We are pleased to announce GenePattern 3.1 and new modules for the analysis of genomic data.
GenePattern 3.1 public server: http://genepattern.broad.mit.edu/gp/.
GenePattern 3.1 download: http://www.genepattern.org/download/.
GenePattern 3.1 release notes: http://www.genepattern.org/doc/relnotes/3.1/.
We welcome your feedback and encourage you to send questions and comments to email@example.com.
The following modules have been updated:
To install new and updated modules, open the GenePattern Web Client and click Modules>Install from Repository.
For comprehensive documentation on the modules in the repository, see our
Our popular GenePattern workshop introduces participants to GenePattern 3.1 features, including:
Registration is free for attendees from academic or other nonprofit organizations and $600 for attendees from for profit organizations.
Register now at http://www.broad.mit.edu/genepattern/workshop/.
Or, if these dates are inconvenient, use the registration form to request
that we notify you of future workshops.
GenePattern Used to Teach Atomistic Modeling
"A fracture in a concrete bridge doesn't begin as a long jagged scar; it starts off as a vibration at the atomic scale and progresses," explains Professor Markus Buehler of MIT's Department of Civil and Environmental Engineering. In his research, Buehler uses complex modeling algorithms to study how the molecular structure of a material relates to the material's response in large scale structures. As a professor, Buehler wants his students to understand and explore how building blocks at the nonscale define material properties at the macroscale. However, the complexity of the modeling algorithms and technical details of running the methods make them difficult for students to access. Working with Ivica Ceraj, a software developer in MIT's Office of Educational Information Technology, Professor Buehler found a solution to the problem: GenePattern.
Prior to using GenePattern, atomistic simulations were difficult to carry out and required students to learn technical details of operating a Linux workstation before they could get to the heart of the numerical method. Ceraj created an interface between GenePattern and the software code Buehler uses in his own research on materials as disparate as collagen and concrete. The combination provides a simple-to-use, but very accurate tool for modeling the behavior of materials under extreme loading. Now, students can learn the basics of atomistic modeling quickly, apply the technique to predict the mechanical properties of various materials, and adopt the methods for their own applications.
For more information, see the article Think small! Think quickly! Atomistic model helps students visualize nanoscale problems published by the MIT News Office.
If you've a GenePattern story to share, we'd love to hear about it.
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is a brief online form that lets you give us feedback about the software and other aspects of using GenePattern.
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