BRF-Software - User contributions [en]

MGE-PortalWiki

2014-05-05T16:06:25Z

Alu: /* Login to the Portal */

__NOTOC__

= MGE-[[PortalWiki]] Overview Page =

This is the primary source of documentation for the
[http://www.cebitec.uni-bielefeld.de/groups/brf/software/mge-portal/ MGE-Portal].
The portal gives you access to the [http://www.cebitec.uni-bielefeld.de/groups/brf/cooperations/marine_genomics_bioinformatics.html Bioinformatics Platform], implementing all activities within the Marine Genomics Europe Network of Excellence.

In this overview page, you will find the following topics:

* [[#gendbaccess|How to access GenDB, SAMS, EMMA, etc...]]
* [[#access|Data access]]
* [[#browsers|Supported Web Browsers]]
* [[#login|Login to the Portal]]
* [[#my|My Projects]]
* [[#request|Request Access to the MGE-Portal]]
* [[#project|Request New Project to the MGE-Portal]]
* [[#tools|Information about Tools]]
* [[#data|Data integrity, data backup and recovery]]
* [[#contact|Contact]]
* [[/DeveloperDocumentation|Developer Documentation]]

[[Image:MGE-PortalWiki$see_stern_small.png]]

The Portal contains datasets and tools for the analysis of ESTs, microarrays, genomes etc., and it is run by the "Bioinformatics Resource Facility ([http://www.cebitec.uni-bielefeld.de/groups/brf/ BRF])".

Powered by the [http://www.cebitec.uni-bielefeld.de/groups/brf/infrastructure.html CeBiTec_Infrastructure], the MGE-Portal contains more than 500 processors
and several Terabytes of disk space. MGE has a private set of processors but can use idle resources of the CeBiTec system.



The individual software packages contained in the platform have their own documentation

* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/ GenDB] Sequence analysis for larger contigs.
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/sams_info/ SAMS] Sequence analysis for ESTs and shotgun reads.
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/ EMMA] Microarray data storage and analysis.


== How to access GenDB, SAMS, EMMA, etc... ==

The three in-house developed software packages: GenDB (procaryotic genome annotation), SAMS (EST processing and annotation) and EMMA (microarray analysis) are provided by the bioinformatics platform to the whole MGE community. The MGE Portal has been designed to grant MGE members access to these tools and projects. All of them work based on projects that are set up by the bioinformatics team at the platform. Please use the MGE Portal in order to request a new project, or request access to an existing one.


== Data access ==

There are two major kinds of project "accessibility" within MGE, according to the Data Policy adopted for the Network:

* "your" projects:
** either you are a project leader and thus have access to your "own" project data,
** or you have already requested access to this project,
** or the project has been made public within the whole MGE community
* "MGE" projects:
** other projects within MGE not yet visible to you, but to which you can request access.

Access to projects is controlled by the project leaders via the GPMS web interface.
All MGE members can request access to these datasets directly to the respective project leader via the Portal.

The General Project Management System ([http://www.cebitec.uni-bielefeld.de/groups/brf/software/gpms/ GPMS]) provides the interface for requesting and granting access to projects.
More information can be found under this [http://www.cebitec.uni-bielefeld.de/groups/brf/software/wiki/GPMSWiki/WebRequestAccess wiki page].


== Supported Web Browsers ==
Please note that not all web browsers are supported with the platform. For security reasons we recommend that users use
[http://www.mozilla.org/products/firefox/ Mozilla/Firefox] or
[http://www.mozilla.org/products/mozilla1.x/ Mozilla].

While other browsers might work, we '''can not test''' with every browser to ensure compatibility. We strive to use standard D-HTML to ensure
maximum compatability.


== Login to the Portal ==
The portal requires a user name and password from every user. The assumption is made that every individual has his/her own private login. If two individuals share one login and use it simultaneously, terrible things will happen to the user settings and data.

Users need to enter user name and password into the login dialog. Since the data is transported via '''https''' all traffic is encrypted and thus secure.

'''Browser Certificates'''

Unfortunately not all institutions that issue certificates are pre-configured into all browsers. Therefore please '''accept permanently''' the CeBiTec certificate.
Doing so will only influence your connections to Bielefeld, no other internet connects will be influenced.
After accepting the certificate once, this question should not need to be answered again ([http://www.mozilla.org/projects/security/pki/psm/help_21/using_certs_help.html Technical Information on using Browser certificates])


[[Image:MGE-PortalWiki$MGE_portal_login.png]]

'''Forgot your password?'''

If you have a login to access the MGE bioinformatics portal or one of our web applications and have forgotten your password, you can use [https://www.cebitec.uni-bielefeld.de/mycebitec/ the following form] to submit a password change request.



== My Projects ==
Once you have logged into the MGE portal, the main page looks like this screenshot:
[[Image:MGE-PortalWiki$mge_portal_overview.png]]

Click on the link "My Projects" in the Action menu.
A page will appear as below where you can see all your projects as a chief.
By clicking on the blue arrow on the right inside, you can jump directly to the corresponding EMMA, SAMS or GenDB project:
[[Image:MGE-PortalWiki$mge_portal_myprojects.png]]


== Request Access to the MGE-Portal ==

All MGE members contained in the MGE list in January 2005 have received an automatical e-mail containing their login to the MGE-Portal and password.

If you are a '''new MGE member''' (registered after February 2005), you can request access to the Portal by sending an e-mail to the [http://www.cebitec.uni-bielefeld.de/groups/brf/cooperations/marine_genomics_bioinformatics.html#contact node representative]. After the validation by the node representative, the contact person will forward your request to the Bioinformatics Platform. You will receive an automatic mail from our General Project Management System (GPMS) containing your login to the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/mge-portal/ MGE-Portal] and password.

Once logged into the Portal, you can request access to any project within MGE by clicking on the link "Request Projects Access" in the Action menu.
Then click onto "Request Project Access via GPMS" which allow you to login to the General Project Management System (GPMS).
For further information, please go to this [http://www.cebitec.uni-bielefeld.de/groups/brf/software/wiki/GPMSWiki/WebRequestAccess wiki page].
[[Image:MGE-PortalWiki$mge_portal_request_access.png]]


== Request New Project to the MGE-Portal ==
By clicking on the link "Request New Project" in the Action menu, a new page will appear as below where you need to fill in the page according to what type of data you have. A email will be sent automatically to the node representative to grant or deny the request.
Once the request is granted, we setup your project and let you know by email.
[[Image:MGE-PortalWiki$mge_portal_request_newproject1.png]]
[[Image:MGE-PortalWiki$mge_portal_request_newproject2.png]]


== Information about Tools ==
Some public databases are available for analysis with the Platform tools. In addition all sequence data sets created within MGE can be analyzed with the tools.
[[Image:MGE-PortalWiki$mge_portal_tools.png]]

'''Please note:''' Only those data sets that you have access to will be visible within the tool section.

