MetaScope

Figure 1: MetaScope showing genomic annotation, RNA polyermase ChIP-chip, expression profiling data and transcription start site data of E. coil K12 MG1655
Figure 2: MetaScope showing genomic annotation, expression profiling and RNA polymerase ChIP-chip data of E. coli K12 MG1655 and K. pneumoniae MGH 78578.

MetaScope

MetaScope is a genome browser, implementing interactive visualization and data integration for analyzing and integrating genome-scale multiple -omic data.

Use MetaScope in order to

  • Visualize datasets including ChIP-chip data, expression profilingdata and transcription start site data
  • Analyze, validate, curate and integrate datasets bycross-referencing multiple -omic data
  • Build genomic annotations such as TU (transcription unit) annotation
  • Analyze and compare multiple -omic datasets from two or more species

Download MetaScope and sample datasets

To download the newest version of MetaScope (old version is here),
click the link below

MetaScope v1.00 (x86) 2010.09.21

MetaScope v1.00 (x64) 2010.09.21

To download the sample datasets, click the links below

Sample 1. RNAP ChIP-chip
Sample 2. Expression Profiling and Transcript Detection
Sample 3. RNAP-Guided Transcript Segment
Sample 4. Potential ORF
Sample 5. Transcription Start Site
Sample 6. Transcription Unit Annotation

Launch MetaScope

  • MetaScope is implementaed with C# programming language and runs on any platform with .NET framework 4.0 or higher.
  • In order to install .NET framework 4.0, click the link below and follow the instructions on that webpage. Installation of .NET framework might require rebooting the computer. Microsoft .NET framework 4 (Web Installer)
  • After completing .NET framework installation, double-clicking "MetaScope.exe" will launch the application.

Documentation

A draft version of MetaScope User's Guide is available below: User's Guide 2010.09.21

FAQs

Q1: How do I launch MetaScope on Windows?  
A: MetaScope runs on .NET framework, thus if .NET framework is properly installed on your computer, double-clicking   
"MetaScope.exe" will launch the application.

Q2: How do I launch MetaScope on Linux or Mac?  
A: Currently .NET framework only runs on Windows, thus MetaScope does not support Linux or Mac.

Q3: Where can I find the MetaScope documentation?  
A: You can find MetaScope user's guide documentations on the website http://gcrg.ucsd.edu/Downloads/MetaScope

Q4: How do I load the sample dataset?  
A: If you unzip the compressed sample dataset file, you can find one ".workspace" file.   
Drag and drop the .workspace file onto MetaScope or use "File > Open Workspace" menu.

Q5: What is the difference between x86 version and x64 version  
A: x86 version of MetaScope is optimal for smaller size of dataset under 750MB. x64 version of MetaScope   

can load larger datasets, and tested up to 3GB of datasets, but x64 version consumes more memory compared to x86 version.

Contact

For questions or comments, please contact Donghyuk Kim dok023@ucsd.edu

MetaScope News

  • September 18, 2010: x64 version of MetaScope is released!
  • August 5, 2010: MetaScope v1.00 released
  • July 29, 2010: MetaScope v0.99 released

Location

Location

417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

Contact Us

Contact Us

In Silico Lab:  858-822-1144

Wet Lab:  858-246-1625

FAX:   858-822-3120

Website Concerns: sbrgit@ucsd.edu

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