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Posted: Sunday, January 7, 2018 11:37 AM

The goal of the Allen Institute for Cell Science is to understand cellular behaviors by studying variance and changes in cell structure over time and under different environmental conditions. The Institute, located in a new facility on South Lake Union in Seattle, Washington, employs cutting edge biology with an open-source, big data, multi-disciplinary team approach to generate novel data sets, analysis tools, and cellular models. We aim to understand how thousands of different cellular components organize and work together as complex systems that can generate the plethora of observed cellular behaviors. We approach this challenge using human induced pluripotent stem cells (hiPSc), genome editing, a large live cell microscopy pipeline for data collection and cell biology experimentation. We analyze the data using visual and qualitative analysis tools, predictive modeling and theory, and ultimately aim to present our results as a novel multi-scale, dynamic and visual output that can engage a broader community.

Position Summary

The Animated Cell team at the Allen Institute for Cell Science is looking for a game developer and software engineer to join our small team. We build visual, animated, and simulated models of cells to allow the scientific community and the general public to intuitively explore our data for analysis, hypothesis generation, and education.

One of our major projects is an online cellular and molecular simulation engine that will run on This engine displays 3D models generated with data from our microscopy pipeline and from other public databases. This engine will enable scientists, through visual scripting with general components, to build their own agent-based cell biology simulations that they can contribute to the community.

We seek a Game Developer/Software Engineer to help build the architecture of this engine, including a visual scripting framework. You will work with our interdisciplinary team of biologists, scientific animators, game developers, front-end engineers and graphics programmers on this effort.

Primary Job Responsibilities

* Design and implement a modular simulation framework with input from an interdisciplinary team

* Translate simulation prototypes from Unity3D C# into this framework

* Maintain and extend a server-side visualization framework built in C++ QT

* Contribute expertise to discussions of platform selection, file-formats, data storage, user account management, and crowd-sourcing technologies

* Develop a user interface and underlying architecture for a visual scripting system

* Help design and implement an agent brain with a user interface that will allow users to apply, modify and define parameter driven behaviors to molecular agents.

* Help to establish a well-documented API that will enable team members or open-source contributors to easily modify or extend the software

* Transform complex and high-level requirement specifications into code

* Actively participate in design sessions and provide thoughtful solutions and alternatives in a team setting

* Perform software development duties using best practices (version control, issue tracking, unit testing, documentation)

* Collaborate with user experience researchers on the implementation and iterative testing of user interfaces

* Coordinate with other groups in the Institute to ensure seamless integration and sharing of resources and data.

* Prepare written summaries and present activities internally and publicly

Basic Qualifications

* Bachelors or equivalent experience in computer science

* Minimum of 3 years relevant experience.

* Experience working on a team with other developers on the same project and in a collaborative, multi-disciplinary environment

* Proficiency with gaming or simulation programming

* Experience with optimization for displaying large amounts of data in real time

* Demonstrated interest in biology

* Broad programming language experience (Python, C++, JS, C# preferred)

* Experience with software version control management systems (e.g. git)

Desirable Qualifications

* Experience with the Unity3D Editor and scripting in C#

* Experience implementing visual scripting systems

* Experience designing architectures for large software systems

* Experience writing and maintaining QT applications in C++

* Experience with database systems

* Experience implementing user accounts and communicating with backend systems

* Experience with crowd-sourcing platforms

* Understanding of cell imaging and image processing techniques

* Experience with visualization and analysis of medium to large scale scientific data

* Basic statistics and strong 3D math skills

* Experience with agent-based or behavioral simulation

* Some coursework in biology

It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.


Associated topics: application, c#, devops, java, php, sde, sdet, software development engineer, software engineer, software programmer


• Location: Seattle

• Post ID: 60880812 seattle is an interactive computer service that enables access by multiple users and should not be treated as the publisher or speaker of any information provided by another information content provider. © 2018