BRF-Software - User contributions [en]

Main Page

2011-10-26T06:21:30Z

Admin: imported contents from former frontpage

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= BRF Software Documentation =

[[Image:FrontPage$BRIDGE-2007_small.png]]

The following Wiki pages contain the documentation of the bioinformatics tools developed and provided by the team of the Bioinformatics Resource Facility ([http://www.cebitec.uni-bielefeld.de/groups/brf/ BRF]) of the Center for Biotechnology ([http://www.cebitec.uni-bielefeld.de/ CeBiTec]) at Bielefeld University.

* [[GenDBWiki]] (how to use the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/ GenDB] genome annotation system)
* [[SAMSWiki]] (how to use the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/sams_info/ SAMS] Sequence Analysis and Management System)
* [[EMMAWiki]] (how to use the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/ EMMA] microarray analysis tool)
* [[ArrayLIMSWiki]] (how to store microarray experimental data in the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/arraylims/ Laboratory Information Management System])
* [[ProDBWiki]] (how to use the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/prodb_info/ ProDB] proteomics analysis tool)
* [[MGE-PortalWiki]] (how to use the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/mge-portal/ MGE-Portal] bioinformatics portal)
* [[BACDIVERS-PortalWiki]] (how to use the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/bacd-portal/ BACDIVERS-Portal] bioinformatics portal)
* [[MeltDBWiki]] (how to use the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/MeltDB_info/ MeltDB] metabolomic framework)
* [[OntologyDBWiki]] (how to use the OntologyDB framework)
* [[IGetDBWiki]] (how to use the IGetDB data warehouse)

/!\ '''See important information for [[Firefox3|Firefox 3 users]]''' /!\

----

All projects are managed via the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/gpms/ General Project Management System]. The following link contains the GPMS documentation:

* [[GPMSWiki]]

----

The current installation and update mechanism is called General Installation System (GIS). The following link contains the GIS documentation:

* [[InstallationSystemWiki]]

EMMAWiki/AdministratorDocumentation

2011-10-26T06:19:13Z

Admin: 6 revisions

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= Documentation for Administrators =

* [[/SoftwareRequirements|Software Requirements]]
* [[/HardwareRequirements|Hardware Requirements]]
* [[/InstallationInstructions|Installation Instructions]]
* [[/AccountManagement|Account Management]]
* [[/ProjectSetup|Project Setup]]

ProDBWiki/DeveloperDocumentation/ImportMultiScans

2011-10-26T06:19:13Z

Admin: 8 revisions

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= Import Multi Scans =

== Overview ==

If you have a gel picture with many protein spots from a tissue, and you want to know what kind of proteins that are, you take a sample from the spots and analyse them with mass spectrometry. As a result you get a file with the peptide masses. Now you can import the files and connect them with the corresponding gel spots. This is a lot of work, especially if you have a large number of spots/files. Therefore you can use the Multi Files Importer. Here you can import all files from spots from one gel at once. You save all the files and the config-file from the spot selector in a compressed file. The compressed file has to be a .tgz-, .tar.gz-, .tar- or .zip-file. Also you have to observe that the compressed file has to be from a special form. This tool uploads all files at once and connects them automatically with the right gel spot. At the moment it only works for Maldi-Files.

== How to use ==

At first you have to import a gel-picture and select the spots you want to analyse. In the config-file you find the the directories where the ms-files for one spot have to be saved (normally the mass spectrometer does it automatically). Be aware that the config file has to be in a specific format, described below. Now you need to save the config-file as '''geometry.config'''. After you selected the spots and send them into the mass spectrometer, you have to create a workstep for ms import and select all samples(spots) that were used by the spot selector. Then you will see all your selected samples, normally with the name SpotPicking(X). Now you can click on "Import Scan" and you will be forwarded to the Mass Spectra Data site. Here you find two sections: "Mass Spectra Browser" and "Mass Spectra Importer". In the second field (Mass Spectra Importer) you choose "Maldi" for the mass spectra type (it doesn't work correctly for Esi-files at the moment) and select "many" for the number of files. Now you can browse and insert your file into the file-window. After you click on "Import", the system starts importing the file. The file has to be a .tgz-, .tar.gz-, .tar- or .zip-file otherwise there will be an error. For the format of the file see the section below. The system automatically connects every maldi file with the corresponding sample. After you imported the file, you can select a sample from the field (Mass Spectra Browser) above and you will see the mass spectrum for this sample.

If you want to make a search with mascot or emowse against a database, you have to return to the Experiment Editor by clicking on the link on the left site of the web-page. There you click on Experiment Selection and choose the link Mass Spectra Data. From there you select MS for scan type and choose one or more scans for the search. To get to the search form you have to click on the "Peptide Mass Fingerprint" link.

== Formats ==

=== Format of the Config File ===

The config file has to be in a special format. Only then the connection between the files and the samples can be made correctly. First of all, it is important that you save the config file, after you selected the spots on the gel, with the name '''geometry.config'''. Here is an example for a config file with 14 spots in it:

<pre><nowiki>Comment_1 Pos_on_Scout AutoX_Method Spectrum_Directory Spectrum_Filename Probe_Geometry Chip_on_Scout
************ ************ ************ ************ ************ ************ ************
standard A:1 calibrate_sbd Standard_A1 1
probe A:1 measure_sbd I_A_01 0
probe B:1 measure_sbd I_B_01 0
standard C:1 calibrate_sbd Standard_C1 1
probe C:1 measure_sbd I_C_01 0
probe D:1 measure_sbd I_D_01 0
standard E:1 calibrate_sbd Standard_E1 1
probe E:1 measure_sbd I_E_01 0
probe F:1 measure_sbd I_F_01 0
standard G:1 calibrate_sbd Standard_G1 1
probe G:1 measure_sbd I_G_01 0
probe H:1 measure_sbd I_H_01 0
probe A:2 measure_sbd I_A_02 0
probe B:2 measure_sbd I_B_02 0
probe C:2 measure_sbd I_C_02 0
probe D:2 measure_sbd I_D_02 0
probe E:2 measure_sbd I_E_02 0
probe F:2 measure_sbd I_F_02 0
</nowiki></pre>

This is a standart config file. It is automatically generated by ProDB. It is important that there is only the '''name''' of the Spectrum_Directory in the config file (forth tab) and not the whole path. Furthermore each row containing a spot has to start with the word '''probe''' and every row containing a calibration has to start with something else (default is '''standart'''). Normally, if you take the autogenerated file you don't have to change anything. Try to change as little as possible in the file.

=== Format of the compressed File ===

First create a directory (take any name you want) and copy all directorys (with the scan files in it) in the new directory. The geometry.config file has to be copied there, too. For example you create a directory with the name '''massensp''' and you have the directories from above with the maldi files in it. Now you copy the scan directories (I_A_01, I_B_01, ... , I_E_02, I_F_02) and the geometry.config in the directory massensp.

<pre><nowiki>
massensp: I_A_01
I_B_01
I_C_01
I_D_01
I_E_01
I_F_01
I_G_01
I_H_01
I_A_02
I_B_02
I_C_02
I_D_02
I_E_02
I_F_02
geometry.config
</nowiki></pre>

Now you compress the directory massensp (with tar, zip, ...) so that you get massensp.tgz, massensp.tar.gz, massensp.tar or massensp.zip. If you are working with linux or unix you can use one of the following commands (you have to be in the same directory as massensp):

<pre><nowiki>
.tgz and .tar.gz: tar -cvzf name.tgz directory -> tar -cvzf massensp.tgz massensp/ or tar -cvzf massensp.tar.gz massensp/
.tar: tar -cvf name.tar directory -> tar -cvf massensp.tar massensp/
.zip: zip -r name.zip directory -> zip -r massensp.zip massensp/
</nowiki></pre>

== What did I do ==

For the this function I wrote a new modul: '''ImportMultiFiles'''. You can find it in prodb/share/www/cgi-bin/. This modul has two functions import_multifiles_maldi and import_multifiles_esi. But the second function doesn't work correctly at the moment.

The function import_multifiles_maldi is called by msscan.cgi(same directory). I modified the function parseMS (in msscan.cgi), so that it can differ between importing one and many files.

<pre><nowiki>
sub parseMS {
my ($q, $tmpl, $session, $master, $probes) = @_;
my $scans;

#parses one scan
if ($q->param('number')eq 'one') {
........normal import.........
}

#parses many scans (from a .tgz, .tar.gz,.tar and .zip File)
elsif ($q->param('number')eq 'many') {
.......imports many files.......
......calls the import function from ImportMultiFiles ......
my $result=import_multifiles_maldi($master, $directory, $probes, $name);
}
</nowiki></pre>

At first the function import_multifiles_maldi decompresses the uploaded file and saves it in /vol/tmp. Then it takes the geometry.config file and reads it. It saves the directories in a hash (%positionScan) with the number of the corresponding sample as key. Now it takes one scan after the other, loads the file up and parses it with the function parseMaldiFileXML or parseMaldiFile, depending on the file format of the scan, from MSTools.pm. It than gets all information for the scan from the parser and creates a new Scanobject and for every peak a new Peakobject. At last the import_multifiles_maldi removes the tempory file.

