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= EMMA 2 Overview Page =
= EMMA 2 - A MAGE-compliant system for storage and analysis of microarray data =


== EMMA 2 - A MAGE-compliant system for storage and analysis of microarray data ==
== Overview ==


EMMA 2 is a web-based system for management and analysis of transcriptomic data. EMMA 2 allows mapping of gene expression data onto proteome data or pathways and vice versa. It provides extensible analysis and visualization Plug-Ins via the R-language. EMMA 2 now supports the MAGE-ML XML-language for the interchange of microarray data.
EMMA 2 is a web-based system for management and analysis of transcriptomic data. EMMA 2 allows mapping of gene expression data onto proteome data or pathways and vice versa. It provides extensible analysis and visualization Plug-Ins via the R-language. EMMA 2 now supports the MAGE-ML XML-language for the interchange of microarray data.
With EMMA you can do normalization of single and multiple microarrays and run statistical tests for inferring differrentially expressed genes. You can also run cluster analysis to find co-regulated genes.
With EMMA you can do normalization of single and multiple microarrays and run statistical tests for inferring differrentially expressed genes. You can also run cluster analysis to find co-regulated genes.


Please have a look at the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/ EMMA  website] for general information.
* [[EMMAWiki/StepbyStep|Step by Step tutorial for complete beginners]]
* Common problems: [https://www.cebitec.uni-bielefeld.de/mycebitec/ change your password] (In case you want to request a new password, please follow this link and click on "Forgot password?")


* /TermsAndConcepts
Please have a look at the [http://www.cebitec.uni-bielefeld.de/polyomics/index.php/emma EMMA info website] for general information.
** [[/TermsAndConcepts/ForUsers| For Users]]
 
** [[/TermsAndConcepts/ForDevelopers| For Developers]]
{{Info}} If you have problems accessing EMMA due to a certificate error please have a look at these pages: '''[[Firefox3|Webbrowsers and certificate errors]]'''
 
* [[EMMAWiki/TermsAndConcepts|Terms and Concepts]]
** [[EMMAWiki/TermsAndConcepts/ForUsers| For Users]]
** [[EMMAWiki/TermsAndConcepts/ForDevelopers| For Developers]]


== Documentation ==
== Documentation ==
* /CoreDocumentation (Documentation of the main backend functionality and executable scripts)
* [[EMMAWiki/WebDocumentation|Web Documentation]]
* /UserManual  (Documentation on the use of the web-interface)
** [[EMMAWiki/WebDocumentation/GeneralUsage|General Usage]]
** /WebDocumentation
** [[EMMAWiki/WebDocumentation/HowTos|HowTos]]
** [[Media:EMMAWiki$EMMA_Quickstart.pdf|QuickStart Documentation (PDF)]]  
** [[EMMAWiki/WebDocumentation/HelpSystem|Help System]]
* /DeveloperDocumentation
** [[EMMAWiki/WebDocumentation/OnlineHelp|Online Help]]
** [[/DeveloperDocumentation/GettingStarted| GettingStarted]]
** [[EMMAWiki/WebDocumentation/AnalysisFunctions| Analysis Functions]]
* /AdministratorDocumentation (Installation, project configuration and account management)
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline.pdf QuickStart Documentation (PDF)]
** [[/AdministratorDocumentation/SoftwareRequirements| SoftwareRequirements]]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/EMMA_guideline.html EMMA guidelines]
** [[/AdministratorDocumentation/HardwareRequirements| HardwareRequirements]]
* [http://bieson.ub.uni-bielefeld.de/volltexte/2008/1236/pdf/DissertationDondrup.pdf A little more in-depth description of EMMA and microarray analysis in general]
** [[/AdministratorDocumentation/InstallationInstructions| InstallationInstructions]]
<!-- * [[EMMAWiki/CoreDocumentation|Core Documentation (Functionality of the main backend and executable scripts)]] -->
** [[/AdministratorDocumentation/ProjectSetup| ProjectSetup]]
* [[EMMAWiki/DeveloperDocumentation|Developer Documentation]]
* /FAQs
** [[EMMAWiki/DeveloperDocumentation/GettingStarted|Getting Started]]
* /HowTos
** [[EMMAWiki/DeveloperDocumentation/APIDocumentation|API Documentation]]
<!-- ** [[EMMAWiki/DeveloperDocumentation/BuildingHeatmapViewer|Building the Heatmap Viewer]] -->
<!-- ** [[EMMAWiki/DeveloperDocumentation/DevelopingPlugIns|Developing Plugins]] -->
** [[UsingTheWSInterface|Using the SOAP Web Service ]]
** [[EMMAWiki/DeveloperDocumentation/MagemlExporterGenerator|MAGE-ML Exporter Generator]]
* [[EMMAWiki/AdministratorDocumentation|Administrator Documentation(Installation, project configuration and account management)]]
** [[EMMAWiki/AdministratorDocumentation/SoftwareRequirements|SoftwareRequirements]]
** [[EMMAWiki/AdministratorDocumentation/InstallationInstructions|InstallationInstructions]]
** [[EMMAWiki/AdministratorDocumentation/ProjectSetup|ProjectSetup]]
** [[EMMAWiki/AdministratorDocumentation/ArraylayoutGuide|Arraylayout Guideline - conventions and definitions]]
* [[EMMAWiki/FAQs|FAQs]]
* [[EMMAWiki/HowTos|HowTos]]
** [[EMMAWiki/HowTos/LoggingIn|LoggingIn]]
** [[EMMAWiki/HowTos/CreatingAnExperiment|Creating An Experiment]]
** [[EMMAWiki/WebDocumentation/GeneralUsage/ImportDatafromArrayLIMS| ImportingData]]
** [[EMMAWiki/WebDocumentation/HowTos/DatasetBrowserHowTo| Using the Dataset Browser]]
** [[EMMAWiki/HowTos/EmmaBridgeHowTo|Emma Bridge How To]]
** [[EMMAWiki/HowTos/MAGEExport|MAGE-ML Export]]