* [[/BLAST]]
* [[/EMOWSE]]


== Data integrity, data backup and recovery ==
To ensure the existence of the valuable data sets we perform nightly backup of all data on the platform. In the unlikely event of a disasterous system failure
all data can be retrieved from backup tape.


== Contact ==
Please feel free at any time to send us a email to [[MailTo(mg-bielefeld AT cebitec DOT uni DASH bielefeld DOT de)]] with questions or suggestions for improvements.

EMMAWiki/StepbyStep

2014-05-05T16:05:38Z

Alu: /* How to access EMMA for MGE members */

__NOTOC__

= Step by Step tutorial for beginners =

* [[#mge|For MGE members]]
* [[#genomikplus|For GenoMik-Plus members]]
* [[#others|For other potential users]]
* [[#all|For all users]]


== How to access EMMA for MGE members ==
* Refer to [http://www.marine-genomics-europe.org/ the MGE homepage] to find out if your institution is a member.
* 1) Login to the Portal:
** If you are a MGE member you should have a login and password for the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/mge-portal/ MGE bioinformatics portal]. Your login is usually as follow: Firstname_Surname.
** Forgot your password? If you have a login to access the MGE bioinformatics portal and have forgotten your password, you can use [https://www.cebitec.uni-bielefeld.de/mycebitec/ the following form] to submit a password change request.
** If you don't remember your login, please send a email to mg-bielefeld[at]cebitec.uni-bielefeld.de
* 2) Access to a EMMA project:
** Once you have logged into the MGE Bioinformatics portal, please check if you can already access a EMMA project by clicking on the link "My Projects" in the Action menu. For more info, have a look at this [http://www.cebitec.uni-bielefeld.de/groups/brf/software/wiki/MGE-PortalWiki#my link].
** If you don't have access to a EMMA project, either you can have a look at the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/demo.html Demo project] or you can request access to a MGE project. The procedure is explained under [http://www.cebitec.uni-bielefeld.de/groups/brf/software/wiki/MGE-PortalWiki#request this MGE wiki link] and [http://www.cebitec.uni-bielefeld.de/groups/brf/software/wiki/GPMSWiki/WebRequestAccess this GPMS wiki link].
** Depending on your privileges for the EMMA project(s) you can access, the tasks you can perform inside a EMMA project can be limited. More info can be found under [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/node8.html this EMMA guideline Rights and Roles page].
* 3) Use ArrayLIMS and EMMA with your own data:
** The best is to have your own project as chief. For that you need to request a New Project inside the MGE Bioinformatics Portal. The procedure is explained under [http://www.cebitec.uni-bielefeld.de/groups/brf/software/wiki/MGE-PortalWiki#project this MGE wiki link].
** Once you have access to your project, please read [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info the ArrayLIMS and EMMA documentations] before to start to use EMMA.
* 4) Contact:
** Please feel free at any time to send us a email to mg-bielefeld[at]cebitec.uni-bielefeld.de if you have any problems and/or comments.



== How to access EMMA for GenoMik-Plus members ==
* Refer to [http://www.genetik.uni-bielefeld.de/GenoMikPlus/ the GenoMikPlus homepage] to find out if your institution is a member.
* 1) Login to the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/portal-genomik/ GenomikPlus Portal]
* 2) Access to an existing EMMA project: see above
* 3) Use ArrayLIMS and EMMA with your own data: see above
* 4) Contact: genomik-support[at]cebitec.uni-bielefeld.de



== How to access EMMA for other potential users ==
* 1) How to get a login and password for using EMMA 2.0? Please send a email to emma[at]cebitec.uni-bielefeld.de
* 2) Login into EMMA: more info under [http://www.cebitec.uni-bielefeld.de/groups/brf/software/wiki/EMMAWiki/HowTos/LoggingIn EMMA wiki page].
* 3) Use ArrayLIMS and EMMA with your own data:
** Request access to an existing project: [https://www.cebitec.uni-bielefeld.de/groups/brf/software/gpms/login.html login to GPMS] with your username and password and click ''Request Project Access''.[http://www.cebitec.uni-bielefeld.de/groups/brf/software/wiki/GPMSWiki/WebRequestAccess detailed description of the request process]
** We can provide you with your own project as chief. Please send a email to emma[at]cebitec.uni-bielefeld.de for details.
** Once you have access to your project, please read [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info the ArrayLIMS and EMMA documentations] before to start to use EMMA.


== Step by Step tutorial for all users ==

* Basic terms and concepts used in EMMA: more info under [http://www.cebitec.uni-bielefeld.de/groups/brf/software/wiki/EMMAWiki/TermsAndConcepts/ForUsers this EMMA wiki page].
* What is an arraylayout and why do we need it? More info under [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/node9.html this EMMA guideline Arraylayout Guidelines page].
* What data files are required?
** if ImaGene, two .txt files, one for each channel (versions >= 5.0 supported)
** if GenePix, one .gpr file (supports versions > 1.x)
** if Affymetrix, one CEL file per array
** all other formats: contac emma-devel[at]cebitec.uni-bielefeld.de
** Dual images or single images? one .tiff file or two .tiff files (one for each channel)
** .data files containing the images for Affy are not required
* Storage of the hybridization data together with all relevant biological information into our LIMS (Laboratory Information Management System): More info under [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/ArrayLIMS_guideline/ArrayLIMS_guideline.html the ArrayLIMS Guidelines pages].
* Upload and group your hybridized arrays: for that you need to create a new experiment in EMMA. The procedure is explained under [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/node14.html this EMMA Guidelines page].
* How to Import Data From the ArrayLIMS system: more info under [http://www.cebitec.uni-bielefeld.de/groups/brf/software/wiki/EMMAWiki/WebDocumentation/GeneralUsage/ImportDatafromArrayLIMS this EMMA wiki page] and under [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/node36.html this EMMA Guidelines page].
* Analyzing Data using EMMA: more info under [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/node66.html this EMMA Guidelines page].

EMMAWiki

2014-05-05T16:04:23Z

Alu: /* Documentation */

__NOTOC__
= 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.

* [[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?")

Please have a look at the [http://www.cebitec.uni-bielefeld.de/polyomics/index.php/emma EMMA info website] for general information.

