a relevant degree or coursework in computer science or related fields. Familiarity with common programming languages (such as Java, Python, or C++), version control systems like Git, and basic software development methodologies is typical. Strong communication, eagerness to learn, and adaptability are vital soft skills for success in this role. These skills are essential for quickly growing your technical capabilities, effectively collaborating with your team, and making meaningful contributions to software projects.

What are the most commonly searched types of Software Engineer jobs in Boston, MA? The most popular types of Software Engineer jobs in Boston, MA are:
What are popular job titles related to Software Engineer Trainee jobs in Boston, MA? For Software Engineer Trainee jobs in Boston, MA, the most frequently searched job titles are:
What job categories do people searching Software Engineer Trainee jobs in Boston, MA look for? The top searched job categories for Software Engineer Trainee jobs in Boston, MA are:
What cities near Boston, MA are hiring for Software Engineer Trainee jobs? Cities near Boston, MA with the most Software Engineer Trainee job openings:
Software Engineer Trainee jobs near you
Infographic showing various Software Engineer Trainee job openings in Boston, MA as of August 2026, with employment types broken down into 1% Internship, 85% Full Time, 9% Part Time, and 5% Contract. Highlights an 88% Physical, 4% Hybrid, and 8% Remote job distribution, with an average salary of $160,270 per year, or $77.1 per hour.

Senior Bioinformatics Research

Harvard University

Cambridge, MA • On-site

Full-time

Re-posted 4 hours ago

Harvard University rating

8.5

Company rating: 8.5 out of 10

Based on 12 frontline employees who took The Breakroom Quiz

80th of 617 rated colleges and universities

Job description

Position
Details
Title
Senior Bioinformatics Research
School
Harvard Medical School
Department/Area
Perrimon Lab
Position Description
We are seeking a highly motivated post-doc trainee to join Dr. Norbert Perrimon's group in the Program of Genetics at Harvard Medical School. Perrimon lab is actively generating data sets of omics scale and this position will involve working with other post-doc trainees in the lab who are responsible of design and generating such datasets. In addition, this position involves working with DRSC/TRiP functional genomics core, a multi-disciplinary team of biologists, software engineers and bioinformaticians as we develop and leverage technological breakthroughs to explore the biology of complex systems. Principal Responsibilities include 1.) Design and implement reusable bioinformatics analysis pipelines for processing RNA-seq, single-cell RNA-seq, genomics and proteomics data. Develop novel algorithms and integrated data visualization applications when existing software packages are not available or are not adequate. 2.) Apply computational, statistical, and AI/ML approaches to uncover biological insights and support functional discovery by analyzing multi-omics datasets eg. genomics, transcriptomics, proteomics, metabolomics, and related datasets. 3.) Help develop custom databases, web portals and pipelines for managing raw and processed experimental data as well as reagent identification/designs. 4.) Collaborate closely with Investigator and lab members on research projects including defining the scope of the collaboration, researching the scientific topics and implementing the appropriate bioinformatics solutions that meet project timelines. Coordinate and collaborate with other bioinformaticians, biostatisticians, information technology professionals, and interdepartmental project teams. 5.) Properly document the procedures used in computational analysis, provide the summary reports of results, and contribute to grant and manuscript writing.
Salary and Benefits
This position is salaried and benefits eligible. Information regarding postdoctoral fellow salary, which is determined by the number of years post PhD, and benefits can be found at https://postdoc.hms.harvard.edu/guidelines.
With this appointment, you are represented by the Harvard Academic Workers (HAW) - UAW for purposes of collective bargaining and matters affecting your compensation and working conditions.
Basic Qualifications
Doctoral degree in Bioinformatics or in biology with extensive experience analyzing omics data. Strong background in programming, algorithms and statistics. Familiarity with programming techniques for analyzing data sets and experience working with BIG DATA (eg. NGS data in multi-TB scale). Experience using genome alignment software (bowtie2, bwa, tophat, etc.) is desired. Fluent in one programming language (Python, C, C++ or Java) and familiarity with scripting languages (bash, Perl). Knowledge of Unix operating system, terminal and bash is a plus. Experience using a compute cluster. Excellent information management skills.
Additional Qualifications
Experience using relational databases, SQL and / or structured data formats. Web programming experience (PHP, Django, JavaScript, JQuery, JSON, REST API) is a plus. Excellent oral and written communication skills as well as the ability to collaborate effectively with a diverse team.
Special Instructions
Contact Information
Claire Yanhui Hu
Contact Email
claire_hu@genetics.med.harvard.edu
Salary Range
Information regarding postdoctoral fellow salary, which is determined by the number of years post PhD, can be found at https://postdoc.hms.harvard.edu/guidelines.
Minimum Number of References Required
3
Maximum Number of References Allowed
3
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