Author: Nicole de la Chaux

MarineGenomicsEurope

2011-10-26T06:19:12Z

Admin: 4 revisions

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This page ist just MGE intern....

EMMAWiki/HowTos

2011-10-26T06:19:12Z

Admin: 12 revisions

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== [[HowTos]] ==
=== Synopsis ===
The following chapter covers various use cases of the
EMMA software which you might encounter during dayly work. Before reading one these you should at least have a look at:

* [[EMMAWiki/TermsAndConcepts| TermsAndConcepts]]

=== Contents ===

* [[/LoggingIn|Logging In]]
* [[/CreatingAnExperiment|Creating An Experiment]]
* [[EMMAWiki/WebDocumentation/GeneralUsage/ImportDatafromArrayLIMS|Importing Data]]
* [[/AnalyzingData|Analyzing Data]]
* [[EMMAWiki/WebDocumentation/HowTos/DatasetBrowserHowTo| Using the Dataset Browser]]
* [[/UploadingAnArraylayout|Uploading An Arraylayout]]
* [[/EmmaBridgeHowTo|Emma Bridge How To]]
* [[/MAGEExport|MAGE-ML export]]

EMMAWiki/WebDocumentation/GeneralUsage/GettingStarted

2011-10-26T06:19:12Z

Admin: 1 revision

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= [[GettingStarted]] =

Please have a look at the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/docu.html EMMA PDF documentation].

InstallationSystemWiki

2011-10-26T06:19:12Z

Admin: 6 revisions

__NOTOC__
Software developed at the [[CeBiTec]] use a special installation system for installing, configuring and maintaining components. It can be used for both installing a production version of e.g. GenDB and also for working with CVS based development versions. /InstallationSystemIntro gives a short overview about the installation system itself and the way it installs components. See /InstallationSystemLayout for information about files inside the installation system and /InstallationSystemHacking for a short tutorial on creating a component.

The following pages gives an introduction how to use the installation system for installing components:
* /InstallationSystemProduction
* /InstallationSystemCVS

For installing application downloaded as a tarball from the [[CeBiTec]] web site, you usually do not have to work with the installation system at all. Refer to the documentation on the web site for installation instructions.

Delete added organism

2011-10-26T06:19:11Z

Admin: 5 revisions

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'''Only chiefs of a project are able to use this function'''

To delete an added organism just select the name of it and press '''remove organism from organism list'''. Because of security reasons you have to select the organism twice.
'''Please notice, that deleted organisms are deleted from the organism lists for all users in all projects! So use this function carefully.'''

EMMAWiki/TutorialIntroduction

2011-10-26T06:19:11Z

Admin: 6 revisions

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= Tutorial Introduction =

== Synopsis ==

This tutorial is intended for a ''learning by doing'' audience. While proceeding step by step you will do the following:

* Log in to the EMMA-Demo project
* Create a new experiment
* Create your experimental design
* Import data from the ArrayLIMS
* Normalize your data
* Plot your data
* Run a statistical test for up- and down-regulated genes
* View the results

Prerequisites: The turial requires

* a completely installed EMMA and ArrayLIMS
* a ready-to-use demo project (eg. 'EMMA-Demo') where you can log in
* an ArrayLIMS project containing demo data to import
* some basic skills on using your web-browser

Reading through [[EMMAWiki/TermsAndConcepts|Terms and Concepts]] will help but is not required to complete the tutorial.

ColorizeMSWiki/Downloads

2011-10-26T06:19:11Z

Admin: 3 revisions

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= ColorizeMS Downloads =

Please select the appropriate platform

== Microsoft Windows (64 Bit) ==

[[Media:ColorizeMSWiki$$Downloads$ColorizeMS_win64.zip]]

== Microsoft Windows (32 Bit) ==

[[Media:ColorizeMSWiki$$Downloads$ColorizeMS_win32.zip]]

== Mac OS X (PPC) ==

[[Media:ColorizeMSWiki$$Downloads$ColorizeMS_macppc.zip]]

== Mac OS X (Intel) ==

[[Media:ColorizeMSWiki$$Downloads$ColorizeMS_macintelb.zip]]

== Jar file (platform independent) ==

[[Media:ColorizeMSWiki$$Downloads$ColorizeMS.jar]]

Microarray hybridization

2011-10-26T06:19:11Z

Admin: 12 revisions

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This form is for submitting data of a microarray hybridization. Fill out ''' every ''' field marked with a red star ('''required fields'''). If you just want to enter the data of '''one''' target do '''not''' fill '''any''' of the fields of '''target2'''. An error message will appear on top of the page either if you have submitted data in the wrong format or did not fill all required fields. The fields that were filled with the wrong data are highlighted in red.

== Required fields ==

The following fields are required:

* '''Date''': date of the microarray hybridization
* '''Operator''': the operator who conducts the microarray hybridization (already filled out, only change this if the person who performed the preparation is not the same who is currently logged in!)
* '''Hybridization labeled-target ID''': the labeled-target that was used for the hybridization (default is "None". Make sure you selected the correct labeled-target ID)
* '''Volume of labeled target used''': the volume of the targets that were used for the hybridization
* '''Slide-ID''': the unique identification of the slide that is hybridized (default is "None". Make sure you selected the correct slide-ID that was allocated to you)
* '''Repeat slide-ID''': to make sure that you use the correct slide-ID. Please only use the slide-IDs that were really assigned to you (default is "None". Make sure you selected the correct slide-ID)
* '''Hybridization and wash protocol''': select an existing protocol (default is "None") or upload a new one in .pdf format
* '''Protocol description''': only required if a new protocol is uploaded
* '''Abstract of the protocol''': only required if a new protocol is uploaded. The abstract is needed for the MAGE-ML export in EMMA. Please fill in a short abstract of the protocol. The abstract should embody all important information of the protocol.

== Optional fields ==

You can also add some additional data for your labeling process

* '''Hybridization solution''': the solution used for hybridization
* '''Hybridization remarks''': some remarks of your hybridization process

GenDBWiki/WebDocumentation/DialogWindows/SequenceViewer

2011-10-26T06:19:10Z

Admin: 21 revisions

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= Sequence Viewer =

The Sequence Viewer (available since GenDB 2.4) allows a zoomed view into the genomic sequence along with its six translated frames.
You can easily '''''select''''' some sequence, afterwards copy it with '''''Control+C''''', and finally paste it with '''''Control+V''''' into an arbitrary place.

Pressing the Show Sequence button in the main window of GenDB, will display the [[SequenceViewer]]. Green rectangles represent the CDS. The CDS that is activated in GenDB has a stronger border and a brighter green color (directly reachable with the '''''Center''''' button). CDS that are marked as ignored are dashed and grey. Moving the mouse over a CDS, displays its details into the '''''Region-Information''''' table. The [[SequenceViewer]] allows you to scroll within a 6000nt-window. In order to get the next or previous 6000nt of the contig press the '''''Left''''' or '''''Right''''' button. Thus, its possible to walk easily through the whole contig.

Selecting any sequence will display the selected sequence at the '''''Sequence-Editor'''''. If you select some sequence on the back strands, a '''''Reverse''''' button allows you to reverse the selected sequence, in order to obtain the sequence in the biological right direction. Afterwards you can select this sequence, copy and paste it into e.g. a file.

=== How to select a sequence ===
The behaviour of the [[SequenceViewer]] is similar to common text-editors (e.g. notepad). You have two possibilities to select an arbitrary sequence:
* Press the left mouse button and move it to the right or to the left (recommeneded for short sequences)
* ''Left-Click'' on the start character, move the scroll bar, ''Shift+Left-Click'' on the end character (recommeneded for long sequences)

In order to obtain quickly the whole sequence of a CDS:
* Move the mouse to the left border of a CDS, ''Left-Click'' and pull the mouse slightly under

[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$SequenceViewer$SequenceViewer.png]]

Edit a microarray hybridization

2011-10-26T06:18:55Z

Admin: 5 revisions

__NOTOC__
This page is for editing or deleting an uploaded Hybridization description. If you are no chief or admin of the chosen project you are only allowed to delete or edit your '''own''' Hybridization descriptions.