{{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 ==
* [[EMMAWiki/WebDocumentation|Web Documentation]]
** [[EMMAWiki/WebDocumentation/GeneralUsage|General Usage]]
** [[EMMAWiki/WebDocumentation/HowTos|HowTos]]
** [[EMMAWiki/WebDocumentation/HelpSystem|Help System]]
** [[EMMAWiki/WebDocumentation/OnlineHelp|Online Help]]
** [[EMMAWiki/WebDocumentation/AnalysisFunctions| Analysis Functions]]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline.pdf QuickStart Documentation (PDF)]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/EMMA_guideline.html EMMA guidelines]
* [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]

* [[EMMAWiki/DeveloperDocumentation|Developer Documentation]]
** [[EMMAWiki/DeveloperDocumentation/GettingStarted|Getting Started]]
** [[EMMAWiki/DeveloperDocumentation/APIDocumentation|API Documentation]]


** [[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 ==
* [[EMMAWiki/NewsAndUpdates|Change log]]

== Other Issues ==

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].

* [[EMMAWiki/EMMA_2_DISCLAIMER|Software Disclaimer]]

== Contact ==

Please send ''help requests'', ''bug-reports and feature requests'', or ''account requests'' to the [mailto:emma-devel@cebitec.uni-bielefeld.de EMMA mailinglist]

=== History of EMMA developers ===

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

-----------
[[File:emma_cartoon_by_dkoch_small.png]]

(C) ''Daniel Koch''
-----------

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

EMMAWiki

2014-05-05T16:03:42Z

Alu: /* History of EMMA developers */

__NOTOC__
= 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.

* [[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?")

Please have a look at the [http://www.cebitec.uni-bielefeld.de/polyomics/index.php/emma EMMA info website] for general information.

{{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 ==
* [[EMMAWiki/WebDocumentation|Web Documentation]]
** [[EMMAWiki/WebDocumentation/GeneralUsage|General Usage]]
** [[EMMAWiki/WebDocumentation/HowTos|HowTos]]
** [[EMMAWiki/WebDocumentation/HelpSystem|Help System]]
** [[EMMAWiki/WebDocumentation/OnlineHelp|Online Help]]
** [[EMMAWiki/WebDocumentation/AnalysisFunctions| Analysis Functions]]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline.pdf QuickStart Documentation (PDF)]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/EMMA_guideline.html EMMA guidelines]
* [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]

* [[EMMAWiki/DeveloperDocumentation|Developer Documentation]]
** [[EMMAWiki/DeveloperDocumentation/GettingStarted|Getting Started]]
** [[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 ==
* [[EMMAWiki/NewsAndUpdates|Change log]]

== Other Issues ==

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].

* [[EMMAWiki/EMMA_2_DISCLAIMER|Software Disclaimer]]

== Contact ==

Please send ''help requests'', ''bug-reports and feature requests'', or ''account requests'' to the [mailto:emma-devel@cebitec.uni-bielefeld.de EMMA mailinglist]

=== History of EMMA developers ===

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

-----------
[[File:emma_cartoon_by_dkoch_small.png]]

(C) ''Daniel Koch''
-----------

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

EMMAWiki

2014-05-05T16:02:03Z

Alu: /* List of EMMA developers */

__NOTOC__
= 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.

* [[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?")

Please have a look at the [http://www.cebitec.uni-bielefeld.de/polyomics/index.php/emma EMMA info website] for general information.

{{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 ==
* [[EMMAWiki/WebDocumentation|Web Documentation]]
** [[EMMAWiki/WebDocumentation/GeneralUsage|General Usage]]
** [[EMMAWiki/WebDocumentation/HowTos|HowTos]]
** [[EMMAWiki/WebDocumentation/HelpSystem|Help System]]
** [[EMMAWiki/WebDocumentation/OnlineHelp|Online Help]]
** [[EMMAWiki/WebDocumentation/AnalysisFunctions| Analysis Functions]]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline.pdf QuickStart Documentation (PDF)]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/EMMA_guideline.html EMMA guidelines]
* [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]

* [[EMMAWiki/DeveloperDocumentation|Developer Documentation]]
** [[EMMAWiki/DeveloperDocumentation/GettingStarted|Getting Started]]
** [[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 ==
* [[EMMAWiki/NewsAndUpdates|Change log]]

== Other Issues ==

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].

* [[EMMAWiki/EMMA_2_DISCLAIMER|Software Disclaimer]]

== Contact ==

Please send ''help requests'', ''bug-reports and feature requests'', or ''account requests'' to the [mailto:emma-devel@cebitec.uni-bielefeld.de EMMA mailinglist]

=== History of EMMA developers ===

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

-----------
[[File:emma_cartoon_by_dkoch_small.png]]

(C) ''Daniel Koch''
-----------

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

EMMAWiki

2014-05-05T16:01:28Z

Alu: /* General */

__NOTOC__
= 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.

* [[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?")

Please have a look at the [http://www.cebitec.uni-bielefeld.de/polyomics/index.php/emma EMMA info website] for general information.

{{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 ==
* [[EMMAWiki/WebDocumentation|Web Documentation]]
** [[EMMAWiki/WebDocumentation/GeneralUsage|General Usage]]
** [[EMMAWiki/WebDocumentation/HowTos|HowTos]]
** [[EMMAWiki/WebDocumentation/HelpSystem|Help System]]
** [[EMMAWiki/WebDocumentation/OnlineHelp|Online Help]]
** [[EMMAWiki/WebDocumentation/AnalysisFunctions| Analysis Functions]]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline.pdf QuickStart Documentation (PDF)]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/EMMA_guideline.html EMMA guidelines]
* [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]

* [[EMMAWiki/DeveloperDocumentation|Developer Documentation]]
** [[EMMAWiki/DeveloperDocumentation/GettingStarted|Getting Started]]
** [[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 ==
* [[EMMAWiki/NewsAndUpdates|Change log]]

== Other Issues ==

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].

* [[EMMAWiki/EMMA_2_DISCLAIMER|Software Disclaimer]]

== Contact ==

Please send ''help requests'', ''bug-reports and feature requests'', or ''account requests'' to the [mailto:emma-devel@cebitec.uni-bielefeld.de EMMA mailinglist]

=== List of EMMA developers ===

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

-----------
[[File:emma_cartoon_by_dkoch_small.png]]

(C) ''Daniel Koch''
-----------

Copyright (C) 2011,
Center for Biotechnology, Bielefeld University

EMMAWiki

2014-05-05T16:00:54Z

Alu: /* Documentation */

__NOTOC__
= 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.

* [[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?")

