About the role
As an Algorithms Engineer, you will support Treeline’s drug design, discovery, and development using our computational platform. You will closely collaborate with computational scientists, as they work on their projects, and amplify their efforts to improve our entire computational platform. You will interpret existing and propose new computational experiments, and grow our computational capabilities with respect to small molecules, proteins, and cells. Your knowledge and ownership of the computational platform will empower experimental and computational scientists, software developers, and data managers. We expect that you will have no problem mastering the technologies that we use today (and will adopt tomorrow).
Watertown, MA; San Diego, CA; Remote, depending on seniority.
- Develop software and statistical tools to classify positive and negative controls for computational experiments, propose generation of new experimental data or materials based on necessary or missing items
- Analyze molecular simulations using internally developed libraries, contributing the analyses into our toolkits
- Maintain and query database of previously ran analyses, and suggest follow-up simulations and analyses based on inferred patterns
- Collaborate with computational chemists to generalize simulation/computational setups from a single project to be applicable across projects
- Identify strengths and weaknesses of existing models of small molecule properties, and keep track of models in use
- Improve existing atomistic models for small molecule behavior in models, through methods based on quantum mechanical, neural net, and heuristic approaches
- Monitor internal synthetic chemistry, structural biology, and biochemistry queues and results for outliers, failure modes, and propose diagnostics and self-healing strategies
- Visualize current project and platform status through dashboards
- Develop search functions for querying stored small molecule or protein structures, simulations, regression/classification models; evaluate exact vs fuzzy search strategies
- Design and maintain computational environments and for local, network, and cloud development, including code and model packaging, version control, and auditing
- Automate model application, prediction generation, model improvement, computational environment building through continuous integration/continuous delivery and test based techniques
- Integrate external libraries, both open source and licensed closed source, into computing environment, building crucial “glue” code
- Bachelors, Masters, or Doctorate in natural sciences or computer science
- Familiarity with scientific Python software such as: chemistry toolkits (OEChem/RDKit); bioinformatics toolkits (Biopython); numpy/scipy/sklearn
- Comfort with operating at the command line and UNIX tools.
- Hands on experience with data aggregation, manipulation, integration, mining, and analysis
- Ability to dig deeply through various data types; demonstrated experience in pinpointing resolving incongruities between tools/framework
- Proficiencies in data visualization
- Excellent written and oral communication skills, including an ability to explain complex ideas to computational scientists, experimentalists, and clinicians
- Capable of establishing strong working relationships across a distributed organization.
- Experience with bioinformatics, cheminformatics, structural biology, experimental design; molecular dynamics and/or structure-based neural network experiences a plus
- Experience with version control, continuous integration/continuous delivery, packaging, deployment, Amazon Web Services, SQL, database design a plus
Notice to Search Firms/Third-Party Recruitment Agencies (Recruiters)
The Human Resources team manages the recruitment and employment process for Treeline Biosciences. To protect the interests of all parties involved, Treeline Biosciences will only accept resumes from a recruiter if an executed search agreement directed to the particular position or positions is in place at the start of the recruitment effort. Unsolicited resumes sent to Treeline Biosciences from recruiters do not constitute any type of relationship between the recruiter and Treeline Biosciences and do not obligate Treeline Biosciences in any way to pay fees should we hire from those resumes. Recruiters are requested not to contact or present candidates directly to our hiring manager or employees.