[[Delete a particular Hybridization]]

[[Edit a particular Hybridization]]

ProDBWiki/DeveloperDocumentation/Cluster

2011-10-26T06:18:54Z

Admin: 2 revisions

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= [[SubmitEmowse]].pm =

== Idea ==

Most of the time in proteomics much data is analysed at once and the results are needed fast. So when hundreds of samples are examined one after another, one have to wait a long time for results. But if the work is parallelised, one would get the results much faster. Since '''''emowse''''' works for every sample and every set of parameters independently, all searches can be done at the same time. For this reason, the searches are collected and submit to a cluster. This is realised in the module '''SubmitEmowse.pm''' in prodb/share/www/cgi-bin.

== Implementation ==

The module has only one function of interest: '''submitThemAll'''. The function expects a reference on an array with all '''''emowse'''''calls. These calls are seperated in groups of 200 calls. If more than 200 jobs are calculated at the same time, there is no advantage on time any more. So only an arrayjob of at most 200 calls is submitted. To create an array job and submit it to the cluster, I use the existing module ''Scheduler::Codine.pm'' in bioinfo/common/share/perl. In order to submit the jobs not as single jobs but alltogether, the scheduler has to be freezed. Then every job can be submitted and after all jobs have been collected, the arrayjob can be run.

<pre><nowiki>
Scheduler::Codine->freeze();
foreach emowsecall {
my $job = Scheduler::Codine->new();
#extra option for the scheduler: do the job immediately
$job->options("-now y");
$job->command(emowsecall);
$job->submit();
}
Scheduler::Codine->thaw();
</nowiki></pre>

By parallelising the '''''emowse'''''searches, your work is done in at least half the time.

Author: Anna-Lena Kranz

Delete protocol(s)

2011-10-26T06:18:54Z

Admin: 6 revisions

__NOTOC__
'''Only chiefs of a project are able to use this function.'''

On this page you see all different available protocols/pdfs. Select the click-boxes of the protocols you want to delete and press the '''delete''' button in the upper right corner of the page.

'''The deleted protocols will be totally removed from the database.The protocol/pdf is no longer shown as an available protocol/pdf in the drop-down menues of the Arraylims steps.'''.

Edit RNA description

2011-10-26T06:18:54Z

Admin: 4 revisions

__NOTOC__
This page is for editing or deleting an uploaded RNA description. If you are no chief or admin of the chosen project you are only allowed to delete or edit your own RNA descriptions.

[[Delete a particular target]]

[[Edit a particular target]]

TheMeanPthreadHack

2011-10-26T06:18:54Z

Admin: 1 revision

__NOTOC__

== A little workaround for packages using the PThread library ==

=== Example ===
When trying to compile some bioconductor packages eg. the affyio packages in Biobase you may experinece compilation errors
like ''undefined symbol PTHREAD_STACK_MIN'' or ''undefined symbol PTHREAD_DESTRUCTOR_ITERATIONS''.
These are symbols used in included pthread.h but they are defined in limits.h. with the given compilation options however these macros are
not defined, because of a conditional define checking for a given POSIX_C_SOURCE version. A workaround is to place a mock pthread.h include file
in the directory <R-installdirectory>/lib/R/include, which looks like:

<pre><nowiki>
#include "/usr/include/pthread.h"
#include <limits.h>
#include <unistd.h>
#warning Using selfdefined PTHREAD_ macros in my own pthread.h in R_HOME/lib/R/include

extern long _sysconf(int); /* System Private interface to sysconf() */
#ifndef _SC_THREAD_STACK_MIN
#error _SC_THREAD_STACK_MIN is not defined
#endif

#define PTHREAD_STACK_MIN ((size_t)_sysconf(_SC_THREAD_STACK_MIN))
/* Added for UNIX98 conformance */
#define PTHREAD_DESTRUCTOR_ITERATIONS _POSIX_THREAD_DESTRUCTOR_ITERATIONS
#define PTHREAD_KEYS_MAX _POSIX_THREAD_KEYS_MAX
#define PTHREAD_THREADS_MAX _POSIX_THREAD_THREADS_MAX
</nowiki></pre>

This is a bad workaround, because we include the absolute path and define the missing symbols ourselves. If you have abetter idea feel free to fix
either the affyio package or the Solaris pthread.h, limits.h

EMMAWiki/TermsAndConcepts/ForUsers/Experimental Factors

2011-10-26T06:18:54Z

Admin: 3 revisions

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= Terms and Concepts: Experimental Factors and Values =

''Experimental Factors'' and ''Factor Values'' are the essential concepts for grouping arrays within an Experiment. An Experimental Factor is a condition (like temperature, time, light intensity, concentration of a substance) of which you want to measure the effect on the organism under study. During the Experiment the ''Factor Value'' of the Factor is controlled by the experimenter (e.g. for the ''Factor'' temperature actual ''Factor Values'' could be 10 degr.C., 20 degr.C., ...). An experiment could also involve many factors with different values. Example: Comparison of the effect of different stresses (Factor: Stress, Values: Stress conditions) during growth over time (Factor: Time, Values: Timepoints of measurements).

Arrays sharing the same unique combination of values can be seen as replicates. The choice of Factors, Values and the assignment of Arrays to these constitue the experimental design, and will be used to group replicates for analysis.

----
The following examples illustrate some possible experimental designs:

[[Image:EMMAWiki$$TermsAndConcepts$$ForUsers$$Experimental_Factors$FactorValuesStress.png]]

----

[[Image:EMMAWiki$$TermsAndConcepts$$ForUsers$$Experimental_Factors$FactorValuesTime.png]]

EMMAWiki/WebDocumentation/OnlineHelp/ArrayViewer

2011-10-26T06:18:54Z

Admin: 3 revisions

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== Array Viewer ==

SoftwareRequirements

2011-10-26T06:18:54Z

Admin: 1 revision

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= Software Requirements =

== Synopsis ==
This page is intended for system administrators who intend to install the EMMA-server on a vanilla system.
When you install e.g. on a LINUX box you will find all or most of the required software in the
distribution. Then you can use the package-management of that system (commands like: rpm, emerge, package_add,...) to
install the software. Please consult the documentation provided by your operating system vendor on how to install software. Perl modules can be installed using the [http://www.cpan.org CPAN shell].

== Requirements ==

We list only the software and the minimum required version which is needed to run the server here.
Where special setup options are required for a software it is listed.

'''Operating systems'''

As a Perl application emma should in principle be platform independent.
It has been tested with these operating systems or distributions:

* Solaris 9
* SuSE-Linux >= 9
* [http://www.gentoo.org Gentoo-Linux]
* [http://www.freebsd.org FreeBSD > 5.3]

'''Required libraries'''
{| border="1" cellpadding="2" cellspacing="0"
| ''Library''
| ''Version''
| ''Download URL''
| ''License''
| ''Source build''
| ''Binary packages''
| ''Remarks''
|-
| HDF5
| 1.6.x
| http://hdf.ncsa.uiuc.edu/HDF5/release/obtain5.html
| [ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/unpacked/COPYING University of Illinois/NCSA Open Source License]
| {configure, make}
| (./)
| Only C-API required
|}

'''Programming languages'''
{| border="1" cellpadding="2" cellspacing="0"
| ''Application''
| ''Version''
| ''Download URL''
| ''License''
| ''Source build''
| ''Binary packages''
| ''Remarks''
|-
| R
| 2.1.x
| http://cran.r-project.org/mirrors.html
| [http://www.r-project.org/COPYING GPL]
| {configure, make}
| (./)
| build with --enable-R-shared (most packages have it)
|-
| Perl
| 5.8.x
| http://www.cpan.org/
| [http://dev.perl.org/licenses/artistic.html Artistic License] or [http://dev.perl.org/licenses/gpl1.html GPL]
| {configure, make}
| (./)
|
|}

'''Perl modules'''
{| border="1" cellpadding="2" cellspacing="0"
| ''Library''
| ''Version''
| ''Download URL''
| ''License''
| ''Installation''
| ''Binary packages''
| ''Remarks''
|}

'''R-packages'''
{| border="1" cellpadding="2" cellspacing="0"
| ''Package''
| ''Version''
| ''Download''
| ''Remarks''
|}

'''Language interfaces'''
{| border="1" cellpadding="2" cellspacing="0"
| ''Package''
| ''Version''
| ''Download''
| ''Remarks''
|}

'''Web-server software'''

'''Database software'''

EMMAWiki/TermsAndConcepts/ForUsers

2011-10-26T06:18:53Z

Admin: 13 revisions

__NOTOC__
= Terms and Concepts for Users =

== Synopsis ==

In this chapter basic concepts for the work with EMMA will be explained. Every user wanting to start out using EMMA should at least read this page.
After reading this part you will know:

* What is an ''Experiment''
* What are ''Datasets'' and ''Arrays''
* What are ''Experimental Factors''
* How are these related to each other
* What is an ''Analysis Pipeline''
* What is ''Access Control'' good for

Before reading this, you should at least

* have a basic understanding of microarray technology and the biology behind it or just read [http://www.cebitec.uni-bielefeld.de/groups/brf/software/emma_info/Microarray_introduction.pdf Introduction to Microarrays]
* have basic skills using your web-browser and dealing with web-based applications

== Contents ==

* [[/Experiments]]
* [[/Arrays]]
* [[/Datasets]]
* [[/Experimental Factors]]
* [[/Analysis Pipeline]]
* [[/Access Control]]

GenDBWiki/DeveloperDocumentation

2011-10-26T06:18:52Z

Admin: 13 revisions

__NOTOC__
= Information for Software Developers =

Currently, the developers' version of GenDB which is maintained via the Concurrent Versions System ([https://www.cvshome.org/ CVS]), comprises more than 200 modules and more than 500,000 lines of Perl source code, not including more than 20 common modules that have been implemented for a number of general purpose tasks (e.g. for translating or reversing a DNA sequence. If you are interested in writing your own programs using the GenDB system you can find some useful information in the sections listed below. Of course, you should also read the GenDB API documentation.