Please have a look at the [http://www.cebitec.uni-bielefeld.de/polyomics/index.php/emma EMMA info website] for general information.

{{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 ==
* [[EMMAWiki/WebDocumentation|Web Documentation]]
** [[EMMAWiki/WebDocumentation/GeneralUsage|General Usage]]
** [[EMMAWiki/WebDocumentation/HowTos|HowTos]]
** [[EMMAWiki/WebDocumentation/HelpSystem|Help System]]
** [[EMMAWiki/WebDocumentation/OnlineHelp|Online Help]]
** [[EMMAWiki/WebDocumentation/AnalysisFunctions| Analysis Functions]]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline.pdf QuickStart Documentation (PDF)]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/EMMA_guideline.html EMMA guidelines]
* [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]

* [[EMMAWiki/DeveloperDocumentation|Developer Documentation]]
** [[EMMAWiki/DeveloperDocumentation/GettingStarted|Getting Started]]
** [[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 ==
* [[EMMAWiki/NewsAndUpdates|News And Updates]]

== Other Issues ==

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].

* [[EMMAWiki/EMMA_2_DISCLAIMER|Software Disclaimer]]

== Contact ==

Please send ''help requests'', ''bug-reports and feature requests'', or ''account requests'' to the [mailto:emma-devel@cebitec.uni-bielefeld.de EMMA mailinglist]

=== List of EMMA developers ===

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

-----------
[[File:emma_cartoon_by_dkoch_small.png]]

(C) ''Daniel Koch''
-----------

Copyright (C) 2011,
Center for Biotechnology, Bielefeld University

EMMAWiki

2014-05-05T15:58:28Z

Alu: /* EMMA 2 Overview Page */

__NOTOC__
= 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.

* [[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?")

Please have a look at the [http://www.cebitec.uni-bielefeld.de/polyomics/index.php/emma EMMA info website] for general information.

{{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 ==
* [[EMMAWiki/WebDocumentation|Web Documentation]]
** [[EMMAWiki/WebDocumentation/GeneralUsage|General Usage]]
** [[EMMAWiki/WebDocumentation/HowTos|HowTos]]
** [[EMMAWiki/WebDocumentation/HelpSystem|Help System]]
** [[EMMAWiki/WebDocumentation/OnlineHelp|Online Help]]
** [[EMMAWiki/WebDocumentation/AnalysisFunctions| Analysis Functions]]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline.pdf QuickStart Documentation (PDF)]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/EMMA_guideline.html EMMA guidelines]
* [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]
* [[EMMAWiki/CoreDocumentation|Core Documentation (Functionality of the main backend and executable scripts)]]
* [[EMMAWiki/DeveloperDocumentation|Developer Documentation]]
** [[EMMAWiki/DeveloperDocumentation/GettingStarted|Getting Started]]
** [[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 ==
* [[EMMAWiki/NewsAndUpdates|News And Updates]]

== Other Issues ==

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].

* [[EMMAWiki/EMMA_2_DISCLAIMER|Software Disclaimer]]

== Contact ==

Please send ''help requests'', ''bug-reports and feature requests'', or ''account requests'' to the [mailto:emma-devel@cebitec.uni-bielefeld.de EMMA mailinglist]

=== List of EMMA developers ===

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

-----------
[[File:emma_cartoon_by_dkoch_small.png]]

(C) ''Daniel Koch''
-----------

Copyright (C) 2011,
Center for Biotechnology, Bielefeld University

EMMAWiki

2014-05-05T15:57:37Z

Alu: /* EMMA 2 - A MAGE-compliant system for storage and analysis of microarray data */

__NOTOC__
= EMMA 2 Overview Page =

== EMMA 2 - A MAGE-compliant system for storage and analysis 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.

* [[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?")

Please have a look at the [http://www.cebitec.uni-bielefeld.de/polyomics/index.php/emma EMMA info website] for general information.

{{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 ==
* [[EMMAWiki/WebDocumentation|Web Documentation]]
** [[EMMAWiki/WebDocumentation/GeneralUsage|General Usage]]
** [[EMMAWiki/WebDocumentation/HowTos|HowTos]]
** [[EMMAWiki/WebDocumentation/HelpSystem|Help System]]
** [[EMMAWiki/WebDocumentation/OnlineHelp|Online Help]]
** [[EMMAWiki/WebDocumentation/AnalysisFunctions| Analysis Functions]]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline.pdf QuickStart Documentation (PDF)]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/EMMA_guideline.html EMMA guidelines]
* [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]
* [[EMMAWiki/CoreDocumentation|Core Documentation (Functionality of the main backend and executable scripts)]]
* [[EMMAWiki/DeveloperDocumentation|Developer Documentation]]
** [[EMMAWiki/DeveloperDocumentation/GettingStarted|Getting Started]]
** [[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 ==
* [[EMMAWiki/NewsAndUpdates|News And Updates]]

== Other Issues ==

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].

* [[EMMAWiki/EMMA_2_DISCLAIMER|Software Disclaimer]]

== Contact ==

Please send ''help requests'', ''bug-reports and feature requests'', or ''account requests'' to the [mailto:emma-devel@cebitec.uni-bielefeld.de EMMA mailinglist]

=== List of EMMA developers ===

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

-----------
[[File:emma_cartoon_by_dkoch_small.png]]

(C) ''Daniel Koch''
-----------

Copyright (C) 2011,
Center for Biotechnology, Bielefeld University

EMMAWiki

2014-05-05T15:56:48Z

Alu: /* EMMA 2 - A MAGE-compliant system for storage and analysis of microarray data */

__NOTOC__
= EMMA 2 Overview Page =

== EMMA 2 - A MAGE-compliant system for storage and analysis 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.

* [[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?")

Please have a look at the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/ EMMA info website] for general information.

{{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 ==
* [[EMMAWiki/WebDocumentation|Web Documentation]]
** [[EMMAWiki/WebDocumentation/GeneralUsage|General Usage]]
** [[EMMAWiki/WebDocumentation/HowTos|HowTos]]
** [[EMMAWiki/WebDocumentation/HelpSystem|Help System]]
** [[EMMAWiki/WebDocumentation/OnlineHelp|Online Help]]
** [[EMMAWiki/WebDocumentation/AnalysisFunctions| Analysis Functions]]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline.pdf QuickStart Documentation (PDF)]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/EMMA_guideline.html EMMA guidelines]
* [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]
* [[EMMAWiki/CoreDocumentation|Core Documentation (Functionality of the main backend and executable scripts)]]
* [[EMMAWiki/DeveloperDocumentation|Developer Documentation]]
** [[EMMAWiki/DeveloperDocumentation/GettingStarted|Getting Started]]
** [[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 ==
* [[EMMAWiki/NewsAndUpdates|News And Updates]]

== Other Issues ==

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].