== General ==
== General ==
* /FeatureTable
* [[EMMAWiki/NewsAndUpdates|Change log]]
* /FuturePlans


== Other Issues ==
== Other Issues ==


For more information about project setup, license, application examples, and publications, please go to the  [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info EMMA website].
EMMA 2 is a free software and is distributed under the [http://www.gnu.org/copyleft/gpl.html GNU General Public License] (GPL).
For more information about project setup, license, demo project, guided tour, workshops and PDF documentation, please go to the  [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info EMMA website].


* /SoftwareDisclaimer
* [[EMMAWiki/EMMA_2_DISCLAIMER|Software Disclaimer]]


== Contact ==
== Contact ==


Please send
Please send ''help requests'', ''bug-reports and feature requests'', or ''account requests'' to the [mailto:emma-devel@cebitec.uni-bielefeld.de EMMA mailinglist]
 
* ''help requests'' to [[MailTo(emma AT cebitec DOT uni DASH bielefeld DOT de)]]
* ''bug-reports and feature requests'' to [[MailTo(emma DASH devel AT cebitec DOT uni DASH bielefeld DOT de)]] or use [http://bugs.genetik.uni-bielefeld.de BugZilla]
* ''account requests'' to [[MailTo(emma DASH support AT cebitec DOT uni DASH bielefeld DOT de)]]
/!\ '''Please never send passwords or other confidential information to mailing lists'''


=== Developers ===
=== History of EMMA developers ===


* [http://www.cebitec.uni-bielefeld.de/~mdondrup Michel Dondrup]
* Michael Dondrup
* [http://www.cebitec.uni-bielefeld.de/~agoesman Alexander Goesman]
* [http://www.cebitec.uni-bielefeld.de/~alu Stefan Albaum]
* Stefan Albaum
* [http://www.cebitec.uni-bielefeld.de/~jueneman Sebastian Jünemann]
* Thasso Griebel
* Thasso Griebel
* Tim Kahlke
* Tim Kahlke
* Felix Tille
* Felix Tille
* Manuel Stein
* Kolja Henckel
* Kai Runte
* Dominik Mertens
* [http://www.cebitec.uni-bielefeld.de/~agoesman Alexander Goesmann]


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[[File:emma_cartoon_by_dkoch_small.png]]


''Cartoon by Daniel Koch, 2004''
(C) ''Daniel Koch''
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Copyright (C) 2004,
Copyright (C) 2014,
Center for Biotechnology, Bielefeld University
Center for Biotechnology, Bielefeld University
Author: [http://www.cebitec.uni-bielefeld.de/~mdondrup Michael Dondrup]

Latest revision as of 17:04, 5 May 2014

EMMA 2 - A MAGE-compliant system for storage and analysis of microarray data

Overview

EMMA 2 is a web-based system for management and analysis of transcriptomic data. EMMA 2 allows mapping of gene expression data onto proteome data or pathways and vice versa. It provides extensible analysis and visualization Plug-Ins via the R-language. EMMA 2 now supports the MAGE-ML XML-language for the interchange of microarray data. With EMMA you can do normalization of single and multiple microarrays and run statistical tests for inferring differrentially expressed genes. You can also run cluster analysis to find co-regulated genes.

Please have a look at the EMMA info website for general information.

Info.png If you have problems accessing EMMA due to a certificate error please have a look at these pages: Webbrowsers and certificate errors

Documentation

General

Other Issues

EMMA 2 is a free software and is distributed under the GNU General Public License (GPL). For more information about project setup, license, demo project, guided tour, workshops and PDF documentation, please go to the EMMA website.

Contact

Please send help requests, bug-reports and feature requests, or account requests to the EMMA mailinglist

History of EMMA developers

Emma cartoon by dkoch small.png

(C) Daniel Koch

Copyright (C) 2014, Center for Biotechnology, Bielefeld University

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