* [[/CVSAccess]]
* /UseTheSource
* /DocumentationGuidelines
* /SystemDesign
* [[/GenDBDemoScript]]
* [[/GenDBProgrammingTutorial]]
* /ContributedScripts
* /ToolIntegration
* /ClassDiagram
* /PersonalWebServer

Delete a particular labeled target

2011-10-26T06:18:52Z

Admin: 4 revisions

__NOTOC__
On this page you have to choose a labeled_target ID you want to delete. Because of security reasons you have to select the labeled_target ID twice. The chosen labeled_target ID will be totally removed from the database.

Note: Only labeled targets that have not been hybridized are listed. To delete labeled targets that already have been hybridized you first have to delete the hybridization associated with the labeled targets.

'''Make sure you delete the right labeled_target!!'''

EMMAWiki/TaskList

2011-10-26T06:18:52Z

Admin: 1 revision

__NOTOC__
Describe EMMAWiki/TaskList here.

GPMSWiki/WebListOfMembers

2011-10-26T06:18:51Z

Admin: 5 revisions

__NOTOC__

= GPMSWiki Documentation - Web Interface =

== List of Project Members ==

The '''Show Project Members''' menu lists all users (and members - see "[[GPMSWiki/WebManageMembers]] for details) of the selected project. Each entry of this list consists of the user's login and its full name and corresponding role in brackets.

file:///vol/bioinfo/share/doku/gpms-wiki/list_memb.png

A more detailed information about a specific user can be obtained by clicking on its corresponding entry in the list. This information provides the user's full name, login and email address, as well as a flag determining whether the user is an internal or external user. Finally, the assigned role is also displayed (see [[GPMSWiki/RolesAndRights]] for details).

file:///vol/bioinfo/share/doku/gpms-wiki/list_memb2.png

----

Go back to the [[GPMSWiki]] overview page or to the [[GPMSWiki/WebDocumentation]].

Add new organism

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Admin: 4 revisions

__NOTOC__
'''Only Chiefs of a project are able to use this function'''

If you want to add a new organism to the global organism list just insert the name of the organism into the text field and press the '''add organism to organism list''' button.

GPMSWiki/DeveloperDocumentation/MigrationHelp/SessionManagementChanges

2011-10-26T06:18:51Z

Admin: 13 revisions

__NOTOC__
= Changes in the Session Management =

The new Sessionmanagement module is completely new and build from scratch. It supports hierarchical sessions,
and also anonymous sessions.
Complete redesign implies vast changes throughout the API. Most functions do no longer exist or have changes.
So this thing is still a real pain in the ass.

== Classes ==

You can have multiple sessions of different classes. An application specific subclass of Session::GPMS is mandatory. It has to be placed in the application subdirectory share/perl/Session/GPMS.

Here is a simple example:

<pre><nowiki>

package Session::GPMS::EMMAII;

=head1 NAME

Session::GPMS::EMMA2

=head1 DESCRIPTION

Sample implementation of a Session::GPMS::Application class, using GPMS::Application_Frame::Sample

=cut

use strict;
use warnings;
use GPMS::Application_Frame::EMMAII;

use base qw(Session::GPMS::Application);

1;

### Begin Class Methods ###

sub AppFrameClass {
# we use GPMS::Application_Frame::EMMAII
return "GPMS::Application_Frame::EMMAII";
}

sub NeedSingleton {
# we cannot have multiple instances of an EMMA apllications at the moment
# this could change in the future....
return 1;
}

### End Class Methods ###

__END__

</nowiki></pre>

== Initialization of Sessions ==

With the new session management there are normally al least two session:
* Session::Master -- the root session from which others can be derived
* Session::GPMS::<[[YourApp]]> -- an application-specific session, sublclass of Session::GPMS as given above

The session management supports multiple sessions of the same type, if your application does not: use singleton session. currently most of our apps
only support a single instance.

To retrieve valid sessions for your application the following steps have to be performed:

# No Session at all -> check if browser accepts cookies
# Check if you can resume Session::Master, if not: new Session::Master. The master session already sets the cookie.
# Check if you are having an authenticated session, that is have already given login/passw
# If not: get credentials and
# authenticate, getting a Session::GPMS::<[[YourApp]]>
# Set the project for this session

once you have and authenticated Session::GPMS::<[[YourApp]]> the session can be resumed using <code><nowiki>Session::GPMS::<[[YourApp]]>->loadSingleton($masterSession);</nowiki></code> if it is a singleton session.

Here is a lengthy stub for a login script (taken from GenDB login script). The code fragment is encapsulated in a function, so ''return'' is used several times to exit the function.

<pre><nowiki>

# resume master session and print HTTP header
my $master_session;
eval {
$master_session = Session::Master->new();
print $master_session->header();
};
if (ref ($@) && $@->isa("Session::NoActiveSessionException")) {
# we do not have an active session
# check whether this is the cookie-test invocation
if ($q->param('cookie_test')) {

# show error about not accepting cookies ....

return;
}
else {
# first invocation, let's check whether the user accepts cookies
$master_session = Session::Master->new(1);
my $url = $q->self_url()."?cookie_test=1";
print $master_session->header();
print $q->start_html(-head=>$q->meta({-http_equiv=>'refresh',
-content => "2;$url"}));

print "Checking for cookies, you will be redirected to ".$q->a({-href=>$url},"this page.");
print $q->end_html();
return;
}
}
elsif (ref($@)) {
# some other error, show some error message to the user
return;
}

unless ($master_session->isAuthenticated()) {
unless ($q->param('login')) {

# show the login form

return;
}
else {
# try to authenticate the user and show the
# project selection list
eval {
# this only creates a GPMS sub session, not a GenDB sub session
# otherwise you would end up with a dangling GenDB sub session if the
# user closes the window after authetication
$master_session->addGPMSSubSession($q->param('login'), $q->param('pass'));
};
if ($@) {

# failed to authenticate, show an error message to the use

return;
}
}
}

# try to load an exiting GenDB session. This will return undef if no
# GenDB sub session exists yet
my $session = Session::GENDB->loadSingleton($master_session);

if ($q->param('project')) {
if (ref($session)) {
# we have a request to set a project and an active GenDB session
# there may be another GenDB window open, so we cannot change to
# a different project
# Session::GPMS::Application stored the selected project in the
# session parameter 'project_name'
if ($session->param('project_name')) {
if ($session->param('project_name') ne $q->param('project')) {

# print some error message about the concurrent project

return;
}
}
}
else {
# no session yet, create a new one
$session = Session::GENDB->create($master_session);
}

# set the requested project
my $project = $master_session->getGPMSSubSession()->
getApplicationFrame()->
gpms_master()->
Project->init_name($q->param('project'));
$session->setProject($project);
}

if (ref($session) && $session->param('project_name')) {

# session is initialized and project is set, show the main window
# of your application
}
else {

# no project selected yet, display project selection

}

</nowiki></pre>

== API ==

The API has been rewritten to be consistent and easy to use.

=== Session parameter ===

Session parameters are handled by a number of functions:

* '''param(name, [value])''' gets or sets a session parameter
* '''hasParam(name)''' returns true if a session parameter with the given name exists
* '''deleteParam(name)''' removed the session parameter
* '''getParams()''' returns a list of all session parameter names

Certain functions of the old API are not supported anymore; they can be easily substituted by short chunks of code. Permanent session parameters are also not implemented in the new session management due to its limited use and added maintance overhead.

=== Other discontinued methods ===

These methods were specific for GPMS based sessions in the former session management; they counterparts (if existing) are implemented for Session::GPMS::Application sub classes only.