* [[EMMAWiki/EMMA_2_DISCLAIMER|Software Disclaimer]]

== Contact ==

Please send ''help requests'', ''bug-reports and feature requests'', or ''account requests'' to the [mailto:emma-devel@cebitec.uni-bielefeld.de EMMA mailinglist]

=== List of EMMA developers ===

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

-----------
[[File:emma_cartoon_by_dkoch_small.png]]

(C) ''Daniel Koch''
-----------

Copyright (C) 2011,
Center for Biotechnology, Bielefeld University

EMMAWiki

2014-05-05T15:55:07Z

Alu: /* EMMA 2 - A MAGE-compliant system for storage and analysis of microarray data */

__NOTOC__
= EMMA 2 Overview Page =

== EMMA 2 - A MAGE-compliant system for storage and analysis 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.

* [[EMMAWiki/StepbyStep|Step by Step tutorial for complete beginners]]
* Common problems: [https://www.cebitec.uni-bielefeld.de/mycebitec/ change your password or request a new one]

Please have a look at the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/ EMMA info website] for general information.

{{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 ==
* [[EMMAWiki/WebDocumentation|Web Documentation]]
** [[EMMAWiki/WebDocumentation/GeneralUsage|General Usage]]
** [[EMMAWiki/WebDocumentation/HowTos|HowTos]]
** [[EMMAWiki/WebDocumentation/HelpSystem|Help System]]
** [[EMMAWiki/WebDocumentation/OnlineHelp|Online Help]]
** [[EMMAWiki/WebDocumentation/AnalysisFunctions| Analysis Functions]]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline.pdf QuickStart Documentation (PDF)]
* [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/EMMA_guideline/EMMA_guideline.html EMMA guidelines]
* [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]
* [[EMMAWiki/CoreDocumentation|Core Documentation (Functionality of the main backend and executable scripts)]]
* [[EMMAWiki/DeveloperDocumentation|Developer Documentation]]
** [[EMMAWiki/DeveloperDocumentation/GettingStarted|Getting Started]]
** [[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 ==
* [[EMMAWiki/NewsAndUpdates|News And Updates]]

== Other Issues ==

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].

* [[EMMAWiki/EMMA_2_DISCLAIMER|Software Disclaimer]]

== Contact ==

Please send ''help requests'', ''bug-reports and feature requests'', or ''account requests'' to the [mailto:emma-devel@cebitec.uni-bielefeld.de EMMA mailinglist]

=== List of EMMA developers ===

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

-----------
[[File:emma_cartoon_by_dkoch_small.png]]

(C) ''Daniel Koch''
-----------

Copyright (C) 2011,
Center for Biotechnology, Bielefeld University

ProMeTraWiki/CSVFormat

2012-03-21T14:04:08Z

Alu: /* CSV and TSV data files */

__NOTOC__
== CSV and TSV data files ==

* ProMeTra supports the simple file formats CSV and TSV (comma separated and tab separated values)
* The first line of these files contains the experimental factors that will be used in the legend of the generated image.
* Every following line contains an identifier and a tab or comma separated list of values.

[[File:ProMeTra_CSVFormat_tsv.png]]

[[Media:ProMeTra_CSVFormat_sample.csv| ProMeTra sample file in csv format]]

* Only put one type of ''omics'' data into a single file

File:ProMeTra CSVFormat sample.csv

2012-03-21T14:03:19Z

Alu:

ProMeTraWiki/Animation

2012-03-21T13:25:19Z

Alu:

__NOTOC__
== Animation features of ProMeTra ==

* ProMeTra can animate Pathway- and GenomeMaps using ColorAnimation defined in the SVG specification.
During the animation, the background color of an Enzyme or Metabolite element changes and the current
timepoint / factor is being highlighted in the legend. This is useful if large time series of ''Omics'' data need to be visualized.

* Please bear in mind that currently only the Opera Browser supports these animations features natively. The Adobe [http://www.adobe.com/svg/viewer/install/ SVG Plugin] provides animation features for other browsers as well.
* The following example SVG image was created with ProMeTra and contains the color animation of metabolite pool sizes in the Methionine pathway of ''C. glutamicum''. Click on the link to download the image and/or open it in your browser.

[[Media:Prometra_animation.svg| ProMeTra Animation SVG example]]

* If your browser displays changing background colors for some of the metabolites in this SVG, you may also use the ''Animation'' feature of ProMeTra to visualize your data.

File:Prometra animation.svg

2012-03-21T13:24:21Z

Alu:

ProMeTraWiki/Animation

2012-03-21T12:58:16Z

Alu: /* Animation features of ProMeTra */

__NOTOC__
== Animation features of ProMeTra ==

* ProMeTra can animate Pathway- and GenomeMaps using ColorAnimation defined in the SVG specification.
During the animation, the background color of an Enzyme or Metabolite element changes and the current
timepoint / factor is being highlighted in the legend. This is useful if large time series of ''Omics'' data need to be visualized.

* Please bear in mind that currently only the Opera Browser supports these animations features natively. The Adobe [http://www.adobe.com/svg/viewer/install/ SVG Plugin] provides animation features for other browsers as well.
* The following example SVG image was created with ProMeTra and contains the color animation of metabolite pool sizes in the Methionine pathway of ''C. glutamicum''. Click on the link to download the image and/or open it in your browser.

[[Media:Prometra_animation.svg]]

* If your browser displays changing background colors for some of the metabolites in this SVG, you may also use the ''Animation'' feature of ProMeTra to visualize your data.

File:ProMeTra UploadPathway pathway2.png

2012-03-21T09:28:39Z

Alu:

File:ProMeTra UploadPathway pathway1.png

2012-03-21T09:28:29Z

Alu:

ProMeTraWiki/UploadPathway

2012-03-21T09:28:21Z

Alu:

__NOTOC__


== Uploading your own annotated pathways in SVG format ==

* Login to [[ProMeTra]] using your authorized account:
* [http://prometra.cebitec.uni-bielefeld.de/ ProMeTra login]
* To upload and import a single pathway, please select 'Import your own SVG pathways' from the main page. The pathway import dialog will show up.

[[File:ProMeTra_UploadPathway_pathway1.png]]

* Enter a unique name for your pathway and select the file in SVG format in the file browser. You can use the description field to include additional notes in free text that describe your pathway in more detail.

