Sr. Staff, Instrument Software Engineer

atlas-data-storage; South San Francisco (CA); On-site; USD 190,000 - 230,000; Full time

Job summary

Atlas is seeking a Senior Staff Instrument Software Engineer in South San Francisco to design and implement high‑performance software for electrochemical CMOS DNA synthesis hardware. You will work closely with hardware, electrical, and chemistry teams to meet demanding timing and reliability targets.

The role requires extensive C/C++/Rust experience, RTOS knowledge, and a hands-on approach to software and hardware development, with emphasis on memory management and low-latency data processing.

Qualifications

• BS in Computer Science or related technical field.
• Expertise in memory management across languages.
• Experience with high‑performance, low‑latency code for large payloads.

Responsibilities

• Develop high‑performance systems for large data payloads.
• Collaborate with hardware and chemistry teams to define requirements.
• Architect using C, C++, or Rust for RTOS-based hardware control.

Skills

C++

C#

Rust

Typescript

Python

OO design

RTOS

Git

Big data handling

Education

BS in CS or related

Tools

SPI

Ethernet 1G/10G

USB

FPGA/ASIC integration

Firmware

Job description

Atlas is charting the future of data and computing by pioneering Molecular Computing technology. We're a recently funded, high-growth startup at the intersection of Information Technology and Bio Technology, tackling some of the most complex IT challenges in the world.

We're looking for an exceptional Senior Staff Instrument Software Engineer to join our core engineering team. This is a unique opportunity to apply your expertise and programming knowledge to build the systems that will make biological data storage a commercial reality.

About the Role

As a Senior Staff Instrument Software Engineer, you will be an essential member of our engineering team. You'll help architect, design, and implement high-performance software to operate the electrochemical CMOS based DNA synthesis instrumentation we are developing. You will also help support the development of a new generation of electronic gene sequencing hardware. All the hardware tightly integrates with back-end web services and bioinformatics pipeline.

• BS in Computer Science or related technical field
• Proficiency in C# and/or C++
• 6+ years industry experience
• Mastery of object oriented programming concepts, and clean software architecture design
• Familiarity with hardware integration, system bring-up and validation
• Ability to take a hands‑on approach to software and hardware development
• Experience with Git or similar version control systems

Your responsibilities will include

• Developing high-performance systems capable of handling very large data payloads while ensuring end-to-end data integrity.
• Help developing software running our highly custom DNA data storage platform
• Working closely with hardware, electrical and chemistry teams to help define requirements and specifications.
• Architecting and implementing using languages such as C, C++ or Rust.
• Bringing expertise in Real‑Time Operating Systems (RTOS) to inform architectural decisions that meet strict timing and reliability requirements for hardware control.

Required Skills

• 10+ years of professional software development experience, with significant experience in a Staff-level or equivalent senior technical leadership role.
• Expertise in broad set of languages such as C, C++, rust, typescript or python.
• Deep, demonstrable understanding of memory management and allocation strategies across multiple languages and runtimes.
• Proven ability to write performant, low‑latency, and highly optimized code, particularly when dealing with very large data payloads (multi‑gigabyte to terabyte scale).
• Experience designing and implementing firmware and working with high‑speed buses (SPI, 1G/10G Ethernet, USB…).
• Knowledge of Real‑Time Operating Systems (RTOS) and their implications on system architecture and design.

Desired Skills

• Prior experience working directly with hardware development, bring‑up, and troubleshooting.
• Front‑end development (typescript, React or similar frameworks)
• Understanding of FPGA and ASIC integration
• Familiarity with data storage technologies
• Experience with cloud platforms (AWS, Azure, GCP) for data storage and deployment infrastructure.
• Bachelor's or master’s degree in computer science, Electrical Engineering, or a related field.
• Mastery of object oriented programming concepts, and clean software architecture design
• Familiarity with hardware integration, system bring‑up and validation
• Ability to take a hands‑on approach to software and hardware development
• Image processing experience
• Experience with Git or similar version control systems

Preferred qualifications

• Master's or PhD in Computer Science or related technical field
• Electrical and mechanical engineering experience is a big plus
• Experience with the latest .NET is a plus
• WPF experience is a big plus, and an eye for clean UI design is greatly appreciated
• Interest and ability to learn other programming languages as needed