Scientific Software Engineer

About Chemaxon

Chemaxon is an industry-leading cheminformatics software company helping early-stage drug discovery and chemistry research for more than 25 years. Our clients are top pharmaceutical companies, innovative biotech startups, and leading academic institutions. We are agile, innovative and friendly, offering compelling opportunities for frequent collaboration and cross-training with teammates and stakeholders

We have been acquired by Certara, a US-based model-informed drug development services and software company. We are in an exciting time of organizational and business growth, so now is the perfect time to join our team!

About Certara

Certara accelerates the potential of bringing medicines to market and to patients using biosimulation software, technology, and services to transform traditional drug discovery and development. Our clients include more than 2,400 biopharmaceutical companies, academic institutions, and regulatory agencies across 70 countries.

Our goal is to enable the life sciences industry’s use of data, modeling, and analytics to make better decisions across the various phases of discovery and drug development. Our software and scientists incorporate modern advances in scientific understanding, drug development experience, data analysis, and AI resulting in significant opportunities to decrease the cost and increase the probability of success for new drug approval and commercialization.

Certara is seeking a Scientific Software Engineer to join our engineering team and help advance Certara IQ, our quantitative systems pharmacology (QSP) modeling and simulation platform. This role focuses on the core modeling language and simulation engine that power the platform’s pharmacological workflows.

You will work on a small and growing team of seven engineers. You’ll collaborate closely with scientific stakeholders to enhance our modeling language, improve numerical performance, and push the boundaries of pharmacological model simulation.

Responsibilities

• Maintain, extend, and evolve Certara’s domain-specific modeling language for ODE-based models, including both graphical and textual representations.
• Design and implement new language features, syntax, semantics, and intermediate representations.
• Improve and extend the compiler/translation pipeline—from high-level model definitions to low-level simulation code.
• Work on numerical solvers and simulation algorithms, improving stability, accuracy, and performance of ODE integrators.
• Implement new model-execution features across Python and C components, with opportunities to leverage CUDA or other low-level acceleration technologies.
• Profile, optimize, and refactor performance-critical code in both Python and C.
• Collaborate with modelers, biologists, and other scientific stakeholders to translate modeling needs into robust software capabilities.
• Contribute to overall code quality, testing, and documentation within an established engineering team.

Qualifications

• Strong proficiency in Python for scientific or technical computing.
• Background in computational biology, pharmacology, systems biology, or a related field involving differential equation–based modeling.
• Experience implementing or using ODE-based modeling frameworks, simulation tools, or numerical solvers.
• Ability to read, understand, and translate scientific algorithms into production software.

Preferred

• Experience with low-level languages such as C (or Rust), especially in performance-critical contexts.
• Exposure to GPU programming (e.g. CUDA) or interest in learning it.
• Experience building or maintaining domain-specific languages, compilers, interpreters, or AST transformations.
• Familiarity with scientific software engineering best practices (testing, profiling, reproducibility).

What we offer

• Hybrid way of working (8 days/month home office)
• Private health insurance (Medicover)
• Generous annual training budget supporting your professional development (off-site training, international conferences, e-books)
• We work with global top 500 companies (R&D) and leading academic institutions, giving you a chance to gain insights into these dynamically evolving industries.
• Inspiring working environment - leisure and recreation area, playing corner for children, English lessons, yearly user conference with social programs, innovation days
• You will be a valued member of a creative and supportive agile team
• Everyday use of English in a multicultural environment
• Influence the evolution of Certara’s modeling language and its long-term technical architecture.
• Develop and integrate state-of-the-art numerical methods for pharmacological modeling.
• Work on performance acceleration across CPU and GPU layers.
• Collaborate directly with scientists to shape future modeling and simulation capabilities.

Certara bases all employment-related decision on merit, taking into consideration qualifications, skills, achievement, and performance. We treat all applicants and employees without regard to personal characteristics such as race, color, ethnicity, religion, sex, sexual orientation, age, nationality, marital status, pregnancy, physical or mental condition, genetic information, military service, or other characteristic protected by law.