[[File:ProMeTra_UploadPathway_pathway2.png]]

* Click the 'Create' button to upload your data and store it in the [[ProMeTra]] database. Depending on your internet connection and the file size this may take some time. After your file has been uploaded, the pathway will be displayed in the browser and you will be able to use it to visualize your datasets afterwards.

ProMeTraWiki

2012-03-21T09:27:59Z

Alu:

__NOTOC__
== ProMeTra - Multi-Omics Viewer ==

ProMeTra is a web based framework for the storage and visualization of
user defined metabolic pathway maps and their visualization with experimental data from
transcriptomics, genomics and proteomics.

Please also have a look at the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/prometra_info ProMeTra website] for general information.

== Important information for users of Firefox ==

* [[Firefox3|Read this if you experience trouble accessing the ProMeTra login page with Firefox]].

== ProMeTra login page ==

* [http://prometra.cebitec.uni-bielefeld.de prometra.cebitec.uni-bielefeld.de]

== ProMeTra User Manual ==

Download the ProMeTra user manual which details the main workflow of ProMeTra and explains how to create own pathway maps:

[[Media:ProMeTra-Manual.pdf|ProMeTra manual]]

== ProMeTra Concepts ==

* [[ProMeTraWiki/PrometraAccount|Using the public ProMeTra account]]
* [[ProMeTraWiki/CebitecAccount|Using your CeBiTec, Bielefeld University account]]
* [[ProMeTraWiki/GenomeMaps|What are the GenomeMaps available via ProMeTra?]]
* [[ProMeTraWiki/Animation|What exactly is the ''Animation'' feature of ProMeTra?]]
* [[ProMeTraWiki/Color|Which methods are employed to colorize the pathway maps?]]

== FAQs and How Tos ==

* [[ProMeTraWiki/Persistency|What happens to my uploaded experimental data?]]
* [[ProMeTraWiki/Inkscape|Which software can I use to draw my own pathway maps?]]
* [[ProMeTraWiki/PathwayMap|How do I create my own PathwayMap for ProMeTra?]]
* [[ProMeTraWiki/PathwayMap|What features do my SVG pathway images need to be used in ProMeTra?]]
* [[ProMeTraWiki/Inkscape|Installing the Inkscape SVG Editor software]]
* [[ProMeTraWiki/WebBrowsers|Which web browsers do support the SVG image format?]]
* [[ProMeTraWiki/DownloadPathway|How can I download existing pathway maps from ProMeTra?]]
* [[ProMeTraWiki/UploadPathway|How can I upload my own pathway maps?]]

== Data formats ==

* [[ProMeTraWiki/ExcelFormat|Which format should the experimental data in my Excel files have?]]
* [[ProMeTraWiki/CSVFormat|Which other data files can I upload?]]

== Contact ==

Please send an e-mail for account requests or questions concerning the use of ProMeTra to the [mailto:prometra@cebitec.uni-bielefeld.de ProMeTra mailinglist]

File:ProMeTra CSVFormat tsv.png

2012-03-21T09:26:03Z

Alu:

ProMeTraWiki/CSVFormat

2012-03-21T09:25:52Z

Alu:

__NOTOC__
== CSV and TSV data files ==

* ProMeTra supports the simple file formats CSV and TSV (comma separated and tab separated values)
* The first line of these files contains the experimental factors that will be used in the legend of the generated image.
* Every following line contains an identifier and a tab or comma separated list of values.

[[File:ProMeTra_CSVFormat_tsv.png]]

[[Media:ProMeTra_CSVFormat_sample.tsv]]

* Only put one type of ''omics'' data into a single file

File:ProMeTra ExcelFormat excel.png

2012-03-21T09:25:11Z

Alu:

ProMeTraWiki/ExcelFormat

2012-03-21T09:25:01Z

Alu: /* Supported Excel Formats */

__NOTOC__
== Supported Excel Formats ==

* Please upload only Excel files in the .xls format (Office 1997-2004).
* ProMeTra does not yet support Office 2008 documents.
* Only the data in the first spreadsheet of your Excel document will be retrieved.
* The ProMeTra parser automatically reads the experimental factors from the first row and the individual identifiers of the proteins, transcripts or metabolites from the first column. ProMeTra does only support numerical data matrices. Please make sure that no text elements occur elsewhere than in the first row and column.
* The following image shows a typical Excel sheet that can be uploaded via the ProMeTra interface.

[[File:ProMeTra_ExcelFormat_excel.png]]

* The number of factors should be adjusted to the width of the rectangular elements in your Pathway- and GenomeMaps. For the standard GenomeMap up to ten factors are a reasonable number, the more factors ProMeTra has to visualize, the smaller the individual divisions of the rectangular elements become in the generated images.

File:ProMeTraWiki CreatePathway form.png

2012-03-21T09:24:18Z

Alu:

File:ProMeTraWiki CreatePathway action.png

2012-03-21T09:24:10Z

Alu:

File:ProMeTraWiki CreatePathway context.png

2012-03-21T09:24:00Z

Alu:

ProMeTraWiki/CreatePathway

2012-03-21T09:23:49Z

Alu:

__NOTOC__
== Upload your own pathway ==

* Select the ''Pathway Maps'' context in the left menu bar.

[[File:ProMeTraWiki_CreatePathway_context.png]]

* Select the ''create'' action to upload one of your SVG pathways and create a new entry in the ProMeTra Pathway Database.
[[File:ProMeTraWiki_CreatePathway_action.png]]

* Fill out the form, select the SVG file to upload and choose an unique and descriptive name for your pathway. You can add additional text to the description field that will help you and others to find your pathway. If you want to share the pathway with other ProMeTra users, check the ''public'' attribute.

[[File:ProMeTraWiki_CreatePathway_form.png]]

* You can later delete or update the entries of your pathway object.

File:ProMeTra DownloadPathway download.png

2012-03-21T09:23:01Z

Alu:

File:ProMeTra DownloadPathway result.png

2012-03-21T09:22:50Z

Alu:

File:ProMeTra DownloadPathway search.png

2012-03-21T09:22:41Z

Alu:

ProMeTraWiki/DownloadPathway

2012-03-21T09:22:29Z

Alu:

__NOTOC__
== Download existing Pathways from ProMeTra ==

* After logging in to ProMeTra you can use the ''Search Bar'' at the top of the interface to find all PathwayMaps and/or GenomeMaps that contain e.g. 'coryne' in their name, filename or description.
* Simply enter your query string in the Search field and press the Search button.

[[File:ProMeTra_DownloadPathway_search.png]]

* ProMeTra will search the internal object relational database containing the Pathway descriptions and present a list with matching pathways.