* '''query''' use CGI->new() to get a CGI object. The CGI module stores an internal copy of an initialized object during page processing, so calling new several times has only very little to no overhead
* '''master''' used to return the /!\ application frame /!\ in the previous session management and was removed for the obvious reason. If you are using a sub class of Session::GPMS::Application, use ''getApplicationFrame()'' to get the application frame of the session and use the ''application_master()'' and ''gpms_master()'' methods to get the master objects.
* '''login_name''','''password''' etc. Also use the application frame to get these values. Keep in mind that the new sessionmanagement uses role accounts. You have to use the ''real_login()'' method of the application frame to get the name of the user. Passwords are only stored as hashes. Clear text passwords '''ARE NOT AVAILABLE ANYMORE'''.

SAMSWiki/WebDocumentation/HowTo/GeNeral

2011-10-26T06:18:50Z

Admin: 1 revision

__NOTOC__
* 1) Sequence data

The different sequence data sets for the current project are listed as ESTs, TCs or singlets. Choose one data set to browse the computational results.

The table lists the best result (e.g., observation) of each tool that has been computed. By clicking on the name of a sequence (e.g., region), you will get a list of all observations computed for this region with this tool.

In case you have chosen either EST or singlet data set, you will additionally get the sequence itself, a visualization of the quality and vector clipped regions and eventually further information on the assembly. By choosing TCs, the additional information consists of the consensus sequence, the list of ESTs used in this TC, as well as a graphical visualization of the assembly. By directly clicking on a specific results description, the results of this particular tool for all regions will be listed.

* [[/ESTs]]
* [[/TCs]]
* [[/Singlets]]
* 2) Search

This option allows you to search by specifying parameters such as:

* Name (exact or regular expression)
* Gene name (exact or regular expression)
* Gene product -CDS only- (exact or regular expression)
* Observation description (contains or regular expression)
* Annotation description (contains or regular expression)
* Annotation comment (contains or regular expression)

IGetDBWiki

2011-10-26T06:18:50Z

Admin: 6 revisions

__NOTOC__
= IGetDB Overview Page =

== IGetDB - Introduction ==

IGetDB is a search facility for expression data. It enables the user to quickly access experiments and their results by formulating queries such as "Give me all temperature-related stress experiments containing gene XY" or "Give me a list of all up-regulated genes in experiments on Xanthomonas campestris". IGetDB combines data from EMMA, GenDB and ProDB. The data is imported from each of these databases and processed for searchability.

The software is currently in development and has no documentation besides this documentation. Other documentation will added when IGetDB is going into production mode.

== Documentation ==
* Developer Documentation
** [[/Specification| Specification]]
** [[/GettingStarted| Getting Started]]
*** [[IGetDBWiki/GettingStarted/VersionControl| Version Control]]
*** [[IGetDBWiki/GettingStarted/EmmaPlugin| Setting up the IGetDB-exporter for EMMA]]
*** [[IGetDBWiki/GettingStarted/WebServer| Web-Server]]
*** [[IGetDBWiki/GettingStarted/Documentation| Documentation]]
*** [[IGetDBWiki/GettingStarted/DirectoryStructure| Directory Structure]]
* [[/ToDoHistory| To Do History]]
* User Documentation
** [[/EmmaExport| EMMA Export to IGetDB]]
* [[/RoadMap| Roadmap]]

== Contact ==

Please send an e-mail for account requests or questions concerning the use of "Software" to:
[[MailTo(krunte AT cebitec DOT uni DASH bielefeld DOT de)]]

For bug reports, please use our bug reporting system [http://bugs.cebitec.uni-bielefeld.de BugZilla].

Author: [http://www.cebitec.uni-bielefeld.de/~krunte Kai Runte]

EMMAWiki/WebDocumentation/HowTos/DatasetBrowserHowTo

2011-10-26T06:18:50Z

Admin: 32 revisions

__NOTOC__
= Browse [[DataSets]] =

This Section describes the use of the Dataset Browser.
A description of shared terms can be found in [[EMMAWiki/WebDocumentation/HelpSystem|HelpSystem]].

This Howto is divided in 2 subsections (chronological by menu prompt):

* [[#select_dataset|Select Dataset(s)]]
* [[#browse_dataset|View Dataset(s)]]


== Select Dataset(s) ==

The following image shows the dialog with three examples of a raw datasets of a current experiment. Each dataset has an unique Identifier, a self explaining Name and if available a short description. The Cube-Order, #BA-Dim,. #DE-Dim and #QT-Dim gives you information about the size and range of the dataset:
* Cube-Order: lay down the following order but is at current state always '''BDQ''',
* #'''B'''A-Dim: show how many arrays were used from this dataset and is also at current state always one,
* #'''D'''E-Dim: stands for the number of rows. Shows how many Designelements were used.
* #'''Q'''T-Dim: stands for the number of columns. Shows how many Quantitationtypes were used.

The Quality is an index for the user. It ranges from very good to insufficient.

[[Image:EMMAWiki$$WebDocumentation$$HowTos$$DatasetBrowserHowTo$brows2_dataset_dialog.png]]

=== Show ===
Clicking the ''Show All'' button shows the selected dataset(s) in one table as described in [[#browse_dataset|View Dataset(s)]].

=== Coincid [[QuantitationType]]-Selection ===
The ''Common Label/Column Selection'' button let you take a preselection of Quantitationtypes which leads to the dialog box (shown below). Thus you can decide which Quantitationtype should be shown for all selected datasets at once. You can get more information about each Quantitationtype by following the link.

[[Image:EMMAWiki$$WebDocumentation$$HowTos$$DatasetBrowserHowTo$browse_dataset_dialog_preselection.png]]

Remarks:
* [[QuantitationType]]-Selection currently works only for data display. The exported datasets always contain the full tables.

=== Individual [[QuantitationType]]-Selection ===
A more sensitive preselection can be made if you click the ''Individual Label/Column Selection'' button. Here you can select which Quantitationtype you want for each
dataset. The dialog box is almost the same as the one shown above and includes all selected datasets.

Remarks:
* [[QuantitationType]]-Selection currently works only for data display. The exported datasets always contain the full tables.


== View Dataset(s) ==
The datasets are shown as one table which can be browsed easily with the navigation bar. Each [[DesignElement]] and Quantitationtype is linked for further detailed information.

[[Image:EMMAWiki$$WebDocumentation$$HowTos$$DatasetBrowserHowTo$browse_dataset_de_range.png]]
[[Image:EMMAWiki$$WebDocumentation$$HowTos$$DatasetBrowserHowTo$browse_dataset_table2.png]]

=== Data Display ===

The actual data is displayed in the table cells. The number format is normally chosen automatically depending on the actual values.
Default is to use floating point representation with eg <code><nowiki> 12.8032050412329 </nowiki></code> with a maximum of 15 digits. For very large numbers or numbers close to zero, exponential representation will be used, like <code><nowiki> 1.2E10 </nowiki></code> = 1.2 * 1010 or <code><nowiki> 1.2E-10 </nowiki></code> = 1.2 * 10-10.

Remarks:
* '''.''' (dot) is used as decimal character, not '','' (comma) for display and export
* The internal precision of the data might be higher than the display precision.
* The number of decimal digits depends on the value, the maximal number of total digits is 15.
* '''NaN''' means Not a Number. It represents a missing or infinite value. Often, values are set to NaN by filter procedures.
* NaN are also found in one-sample statistical tests, for values for the second group. This means, that their calculation is not applicable.

=== Dimension Range ===
The first section of this window is for specifying how many rows ([[DesignElement]]) are shown in each page. Entering a start and end position in the Dimension-Range field enables you to go to the given position. With this option you can also set the number of Designelements per page. The field named ''Search'' offers you a simple possibility to restrict the Designelements by the Identifier.

=== Sort by Quantitationtypes ===
The blue arrows in the first row of the table let you sort the dataset in ascendending or descendending order. Also you can choose between sorting the current shown page or the whole
dataset(s) by switching the radio button above the table between '''Sort only this page''' or '''Sort whole dataset'''. If you pick the option ''whole dataset'' the
assortion remains while browsing the dataset until you click '''Drop Assortment'''.

=== Filter Data ===
The button '''filter data''' opens a new window where you are able to filter the dataset. Start to single out the whished Quantitationtype in the first drop-down menu then
select an operator and leave the value for the comparison in the right text field. If you want to filter for more than one Quantitationtype or one Quantitationtype with
different operation you have to chose '''AND''' at the first drop-down menu of each next line you want to include. The More button leads in as many new lines you want.
As by the sorting the filter keeps by as long until '''Drop Assortment'''. You can reactivate the sorting/filtering by pressing the '''Keep Assortment''' button. This way
you switch between the raw dataset and your last performed sorting/filtering.

