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Computational Scientist and Engineering Summer Intern: Inscripta, Boulder, CO

Inscripta is developing the world’s first scalable platform for benchtop Digital Genome Engineering. The company’s advanced CRISPR-based platform, consisting of an instrument, reagents, and software, will offer a fully automated workflow that enables multiplexed, trackable editing of cells at an unprecedented scale. Inscripta’s goal is to empower scientists whose gene editing research is stifled by current technical and licensing limitations. By providing this unique platform and engaging in collaborative business practices, such as making its MAD7 CRISPR nuclease free for research purposes, the company enables scientists to realize a new era of biological discovery.  Inscripta has an opening for a full-time Computational Scientist and Engineering Summer Intern located in either our Boulder, CO or our Pleasanton, CA office.

This internship will last a minimum of 10 weeks throughout the summer and will have full-time hours, 40 hours per week, Monday through Friday.

The Department of Computational Sciences and Engineering (CoSE) works with diverse multi-disciplinary teams throughout Inscripta to address a number of genomic, proteomic, experimental design, and other relevant questions using mathematical modeling, simulation, data science, machine learning, and other computationally challenging techniques. We are looking for exceptional candidates to spend the summer at Inscripta pursuing projects to build out our automated analytical pipelines, develop novel algorithms and models for genomics and proteomics, and create scalable platforms for large scale computation. This summer internship could be based in either our Pleasanton, California or Boulder, Colorado offices.

Potential project areas

  • Work with a team of pipeline developers to explore novel approaches to variant detection and representation for sequencing libraries composed of highly multiplexed, edited cells. Benchmark competing approaches and optimize pipelines for speed, resource usage and accuracy. Help define the metrics used to characterize these libraries and present your work to other CoSE scientists.
  • Work with a team of scientists to characterize genome editing efficiency in different genomic contexts and use this information to improve the design rules used by our customers. Explore potential machine learning approaches to guide the construction of primer and oligonucleotide sequences used to create genome editing libraries.
  • Evaluate methods of deploying large scale bioinformatics pipelines to HPC and cloud environments. With input from the CoSE team, determine criteria by which to assess pipeline deployment methods, paying close attention to scalability, maintainability, ease of use, and total cost.
  • Support Inscripta’s scientific research by partnering with bench scientists to develop novel genome editing assays and data analysis methods. Create reproducible Jupyter notebooks showcasing newly developed statistical analyses and prototypes of data visualizations.
Requirements

Minimum Qualifications:

  • A graduate student or a rising senior undergraduate student pursuing a degree in computer science, engineering, bioinformatics, biology, biochemistry, physics, statistics, or a related field.
  • Knowledge of Python, C++, or other advanced programming language.
  • Software development skills, including a working knowledge of version control systems such as git.
  • Strong problem solving, statistical, and mathematical skills.
  • Strong communication and presentation skills.

Desired Qualifications:

Projects will vary depending upon the candidate’s background, but experience in one or more of the following skillsets is expected:

  • Familiarity with a broad range of bioinformatics software and algorithms, and experience using them on large data sets.
  • Workflow management systems like WDL, CWL, SnakeMake, Nextflow, etc.
  • Graphical approaches to genome variant detection and representation.
  • Machine learning techniques such as linear and logistic regression, deep neural networks, and ensemble approaches to classification.
  • Ad hoc data analysis using Jupyter notebooks with Python, Matplotlib, Seaborn, Numpy, and R.
  • Big data technologies such as SQL and NoSQL databases and Spark infrastructure.
  • Cloud infrastructure such as AWS’ EC2, S3, ECR, and Batch environment.

Inscripta offers a competitive hourly rate for interns. Join us for the summer and work with a great team of people developing the world’s first scalable platform for benchtop Digital Genome Engineering. Inscripta is headquartered in Boulder, CO with offices in Pleasanton and San Diego, CA.  This internship can be located in either our Boulder, CO or Pleasanton, CA office.

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Lio Tariman

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