[[File:ProMeTra_DownloadPathway_result.png]]

* Click on one of the pathway name and the associated SVG image will be displayed in your browser window. Below the SVG image is a download link.

[[File:ProMeTra_DownloadPathway_download.png]]

* Store the image on your computer and edit it according to your needs using the Inkscape software.

File:ProMeTra PathwayMap editor.png

2012-03-21T09:20:37Z

Alu:

File:ProMeTra PathwayMap xml.png

2012-03-21T09:20:25Z

Alu:

File:ProMeTra PathwayMap xmleditor.png

2012-03-21T09:20:11Z

Alu:

File:ProMeTra PathwayMap glycine.png

2012-03-21T09:20:00Z

Alu:

ProMeTraWiki/PathwayMap

2012-03-21T09:19:50Z

Alu: /* Annotate SVG elements using Inkscape */

__NOTOC__
== ProMeTra PathwayMaps ==

A PathwayMap in ProMeTra is a SVG image designed using e.g. Inkscape which additionally contains
some labeled rectangles. The labeling defines which experimental data associated to
entities from functional genomics (transcripts, proteins, metabolites) can be represented
inside the image. Users can add other graphical elements such as lines, shapes, and text to SVG PathwayMaps, only the specially labeled elements will be modified by ProMeTra.

[[File:ProMeTra_PathwayMap_pathway.png]]

=== Annotate SVG elements using Inkscape ===

To add such a label to a graphical element in the SVG image, functionality of Inkscape can be used.

* Open a SVG Pathway image in Inkscape

[[File:Prometra Inkscape inkscape.png]]

* Select a rectangular image element (e.g. the Glycine rectangle as in the example)

[[File:ProMeTra_PathwayMap_glycine.png]]

* Select XML Editor from the Edit Menu ...

[[File:ProMeTra_PathwayMap_xmleditor.png]]

* Add the ''Metabolite'' attribute and set the value to e.g. C00037

[[File:ProMeTra_PathwayMap_xml.png]]

=== Annotate SVG elements using a text Editor ===

You may also edit the SVG file (XML Format) with any text editor and add the ''Protein'', ''Metabolite''
or ''Transcript'' identifiers to the rectangle elements manually. In the following example the ''Transcript'' element for the ''C.glutamicum'' gene identified by the locus_tag cg1337 is defined and another rectangle is connected to a ''Metabolite'' (KEGG Compound C00441).

[[File:ProMeTra_PathwayMap_editor.png]]

=== Data connection ===

ProMeTra will be able to identify the attributes ''Protein'', ''Metabolite''
or ''Transcript'' in your rectangular SVG elements and use the associated identifiers (e.g. C00037) to connect to
experimental datasets that users upload or obtain from MeltDB, ProSE or Emma2 via WebServices.

ProMeTraWiki

2012-03-21T09:19:19Z

Alu: /* FAQs and How Tos */

__NOTOC__
== ProMeTra - Multi-Omics Viewer ==

ProMeTra is a web based framework for the storage and visualization of
user defined metabolic pathway maps and their visualization with experimental data from
transcriptomics, genomics and proteomics.

Please also have a look at the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/prometra_info ProMeTra website] for general information.

== Important information for users of Firefox ==

* [[Firefox3|Read this if you experience trouble accessing the ProMeTra login page with Firefox]].

== ProMeTra login page ==

* [http://prometra.cebitec.uni-bielefeld.de prometra.cebitec.uni-bielefeld.de]

== ProMeTra User Manual ==

Download the ProMeTra user manual which details the main workflow of ProMeTra and explains how to create own pathway maps:

[[Media:ProMeTra-Manual.pdf|ProMeTra manual]]

== ProMeTra Concepts ==

* [[ProMeTraWiki/PrometraAccount|Using the public ProMeTra account]]
* [[ProMeTraWiki/CebitecAccount|Using your CeBiTec, Bielefeld University account]]
* [[ProMeTraWiki/GenomeMaps|What are the GenomeMaps available via ProMeTra?]]
* [[ProMeTraWiki/Animation|What exactly is the ''Animation'' feature of ProMeTra?]]
* [[ProMeTraWiki/Color|Which methods are employed to colorize the pathway maps?]]

== FAQs and How Tos ==

* [[ProMeTraWiki/Persistency|What happens to my uploaded experimental data?]]
* [[ProMeTraWiki/Inkscape|Which software can I use to draw my own pathway maps?]]
* [[ProMeTraWiki/PathwayMap|How do I create my own PathwayMap for ProMeTra?]]
* [[ProMeTraWiki/PathwayMap|What features do my SVG pathway images need to be used in ProMeTra?]]
* [[ProMeTraWiki/Inkscape|Installing the Inkscape SVG Editor software]]
* [[ProMeTraWiki/WebBrowsers|Which web browsers do support the SVG image format?]]
* [[ProMeTraWiki/DownloadPathway|How can I download existing pathway maps from ProMeTra?]]
* [[ProMeTraWiki/CreatePathway|How can I upload my own pathway maps?]]

== Data formats ==

* [[ProMeTraWiki/ExcelFormat|Which format should the experimental data in my Excel files have?]]
* [[ProMeTraWiki/CSVFormat|Which other data files can I upload?]]

== Contact ==

Please send an e-mail for account requests or questions concerning the use of ProMeTra to the [mailto:prometra@cebitec.uni-bielefeld.de ProMeTra mailinglist]

File:ProMeTra PathwayMap pathway.png

2012-03-21T09:17:08Z

Alu:

ProMeTraWiki/PathwayMap

2012-03-21T09:16:34Z

Alu:

__NOTOC__
== ProMeTra PathwayMaps ==

A PathwayMap in ProMeTra is a SVG image designed using e.g. Inkscape which additionally contains
some labeled rectangles. The labeling defines which experimental data associated to
entities from functional genomics (transcripts, proteins, metabolites) can be represented
inside the image. Users can add other graphical elements such as lines, shapes, and text to SVG PathwayMaps, only the specially labeled elements will be modified by ProMeTra.

[[File:ProMeTra_PathwayMap_pathway.png]]

=== Annotate SVG elements using Inkscape ===

To add such a label to a graphical element in the SVG image, functionality of Inkscape can be used.

* Open a SVG Pathway image in Inkscape

[[File:ProMeTra_PathwayMap_inkscape.png]]

* Select a rectangular image element (e.g. the Glycine rectangle as in the example)

[[File:ProMeTra_PathwayMap_glycine.png]]

* Select XML Editor from the Edit Menu ...