[[Image:EMMAWiki$$WebDocumentation$$HowTos$$DatasetBrowserHowTo$browse_dataset_filter.png]]

The following operators available:

* > : greater
* < : less than
* >=: greater or equal
* <= : less or equal
* != : not equal
* approx ''value epsilon'' : get all values approximately equal to ''value'' within an range of +/-''epsilon'' (default 0.001). e.g.:
''approx 10 0.1'' will return all rows where the selected column value is between 9.9 and 10.1
* not missing : filter rows where selected column has a good value (not NaN)
* missing : the opposite, return all rows with missing values

=== Export ===
It is possible to download the dataset as a tab seperated text file. You can either export the foltered/sorted dataset ore the whole dataset.

ArrayLIMSWiki/WebDocumentation

2011-10-26T06:18:47Z

Admin: 11 revisions

__NOTOC__
= ArrayLIMS =

First login on "https://www.cebitec.uni-bielefeld.de/groups/brf/software/arraylims/".
Fill in your username and password and submit. After that choose a project you are member of/you want to edit and press the submit button. The first page you are directed to is an index page which gives you a short overview of the different pages of the [[ArrayLIMSWiki|ArrayLIMS]] system. On this page are links to every page in the system. There is a second navigation bar on the left of the page so you dont have to go back to the index page. In the upper left part you see your login name and your chosen project.

----

[[Target]]

[[Target labeling]]

[[Microarray hybridization]]

[[Report]]

[[Image and data upload]]

[[[GeneChip|data upload]]]

[[List of protocols]]

[[Project selection]]

[[Edit]]

[[Options]]

[[Search]]

IGetDBWiki/GettingStarted

2011-10-26T06:18:47Z

Admin: 19 revisions

__NOTOC__
= Getting Started =

This HowTo explains briefly how to get started with developing code for IGetDB project.

== Code Example ==

You can download some example source-code showing how to access an IGetDB mart and convert the results into a nice pie-chart: [[Media:IGetDBWiki$$GettingStarted$igetdb_1_0-tutorial.zip]]

== Setup of the IGetDB project class in GPMS 2 ==

[http://www.cebitec.uni-bielefeld.de/groups/brf/internal/AdministrationOverview/SetupNewIGetDBProjectClass Setup of the IGetDB project class in GPMS 2 (internal wiki)]

== DB Access ==

All IGetDB projects are backed by the projectmanagement system [[GPMSWiki| GPMS]].
To be able to work with IGetDB you need an account.

If you are a developer
send an email to: [[MailTo(krunte AT cebitec DOT uni DASH bielefeld DOT de)]] to get a
developer account.

== Version Control ==
[[IGetDBWiki/GettingStarted/VersionControl| Version Control]]

== API Documentation ==

The API documentation of IGetDB is not checked in as this causes more
trouble then it's worth. To generate your own copy of the API
documentation, simply run <code><nowiki>ant doc</nowiki></code> in <code><nowiki>igetdb</nowiki></code> directory.

== Setting up the IGetDB-exporter for EMMA ==
[[IGetDBWiki/GettingStarted/EmmaPlugin| EMMA Plugin]]

== Web-Server ==
[[IGetDBWiki/GettingStarted/WebServer| Web-Server]]

== Documentation ==
[[IGetDBWiki/GettingStarted/Documentation| Documentation]]

== Directory Structure ==
[[IGetDBWiki/GettingStarted/DirectoryStructure| Directory Structure]]

EMMAWiki/DeveloperDocumentation/APIDocumentation

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Admin: 6 revisions

__NOTOC__


== Documentation of concepts ==
See [[ConceptDocumentation]] for an introduction to basic programming concepts and diagrams. This page also describes how the backend-code and core classes are generated.

== EMMA API-Documetation ==
This section is mainly addressing core developers and developers wishing to extend or customize EMMA.
There are several levels of API-documentation available.

=== O2DBI Server Documentation ===

Automatically generated [http://www-test.cebitec.uni-bielefeld.de/~mdondrup/INTERN/EMMA2/API-doc/ HTML-documentation] of the O2DBI-Backend modules.
This includes all modules under the share/perl/EMMA/ hierarchy.

=== MAGE-OM Documentation ===
Sorted by packages:
* Auto generated [http://www-test.cebitec.uni-bielefeld.de/~mdondrup/INTERN/EMMA2/API-doc/MAGE.html HTML-documentation of the MAGE-OM classes] from POD. If you add POD to your modules the documentation will automatically appear here.
* Auto generated [http://www-test.cebitec.uni-bielefeld.de/~mdondrup/INTERN/EMMA2/API-doc/MAGE.pdf PDF-documentation of the MAGE-OM classes] generated from the HTML-file.

External documentation:
* [http://www.ebi.ac.uk/arrayexpress/Schema/MAGE/MAGE.htm MAGE-OM as a set of hyperlinked diagrams] (Mozilla browser required)

=== Generating Documentation ===
To regenerate the HTML-documetation:
* Use the script:
<pre><nowiki>
cd CVS/bioinfo/emma2/share/exec/
./create_html_docs.pl
</nowiki></pre>

GPMSWiki/AdministratorDocumentation/AddingProjectClass

2011-10-26T06:18:44Z

Admin: 5 revisions

__NOTOC__
= Adding a [[ProjectClass]] =

* Define the Roles and Rights of the ProjectClass
* Add the ProjectClass:
gpms add_project_class -c <class name> -d <description>
(e.g. gpms add_project_class -c GenDB-2.2 -d "Class for all GenDB version 2.2 projects")

Search

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Admin: 7 revisions

__NOTOC__
= Search =

On this page you are able to search for certain objects like targets, labeled targets, images, protocols, etc.
# Select the type of data you want to search for.
# There will appear a select box in the row below. In this select box all data objects associated with your chosen data type are listed. Choose one of this data objects.
# A second select box will appear in the same row in which all attributes of the chosen data object are listed. Choose one of the attributes and type in the value of the attribue in the appearing input field.
If you want to search for additional data objects/attributes click on the '''and''' button and repeat the steps 2 and 3.

Submit the search with the '''search''' button.

The results will be shown as links named with the result objects. To see a report of the result objects click on these links. A new page will appear where the attributes of the chosen object are listed. To get back to the search results click on the '''Back to search results''' link on the upper left of the page. To start a new search click on the '''New search''' link on the upper left of the page.

PathwayMap

2011-10-26T06:18:44Z

Admin: 3 revisions

__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.

[[Image: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

[[Image:PathwayMap$inkscape.png]]

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

[[Image:PathwayMap$glycine.png]]

* Select XML Editor from the Edit Menu ...

[[Image:PathwayMap$xmleditor.png]]

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

[[Image: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).

[[Image: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.

Edit image and data files

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Admin: 3 revisions

__NOTOC__
This page is for editing or deleting an uploaded image and its corresponding data file. If you are no chief or admin of the chosen project you are only allowed to delete or edit your '''own''' images and data files.

[[Delete a particular image and its data file]]

[[Edit a particular image and its data file as well as its corresponding image file]]

EMMAWiki/WebDocumentation/HelpSystem/StatusExperiment

2011-10-26T06:18:44Z

Admin: 5 revisions

__NOTOC__
= Status =

An experiment can have three states: in progress, finished and locked.
In Progress is an experiment which can be edited.
Finished represents a final version of an experiment, without the blessing of the chief.
If the chief submits the experiment the status changed to locked, which is an indicator for an closed experiment.

MGE-PortalWiki

2011-10-26T06:18:43Z

Admin: 78 revisions

__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/chpwreq.html 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.

SAMSWiki/WebDocumentation/HowTo/BasicActions

2011-10-26T06:18:24Z

Admin: 2 revisions

__NOTOC__
* Import Sequences:
The SAMS Web Importer will guide you through the import process. On the next pages you are asked to select a file, to check the sequence names and to select the settings for quality and vector clipping, if necessary. Default values are suggested for each step, but custom values can easily be used.

The window on the right hand side lists the 5 steps of the Importer, ticking the processed step off and opening the next one. Step 5 summarises your settings, so that you can easily go back to previous steps to change the parameters, if neccessary, before completing the process of importing your sequences into SAMS.

* [[/Import Step1]]: please select a file to upload.
* [[/Import Step2]]: check sequence names
* [[/Import Step3]]: select quality clipping
* [[/Import Step4]]: select vector clipping
* [[/Import Step5]]: finish the import to SAMS
* [[/Import Step6]]: Import finished
* /CreateandEditlibrary
* /MergeLibraries
* [[/Cluster and Assembly EST data]]
* /AutomaticAnnotation
* /BrowsingSequencedatasets
* /AnnotatingSequencedata
* /AddCustomtool
* /ShowAnnotationstatistics
* /ShowJobstatistics

MeltDBWiki/HowTos

2011-10-26T06:18:24Z

Admin: 11 revisions

__NOTOC__

== Using the public MeltDB experiments ==

* Login to the public MeltDB project using the guest account:
[http://meltdb.cebitec.uni-bielefeld.de/cgi-bin/meltdb.cgi?login=guest&chksum=h/Zx4JEg6sz0I6hi97ZfsA&project=MeltDB_Public MeltDB guest login]

* To analyze the publicly available datasets in MeltDB, please select 'Browse/Analyse an existing Experiment' from the start page.

