Software Developer 2

Mar 28, 2017
Institution Type
Four-Year Institution

Stanford University

Software Developer 2

Job Number:

Software Developer 2 - Job Grade J - 100% FTE, Exempt,

School of Engineering, Bioengineering Department

This position is an opportunity to contribute to one of the most exciting new frontiers of computational biology. Specifically, the creation of a “whole-cell” computer model that explicitly takes all of the known information about each gene and molecule into account to predict cell behaviors was called an “ultimate goal” of biology, and “a grand challenge for the 21st century. The Covert Lab reported completion of the first such model in 2012, an achievement that was recently highlighted in the journal Cell as one of the most important advances reported by that journal in its entire 40-year existence.

Now, with a major new award from the Paul G. Allen Family Foundation, our group is building a top-flight team to develop and advance this modeling approach in order to have the largest possible impact on the world. In particular, we are looking for a computational biology-oriented software engineer to contribute to whole-cell modeling by developing tools to improve workflow and analysis of experimental and/or simulation data, improve distributed computing performance, and support open-source sharing of both simulation and experimental data (including through data visualization) as well as the modeling platform itself.

Bioengineering website:


Execute all programming tasks, including programming, analyzing, designing, developing, implementing, modifying, and maintaining computer programs. Work on systems of moderate size and complexity or segments of larger systems.


  • Conceptualize design, implement, and develop solutions for complex system/programs independently.
  • Work with a variety of users to gain information, and develop intra-system tradeoffs between different users, as necessary; interact with a diverse client base and outside vendor contacts.
  • Document system builds and application configurations; maintain and update documentation as needed.
  • Provide technical analysis, design, development, conversion, and implementation work.
  • Work as a project leader, as needed, for projects of moderate complexity.
  • Serve as a technical resource for applications.
  • Compare, evaluate, and implement new features and technologies, and integrate them into the computing environment.
  • Follow team software development methodology.
  • Mentor lower level software developers.
  • Offload software support tasks from researchers (e.g. adapt to the latest version of Python 2.7 and its packages, and someday to Python 3; facilitate cluster computing)
  • Strengthen and harden the whole-cell modeling code base by increasing test coverage, documentation coverage, execution speed, development speed, and learnability
  • Facilitate the integration of new code contributions into the whole-cell modeling code base
  • Train both internal and external researchers who are new to the code
  • Integrate our data acquisition, analysis and storage pipelines, both on the simulation and experimental data sides
  • Develop and implement new aspects of cellular modeling (e.g., explore relating whole cell models with agent based models)

    Other duties may also be assigned


    Knowledge, Skills and Abilities:

  • Expertise in designing, developing, testing, and deploying applications.
  • Proficiency with application design and data modeling.
  • Ability to define and solve logical problems for highly technical applications.
  • Strong communication skills with both technical and non-technical clients.
  • Ability to lead activities on structured team development projects.
  • Ability to select, adapt, and effectively use a variety of programming methods.
  • Knowledge of application domain.
  • Ability to define and solve logical problems for highly technical applications.
  • Comprehensive understanding of scientific principles.
  • General computer skills and ability to quickly learn and master computer programs, databases, and scientific applications.
  • Strong analytical skills and excellent judgment.
  • Ability to work under deadlines with general guidance is essential.
  • Excellent organizational skills and demonstrated ability to accurately complete detailed work.

    Additional Knowledge, Skills and Abilities:

  • Ability to work closely with research scientists to model and support their laboratory activities (modeling and computation)
  • Extensive experience creating professional software and prior language experience in the following: Python - including the scientific tools such as NumPy, Jupyter, and Cython; C/C++; Java
  • Understanding of large-scale software engineering best practices and tools as well as team-scale software development
  • Experience with data analysis pipelines and data visualization
  • Prior experience with biology, and preferably computational modeling of biology
  • Knowledge of publicly available genomic and systems biology resources.

    Certifications and Licenses:


    Education & Experience

    Bachelor's degree and five years of relevant experience, or a combination of education and relevant experience. Also acceptable would be a bachelor's degree in a related scientific field and three years of relevant experience, a master's degree in a related scientific field, or a combination thereof.


  • Constantly perform desk-based computer tasks.
  • Frequently sit, grasp lightly/fine manipulation.
  • Occasionally stand/walk, writing by hand.
  • Rarely use a telephone, lift/carry/push/pull objects that weigh up to 10 pounds.

    * Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job.


  • May require working in close proximity to blood borne pathogens.
  • May require work in an environment where animals are used for teaching and research.
  • Position may at times require the employee to work with or be in areas where hazardous materials and/or infectious diseases are present.
  • Employee must perform tasks that require the use of personal protective equipment, such as safety glasses and shoes, protective clothing and gloves, and possibly a respirator.
  • May require extended or unusual work hours based on research requirements and business needs.


  • Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations.
  • Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned.
  • Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University's Administrative Guide,

    *We are unable to provide Sponsorship for this position.

    Applicants are required to upload a cover letter and resume to be considered for this opening.

    About Stanford University

    Stanford University, located between San Francisco and San Jose in the heart of California's Silicon Valley, is one of the world's leading teaching and research universities. Since its opening in 1891, Stanford has been dedicated to finding solutions to big challenges and to preparing students for leadership in a complex world.

    Supporting that mission is a staff of more than 10,000 which is rooted in a culture of excellence and values innovation, collaboration, and life-long learning. To foster the talents and aspirations of our staff, Stanford offers career development programs, competitive pay that reflects market trends and benefits that increase financial stability to promote healthy and fulfilling lives. An award-winning employer, Stanford offers an exceptional setting for professionals looking to advance their careers.

    Stanford is an equal employment opportunity and affirmative action employer and is committed to recruiting and hiring without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, veteran status, or any other characteristic protected by law.

    Thank you for your interest!

    Job: Information Technology Services

    Location: School of Engineering
    Schedule: Full-time
    Classification Level:

    To be considered for this position please visit our web site and apply on line at the following link:

    Stanford is an equal opportunity employer and all qualified applicants will receive consideration without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, veteran status, or any other characteristic protected by law.


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