[[File:ProMeTra_PathwayMap_xmleditor.png]]

* Add the ''Metabolite'' attribute and set the value to e.g. C00037

[[File:ProMeTra_PathwayMap_xml.png]]

=== Annotate SVG elements using a text Editor ===

You may also edit the SVG file (XML Format) with any text editor and add the ''Protein'', ''Metabolite''
or ''Transcript'' identifiers to the rectangle elements manually. In the following example the ''Transcript'' element for the ''C.glutamicum'' gene identified by the locus_tag cg1337 is defined and another rectangle is connected to a ''Metabolite'' (KEGG Compound C00441).

[[File:ProMeTra_PathwayMap_editor.png]]

=== Data connection ===

ProMeTra will be able to identify the attributes ''Protein'', ''Metabolite''
or ''Transcript'' in your rectangular SVG elements and use the associated identifiers (e.g. C00037) to connect to
experimental datasets that users upload or obtain from MeltDB, ProSE or Emma2 via WebServices.

File:Prometra Inkscape inkscape.png

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ProMeTraWiki/Inkscape

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__NOTOC__
== Inkscape ==

Inkscape is a Vector Graphics Editor that is SVG compliant, open source, responsive and extensible.
The [http://www.inkscape.org project] homepage contains the links to the free [http://www.inkscape.org/download/?lang=en download] of the latest release and extensive tutorials. Inkscape will help you to design your own PathwayMaps for ProMeTra and
can also be used to review the generated results of PathwayMaps that you have colored with your experimental datasets using the ProMeTra web interface.

[[File:Prometra_Inkscape_inkscape.png]]

File:Prometra Color range.png

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File:Prometra Color colors.png

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File:Prometra Color legend.png

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Alu: uploaded a new version of "File:Prometra Color legend.png"

File:Prometra Color legend.png

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ProMeTraWiki/Color

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__NOTOC__
== Color Mappings in ProMeTra ==

* ProMeTra visualizes numerical values from ''Omics''-experiments by mapping them onto
several predeined color gradients (e.g. Red-to-Green, Yellow-to-Blue, etc). Elements representing transcripts, proteins, or metabolites in !Pathway- or GenomeMaps are
highlighted with the respective colors. The following ColorLegend shows an M-value
mapping that can for example be used for Transcriptomics datasets.

[[File:Prometra_Color_legend.png]]

* Various color gradients have been defined and are available via the web interface.

[[File:Prometra_Color_colors.png]]

* Users can select the numerical range of the color gradient mapping. Experimental values that
are outside the range will be mapped to the colors at the respective end of the gradient.
Alternatively, an automatic computation of maximal and minimal values can be employed ('auto'). The color
gradient range is then dynamically adapted to the submitted experimental data.

[[File:Prometra_Color_range.png]]

* The 'zero-centered' option computes the maximal absolute value found in the dataset and defines a symmetric range.
The value 0 is always at the center of the color gradient. If the minimal value of the experimental data is -8.9 and the maximal value is 5.6, 'zero-centered' will set the range from -8.9 to 8.9.

ProMeTraWiki

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__NOTOC__
== ProMeTra - Multi-Omics Viewer ==

ProMeTra is a web based framework for the storage and visualization of
user defined metabolic pathway maps and their visualization with experimental data from
transcriptomics, genomics and proteomics.

Please also have a look at the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/prometra_info ProMeTra website] for general information.

== Important information for users of Firefox ==

* [[Firefox3|Read this if you experience trouble accessing the ProMeTra login page with Firefox]].

== ProMeTra login page ==

* [http://prometra.cebitec.uni-bielefeld.de prometra.cebitec.uni-bielefeld.de]

== ProMeTra User Manual ==

Download the ProMeTra user manual which details the main workflow of ProMeTra and explains how to create own pathway maps:

[[Media:ProMeTra-Manual.pdf|ProMeTra manual]]

== ProMeTra Concepts ==

* [[ProMeTraWiki/PrometraAccount|Using the public ProMeTra account]]
* [[ProMeTraWiki/CebitecAccount|Using your CeBiTec, Bielefeld University account]]
* [[ProMeTraWiki/GenomeMaps|What are the GenomeMaps available via ProMeTra?]]
* [[ProMeTraWiki/Animation|What exactly is the ''Animation'' feature of ProMeTra?]]
* [[ProMeTraWiki/Color|Which methods are employed to colorize the pathway maps?]]

== FAQs and How Tos ==

* [[ProMeTraWiki/Persistency|What happens to my uploaded experimental data?]]
* [[ProMeTraWiki/Inkscape|Which software can I use to draw my own pathway maps?]]
* [[ProMeTraWiki/PathwayMap|How do I create my own PathwayMap] for ProMeTra?]]
* [[ProMeTraWiki/PathwayMap|What features do my SVG pathway images need to be used in ProMeTra?]]
* [[ProMeTraWiki/Inkscape|Installing the Inkscape SVG Editor software]]
* [[ProMeTraWiki/WebBrowsers|Which web browsers do support the SVG image format?]]
* [[ProMeTraWiki/DownloadPathway|How can I download existing pathway maps from ProMeTra?]]
* [[ProMeTraWiki/CreatePathway|How can I upload my own pathway maps?]]

== Data formats ==

* [[ProMeTraWiki/ExcelFormat|Which format should the experimental data in my Excel files have?]]
* [[ProMeTraWiki/CSVFormat|Which other data files can I upload?]]

== Contact ==

Please send an e-mail for account requests or questions concerning the use of ProMeTra to the [mailto:prometra@cebitec.uni-bielefeld.de ProMeTra mailinglist]

ProMeTraWiki/Animation

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__NOTOC__
== Animation features of ProMeTra ==

* ProMeTra can animate Pathway- and GenomeMaps using ColorAnimation defined in the SVG specification.
During the animation, the background color of an Enzyme or Metabolite element changes and the current
timepoint / factor is being highlighted in the legend. This is useful if large time series of ''Omics'' data need to be visualized.

* Please bear in mind that currently only the Opera Browser supports these animations features natively. The Adobe [http://www.adobe.com/svg/viewer/install/ SVG Plugin] provides animation features for other browsers as well.
* The following example SVG image was created with ProMeTra and contains the color animation of metabolite pool sizes in the Methionine pathway of ''C. glutamicum''. Click on the link to download the image and/or open it in your browser.

[[File:Prometra_animation.svg]]

* If your browser displays changing background colors for some of the metabolites in this SVG, you may also use the ''Animation'' feature of ProMeTra to visualize your data.

File:GenomeMaps genomemap.png

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