[[Image:MeltDBWiki$$HowTos$startpage.png]]

* Select the 'Three carbon sources' experiment by clicking on the folder icon to the left.

[[Image:MeltDBWiki$$HowTos$experiments.png]]

* The textual display of the experiment is presented and a number of potential actions together with their short descriptions are listed below.

[[Image:MeltDBWiki$$HowTos$carbon_sources.png]]

* Please select 'Show PCA' to start the PCA analysis on the previously imported peaks found by Xcalibur preprocessing methods.
* Select all chromatograms and a list of metabolites and click the 'Compute PCA' button. If you would like to log-transform the measured and normalized metabolite values, mark the 'log' checkbox.

[[Image:MeltDBWiki$$HowTos$pca.png]]

ArrayLIMSWiki

2011-10-26T06:18:24Z

Admin: 19 revisions

__NOTOC__
= ArrayLIMS Overview Page =

== ArrayLIMS - Laboratory information management system for microarray hybridizations ==

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

* /TermsAndConcepts
** /ForUsers
** /ForDevelopers

== Documentation ==
* /CoreDocumentation (Documentation of the main backend functionality and executable scripts)
* /UserManual (Documentation on the use of the web-interface)
** /WebDocumentation
* /DeveloperDocumentation
** /GettingStarted
* /[[FAQs]]
* /HowTos

== General ==
* /ToDos (Tasks on the road to an ArrayLIMS2 release candidate)
* /FeatureTable
* /FuturePlans

== 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 ArrayLIMS website].

== Contact ==

Please send an e-mail for account requests or questions concerning the use of ArrayLIMS to:
[[MailTo(Emma AT cebitec DOT uni DASH bielefeld DOT de)]]

For bug reports, please use our bug reporting system [http://bugs.cebitec.uni-bielefeld.de BugZilla].

Author: [http://www.cebitec.uni-bielefeld.de/~druffi Tim Kahlke]

MeltDBWiki/PerformFBCA

2011-10-26T06:18:23Z

Admin: 4 revisions

__NOTOC__


== Perform the Feature Based Chromatogram Alignment of MeltDB ==

* After logging in to MeltDB, select your experiment by either a) browsing through the list of available experiments or b) via the search function available at the top.

a)

[[Image:MeltDBWiki$$PerformFBCA$browse.png]]

b)

[[Image:MeltDBWiki$$PerformFBCA$search.png]]

* After selecting your experiment, you can generate a multiple TIC view of the associated chromatograms via the following function:

[[Image:MeltDBWiki$$PerformFBCA$tic2.png]]

* The first call to this may take some time since the image needs to be rendered from the raw datasets. Consecutive calls will reuse the generated image. If you change your experiment by adding or removing chromatograms to the chromatogram groups you can repaint the image with the 'recreate image' link.

[[Image:MeltDBWiki$$PerformFBCA$tic.png]]

* Feature based alignment is only possible if a peak detection and/or import was performed on your chromatograms. In order to compute an alignment using the FBCA tool of MeltDB select a representative chromatogram of your experiment. (e.g. click on one peak marked as blue or green spot and select the chromatogram name below). Select the 'Compute aligment' action from the chromatogram context menu.

[[Image:MeltDBWiki$$PerformFBCA$fbca1.png]]

* The FBCA algorithm will generate pairwise alignments of your selected chromatogram with all other chromatograms of the selected experiment. Click 'Compute aligment' to start the processing. This may take some time...

[[Image:MeltDBWiki$$PerformFBCA$fbca2.png]]

* After the computation is finished, use the 'Show alignment' action of your chromatogram to review the results. You can reorder the chromatograms and/or select only subsets of the aligned chromatograms in the dialog. Select the peak detection or importer tools for which you would like to view peaks in the alignment.

[[Image:MeltDBWiki$$PerformFBCA$fbca3.png]]

* The rendering of the aligned image takes some seconds, it allows to quickly spot differences in the aligned chromatograms.

[[Image:MeltDBWiki$$PerformFBCA$fbca4.png]]

HelpOnInstalling/ApacheOnMacOsx

2011-10-26T06:18:22Z

Admin: 2 revisions

__NOTOC__

== installing [[MoinMoin]] on OS X ==
An install report of a succesfull install on a powermac G4 running mac OS X 10.2.6.
In the examples you will see that the machine name is `pm142` and the administrator account is `giels`. The wiki site that is created is called `mgwiki`.

=== before you begin ===

* You should have activated the `root` user
* You must not be afraid to use the terminal ;)
* some practice with the pico editor might be useful as well

=== download ===

Download the source on the desktop: you should see a `moin-x.x.tar.gz` file.
Extract this file on the desktop with Stuffit. You will get a folder `moin-x.x`.

=== install ===

All code examples are taken form a terminal session.

First check everything:

<pre><nowiki>
[pm142:~] giels% su root
Password:
[pm142:/Users/giels] giels# whoami
root
[pm142:/Users/giels] giels# python -c 'import sys; print sys.prefix'
/usr
[pm142:/Users/giels] giels#
[pm142:/Users/giels] giels# cd Desktop/moin-1.0
[pm142:giels/Desktop/moin-1.0] giels# ls -al
total 264
drwxr-xr-x 15 giels staff 510 May 10 2002 .
drwxr-xr-x 9 giels staff 306 May 12 19:39 ..
-rw-r--r-- 1 giels staff 19118 May 10 2002 CHANGES
-rw-r--r-- 1 giels staff 17992 Jun 9 2001 COPYING
-rw-r--r-- 1 giels staff 42827 May 9 2002 INSTALL.html
-rw-r--r-- 1 giels staff 837 Feb 27 2002 MANIFEST.in
drwxr-xr-x 37 giels staff 1258 May 10 2002 MoinMoin
-rw-r--r-- 1 giels staff 553 May 10 2002 PKG-INFO
-rw-r--r-- 1 giels staff 5831 Apr 17 2002 README
-rw-r--r-- 1 giels staff 908 Jan 16 2002 TODO
drwxr-xr-x 5 giels staff 170 May 10 2002 contributions
-rw-r--r-- 1 giels staff 13878 Jul 5 2001 moinlogo.bmp
-rw-r--r-- 1 giels staff 229 Jul 5 2001 setup.cfg
-rw-r--r-- 1 giels staff 6586 May 9 2002 setup.py
drwxr-xr-x 5 giels staff 170 May 10 2002 wiki
[pm142:giels/Desktop/moin-1.0] giels#
</nowiki></pre>

the real install:

<pre><nowiki>
[pm142:giels/Desktop/moin-1.0] giels# python setup.py install --record=install.log
running install
running build
running build_py
creating build
....
creating /usr/share/moin/htdocs/applets
creating /usr/share/moin/htdocs/applets/TWikiDrawPlugin
writing list of installed files to 'install.log'
</nowiki></pre>

Now installation is finished. You will find a file `install.log` on the desktop in the folder `moin-x.x`.

=== configuration ===
First make a copy of the original [[MoinMoin]] site:

<pre><nowiki>
[pm142:giels/Desktop/moin-1.0] giels#
[pm142:giels/Desktop/moin-1.0] giels# egrep "^User|^Group" /etc/httpd/httpd.conf
User www
Group www
[pm142:giels/Desktop/moin-1.0] giels# cd /usr/share/moin/
[pm142:/usr/share/moin] giels# ls -al
total 0
drwxr-xr-x 5 root wheel 170 May 12 19:49 .
drwxr-xr-x 44 root wheel 1496 May 12 19:49 ..
drwxr-xr-x 4 root wheel 136 May 12 19:49 cgi-bin
drwxr-xr-x 9 root wheel 306 May 12 19:49 data
drwxr-xr-x 6 root wheel 204 May 12 19:49 htdocs
[pm142:/usr/share/moin] giels#
[pm142:/usr/share/moin] giels# mkdir mgwiki
[pm142:/usr/share/moin] giels# cp -r data mgwiki
[pm142:/usr/share/moin] giels# cp cgi-bin/* mgwiki
[pm142:/usr/share/moin] giels# chown -R www.www mgwiki
[pm142:/usr/share/moin] giels# chmod a+rx mgwiki/*.cgi
[pm142:/usr/share/moin] giels#
</nowiki></pre>

Configure Apache. We'll use the pico editor:

<pre><nowiki>
[pm142:/usr/share/moin] giels# pico /etc/httpd/httpd.conf
</nowiki></pre>

Scroll to the end of the file and edit like the example below, (only the last two lines are added; use control-x to save the file):

