Lattice microbes

1/10/2014 Elijah Roberts, John E. Stone and Zaida Luthey-Schulten, Journal of Computational Chemistry, 2013, Volume 34, Pages: 245255.

Cytoplasmic membrane
Cytoplasmic membrane
Spatially resolved stochastic simulation is a valuable technique for studying reactions on time and size scales relevant for biological systems. Here, CPLC faculty ZLS and postdoc ER introduce the Lattice Microbes GPU-based software package for simulating complex biochemical reaction networks on the level of the whole cell. Our approach integrates data from cyroelectron tomography, proteomics, and single molecule spectroscopy to capture the molecular crowding within cells. The software performs either well-stirred or spatially resolved stochastic simulations with approximated cytoplasmic crowding in a fast and efficient manner. Our new algorithm efficiently samples the reaction-diffusion master equation using NVIDIA graphics processing units and is shown to be two orders of magnitude faster than exact sampling for large systems while maintaining an accuracy of 0.1%. Display of cell models and animation of reaction trajectories involving millions of molecules is facilitated using a plug-in to the popular VMD visualization platform.

The Lattice Microbes software is open source and available for download at Lattice Microbe has been implemented on Blue Waters and other NSF/DOE supercomputers.

12/13/2013 PivotRise

PivotRise is an internet startup company headquartered in Palo Alto, CA, that uses web technology and social science to strive for the grand mission of helping people redirect and pursue new careers beyond their experience and current expertise.

We are looking for two passionate, hard-working, and initiative Software Engineer Interns who are passionate in learning and building cloud application(s) in a mission-driven environment. You will have an enormous opportunity to make a large impact on the design, architecture, and implementation of a brand new Web2.0 online application facing tens of millions audience.

- Responsible for the development and maintenance of key system features from scratch, with guidance from other software engineers.
- Will work closely with software engineers and CTO to investigate design approaches, prototype new technology and evaluate technical feasibility.
- Will work in a Mission-Driven environment to quickly adapt and comprehend overall strategies and translate into technical details, and deliver high quality software against aggressive schedules.
- Will read, adapt, and improve existing codebase for better maintainability and integration with new features.
- Will learn quickly on a daily basis.

Basic Qualifications
- Students in Computer Science or a field with equivalent skills set. Post-graduate applicants who are looking for a career pivot into software development and possess strong hands-on skills are also encouraged to apply
- The ability to comprehend strategic objectives and business logic, and center technical decisions on such understanding.
- The ability to take raw product requirements and develop software features to bring them to life. - Excellent of hands-on programming skills and tools of trade, including some of the following: JavaScript, Jquery, Ruby on Rails, Bootstrap 3, PHP, Python, and tools (i.e.PostgreSQL, GitHub, Linux, Heroku, Jira/Asana, New Relics, etc).
- The ability to learn quickly on their own.
- Common sense in typical web application workflows, user experience and business logic.

Preferred Qualifications
- Experience building successful cloud production software systems and an understanding of design for scalability, performance and reliability.
- Excellence in technical communication with peers and non-technical cohorts.
- Hands-on experience using REST based social network APIs.
- Experience building recommendation engines
- Experience building Web 2.0 applications.
- Data Science and Data Mining experience preferred.

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PivotRise, Inc. is an equal opportunity employer.