February 2008, Number 8http://www.broad.mit.edu/genepattern/

Now Available: GenePattern 3.1

We are pleased to announce GenePattern 3.1 and new modules for the analysis of genomic data.

  1. GenePattern 3.1 Features
  2. New and Updated Modules
  3. GenePattern 3.1 Workshops
  4. GenePattern Case Study

 1. GenePattern 3.1 Features

GenePattern 3.1 is now available. New features in this release include:
  • Public GenePattern Server: The Broad Institute now hosts a public GenePattern server where you can run your analyses. The GenePattern 3.1 server is available at: http://genepattern.broad.mit.edu/gp/.

  • Support for Vista and Leopard: GenePattern 3.1 adds support for Windows Vista and Mac OS X 10.5 (Leopard) and can be used on any operating system that has a Java 1.5 virtual machine installed. GenePattern 3.1 is available for download at: http://www.genepattern.org/download/.

  • Protocols for Common Analyses: The GenePattern Web Client now provides step-by-step instructions ("protocols") to guide you through which modules to use at each step of several common analyses, such as marker selection, clustering, prediction, and others. Give us your feedback or requests for other protocols by following the Comments/Suggestions link on the protocols pages.

  • Upgrade to R 2.5: GenePattern 3.1 uses R 2.5. For more information, including information on how to preserve your existing R 2.0.1 installation, see the GenePattern 3.1 release notes.

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 gp-help@broad.mit.edu.

 2. New and Updated Modules

A number of modules have been added to the GenePattern module repository since our last newsletter:

The following modules have been updated:

  • All R-based modules have been updated for R 2.5: AreaChange, CART, CARTXValidation, CompareSpectra, ComparativeMarkerSelection, ConsensusClustering, ExpressionFileCreator, GEOImporter, GLAD, ImputeMissingValues.KNN, LocatePeaks, NMFConsensus, Peaks, PlotPeaks, ProteomicsAnalysis, and SVM.

  • ExpressionFileCreator has been updated to include Affymetrix probe ID annotations in the generated RES or GCT file.

  • HierarchicalClusteringViewer, HierarchicalClusteringImage, HeatMapViewer, and HeatMapImage have been updated to convert values to colors using either a linear color gradient or a discrete color map.

  • PCAViewer has been updated to provide 2D and 3D visualizations of the results from principal component analysis (the PCA module). Plot the eigenvectors of selected principal components, display a 2D plot that projects experiments/genes onto two principal components, or a 3D plot that projects experiments/genes onto three principal components.

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 module page.

 3. GenePattern 3.1 Workshops

Our popular GenePattern workshop introduces participants to GenePattern 3.1 features, including:

  • intuitive web interface for users at all levels of computational sophistication
  • comprehensive repository of analysis and visualization modules for analyzing gene expression data, proteomic data, and high-density SNP array data
  • pipelines that allows users to chain modules together to create and share methodologies
This one-day workshop will be held 9am-5pm at MIT's Digital Instruction Resource Center (14N-132) in Cambridge, Massachusetts on the following dates:
  • Friday, March 28 (Broad/MIT community only)
  • Friday, April 4 (Open to everyone)

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.

 4. GenePattern Case Study

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.

 Let Us Know How You're Using GenePattern

If you've a GenePattern story to share, we'd love to hear about it. If you're using GenePattern for your research, to share analysis methods, or to publish analysis results, please let us know:
email the GenePattern team.

User Survey

We'd like to know more about your day-to-day experiences with GenePattern. Our user survey is a brief online form that lets you give us feedback about the software and other aspects of using GenePattern. Your responses are greatly appreciated - they help us to understand how GenePattern is being used and how to make it a more valuable tool.

Early Adopters

If you'd like early access to new GenePattern releases to help us test new GenePattern features,
join the early adopters mailing list.

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