<pre><nowiki>
RegisterDefaultSite
</IfModule>

Include /private/etc/httpd/users

Alias /wiki/ "/usr/share/moin/htdocs/"
ScriptAlias /mgwiki "/usr/share/moin/mgwiki/moin.cgi"

^G Get Help ^O WriteOut ^R Read File ^Y Prev Pg ^K Cut Text ^C Cur Pos
^X Exit ^J Justify ^W Where is ^V Next Pg ^U UnCut Text ^T To Spell
</nowiki></pre>

Restart Apache:

<pre><nowiki>
[pm142:/etc] giels# apachectl help
usage: /usr/sbin/apachectl (start|stop|restart|fullstatus|status|graceful|configtest|help)

start - start httpd
stop - stop httpd
restart - restart httpd if running by sending a SIGHUP or start if
not running
fullstatus - dump a full status screen; requires lynx and mod_status enabled
status - dump a short status screen; requires lynx and mod_status enabled
graceful - do a graceful restart by sending a SIGUSR1 or start if not running
configtest - do a configuration syntax test
help - this screen

[pm142:/etc] giels#
[pm142:/etc] giels# apachectl graceful
/usr/sbin/apachectl graceful: httpd gracefully restarted
[pm142:/etc] giels#
</nowiki></pre>

=== testing ===

In a web-browser surf to the site: `pm142/mgwiki`

== Comments ==

Here are a couple of issues with my Mac OS X install I needed to fix:

# The TWiki drawing jar file is not installed, so drawings do not work. You have to find the twikidraw.jar file (download the latest stable [[MoinMoin]] tar.gz file and uncompress like: `tar xzvf moinmoin.tar.gz`), and copy the twikidraw.jar file (under `htdocs/applets/TWikiDrawPlugin`) to this folder `/usr/share/moin/htdocs/applets/TWikiDrawPlugin/`. You'll probably need to use sudo: `sudo cp twikidraw.jar /usr/share/moin/htdocs/applets/TWikiDrawPlugin/` and set permissions: `sudo chmod 755 /usr/share/moin/htdocs/applets/TWikiDrawPlugin/twikidraw.jar`
# The RSS feed for your [[Special:Recentchanges|RecentChanges]] page may be broken. You need to install the most recent version of [http://sourceforge.net/projects/pyxml/ PyXML]. Here's how I did so and the RSS feed was fixed. `curl -O http://aleron.dl.sourceforge.net/sourceforge/pyxml/PyXML-0.8.3.tar.gz` `tar xzvf PyXML-0.8.3.tar.gz` `cd PyXML-0.8.3` `sudo python setup.py --without-xpath build` `sudo python setup.py install`

OS X users with a fink install need to chance the path `/usr/share/moin` to `/sw/share/moin`. see `install.log`.

O2DBIWiki/IntroRequirements

2011-10-26T06:18:22Z

Admin: 4 revisions

__NOTOC__

= O2DBI - Introduction - Requirements =

-> Back to [[O2DBIWiki| Overview page]] <-

O2DBI uses a number of Perl modules. Most of them are either default modules (bundled with the Perl distribution itself) or are available at [http://www.cpan.org CPAN].

* Code generator:
** XML::DOM
** XML::Writer
* Graphical schema design interface
** Gtk
** Gtk::Gdk::[[ImlibImage]]
* drawing of class graphes within the GUI
** Graph
** Graph::Directed
** Graph::Writer::Dot
** Graph::Writer::VCG
* generated code
** DBI
** DBI backend modules for MySQL, PostgreSQL
* experimental SOAP client/server code
** Compress::Zlib
** SOAP::Lite

-> Back to [[O2DBIWiki| Overview page]] <-








Author: [http://www.cebitec.uni-bielefeld.de/~blinke]

EMMAWiki/WebDocumentation/HelpSystem/FactorsExperiment

2011-10-26T06:18:22Z

Admin: 3 revisions

__NOTOC__
= Experimental Factors in experiment =

All factors under which the experiment was conducted.

See also [[EMMAWiki/WebDocumentation/HelpSystem/FactorsGeneral|ExperimentalFactor]]

GenDBWiki/WebDocumentation/DialogWindows/PatScan

2011-10-26T06:18:22Z

Admin: 22 revisions

__NOTOC__
= [[PatScan]] =
PatScan is used to identify patterns in large sequences. It is possible to search patterns by specifying the number of insertions, deletions and substitutions or by defining a weight-matrix.

[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_a.png]]

The interface consists of 4 categories:
{| border="1" cellpadding="2" cellspacing="0"
| '''Options'''
| Define the type of regions to be searched (DNA or Protein)
|-
|
| Define search strand
|-
|
| Defined the offset which is used to search also characters infront or behind the actual search-region
|-
| '''Search definition'''
| Enter your search pattern here.
|-
|
| Optionally you can check the "use" checkbox to define the insertions/deletions/substitutions if you have not already defined it in your pattern
|-
|
| Above the textfield are two links. "Ambiguity codes" shows you the available IUPAC codes which can be incorporated into your pattern
|-
|
| The second link "Examples" shows you some common example queries for a quick start building your own search patterns
|-
| '''Filter'''
| GenDB tries to associate regions with the PatScan matches. Sometimes you are only interested in matches which are infront
|-
|
| or behind a region,like promotors. So here you can define whether all matches should be displayed, only matches which lie within the bounds of
|-
|
| a region or only intergenic matches.
|-
| '''PatScan'''
| These values should normally not be touched. Only if performance is an issue and you know what you are doing change these values.
|-
|
| Mainly these are commandline options for the scan_for_matches (PatScan) program. For a better description please take a closer look at the [http://www-unix.mcs.anl.gov/compbio/PatScan/HTML/readme_scan_for_matches.html PatScan manual]
|}

== How does the search work ==

Basically GenDB fetches all regions of the type you specified in the options section and runs PatScan for each region. By default only upstream sequences are searched. But you can override this behaviour by selecting the "both strands" radiobox.
The result shows the region marked as big red bars and the PatScan matches are shown as small yellow bars.

== Interpretation of Results ==

[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b1.png]]

The result shows the name of the region which the match belongs to, the position in the contig and the distance to the start of the region.
Every row has on its far right a link to the [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog|AnnotationDialog]]. Sometimes its handy to annotate few matches at once without clicking on every rows annotate link.
For that reason there is a button called '''"Annotate selection"''' which opens the [[GenDBWiki/WebDocumentation/DialogWindows/MultiAnnotator|MultiAnnotator]] to annotated many regions at once.

We specified a offset of 100 bases and filtered all matches which lie within the bounds of a region. As a result we get all intergenic matches which start at maximum 100 bases infront of a region. This can be very handy for identifying promotor regions.

== Exporter for Results ==

[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b2.png]]

'''This feature is available since GenDB version 2.4.'''

The exporter for the results of the pattern search is shown after clicking the '''"Show exporting fields"''' button. This button is only visible next to the '''"Annotate"''' button, if your status allows you to export data.

You can choose the values, which should be exported, by clicking in the associated checkboxes.
Beneath this, there is a checkbox for adding a ''comment line'' to the export-file, which contains the name of the checked values.
You also can choose the type of separation between '''"tabulator"''' (recommended) and '''"comma"'''.

By clicking the '''"Export values"''' button, the export-file will be generated and a save dialog will be opened.

== Q/A Troubleshooting ==

'''Q: My pattern was not found. It was expected to be an intergenic match.'''

A: You possibly specified the offset too low. Imagine there exist 2 regions which are divided by a 100 bases raw sequence which has no region there.
If your offset reads e.g. 30 bases upstream you loose the the information if the pattern occurs in the remaining 70 bases sequence.
So, setting your offset higher may solve your problem

'''Q: Why does the result always show my selected contig as associated region?'''

A: You didn't select a region and selected '''"current"''' as '''Search Region'''. As a result, PatScan searches only the contig (which is also a region).
To solve this problem select '''all''' as Search Region and select an applicable type from the listbox. A value of '''Region''' will search all regions except the contig.

ProMeTraWiki/CSVFormat

2011-10-26T06:18:20Z

Admin: 2 revisions

__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.

[[Image:ProMeTraWiki$$CSVFormat$tsv.png]]

[[Media:ProMeTraWiki$$CSVFormat$sample.tsv]]

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

EMMAWiki/WebDocumentation/HelpSystem/NameGeneral

2011-10-26T06:18:20Z

Admin: 2 revisions

__NOTOC__
= Name =

Name of the specific object.

AufgegebeneSeiten

2011-10-26T06:18:20Z

Admin: 2 revisions

__NOTOC__



Seiten, die seit Urzeiten nicht mehr geändert wurden; dies ist eine Liste der ältesten Einträge im Editlog.

[[AbandonedPages]]