Recent changes to Modules

WikiPage Modules modified by Vincent WALTER

Vincent WALTER — Fri, 01 Mar 2013 20:20:39 -0000

--- v32
+++ v33
@@ -82,8 +82,9 @@

 #####Combined best p-values#####

-
-
+This scoring method consists in comparing tissular expression profiles of candidate gene with those of known genes. The similarity of these tissular expression profiles is evaluated using the ___Pearson Correlation Coefficient___. For each candidate gene and known genes, we keep the best p-value that corresponds to the closest profiles. Then the best p-values obtained against each known genes are ___merged using the Fisher omnibus anlysis___.
+
+The Pearson Correlation Coefficient is made only for positive correlation signal. One one hand, low expression of a gene does not necessarily means that it is repressed by the other. It may not be expressed in the observed tissue. On the other hand, the coexpression is more interesting because it can reflect an interaction (direct or not) between two genes.

 ###IDGP###

WikiPage Modules modified by Vincent WALTER

Vincent WALTER — Fri, 01 Mar 2013 19:51:26 -0000

--- v31
+++ v32
@@ -74,6 +74,9 @@
 During the recent years gene expression profiling through transcriptomics has become an essential tool in many domains of research. This technique generates large quantities of data that may be exploited in many different ways allowing to reveal different aspects of the nature of the original data. The analysis and the meta- analysis of such data still remain quite laborious and often are not easily accessible to biologists. In this context, we develop an innovative platform, called GxDb, in order to offer an integrative tool for the analysis of transcriptomics data analysis. This platform is accessible through a secured web- portal and allows convenient upload of data, storage in a relational database and running many treatment and analysis procedures automatically. At the user interface, data query and analysis is greatly facilitated through the various modules and options for graphical display. GxDb clearly extends the opportunity to compare results from different treatment and analysis procedures (including human expert analysis) and/or different experiments. This also gives to the biologist tools for investigating and understanding the strengths and weaknesses of the data-treatments or combination thereof used during analysis, thus allowing to choose the best approach and tools for a given experimental question or a given gene.

 ![alternate "GenomicContext](http://lbgi.igbmc.fr/~walterv/gepetto/sourceforge/images/0gxdb.png)
+
+The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom arrays that interrogate the expression of the vast majority of protein-encoding human and mouse genes and have used them to profile a panel of 79 human tissues. The resulting data set provides the expression patterns for thousands of predicted genes, as well as known and poorly characterized genes, from humans. We have explored this data set for global trends in gene expression, valuated commonly used lines of evidence in gene prediction methodologies, and investigated patterns indicative of chromosomal organization of transcription.
+

 ####Methods####

WikiPage Modules modified by Vincent WALTER

Vincent WALTER — Thu, 28 Feb 2013 23:31:37 -0000

--- v30
+++ v31
@@ -183,15 +183,6 @@

 ####Others####

-#####Logging#####
-
-* ___GEPETTOLogger___ : to log informations, errors, etc.
-
-#####Exceptions#####
-
-* ___DependenciesNotFoundException___ : when dependencies are not satisfied
-* ___GEPETTOModuleException___ : when a _general_ exception occured
-
 #####Manipulated features#####

 * ___GEPETTOSet___ : set of genes / proteins and the correspondence between them
@@ -209,9 +200,17 @@

 #####Global prioritization#####

-
 * ___GEPETTOGlobal___ : results of global prioritization (scores and annotations)
 * ___GlobalPrioritization___ : result of global prioritization for one feature.
+
+#####Logging#####
+
+* ___GEPETTOLogger___ : to log informations, errors, etc.
+
+#####Exceptions#####
+
+* ___DependenciesNotFoundException___ : when dependencies are not satisfied
+* ___GEPETTOModuleException___ : when a _general_ exception occured

 ###MANIFEST file###

WikiPage Modules modified by Vincent WALTER

Vincent WALTER — Thu, 28 Feb 2013 23:30:19 -0000

--- v29
+++ v30
@@ -152,27 +152,66 @@

 ###GEPETTOModel-based classes implementations###

-####Prioritization class####
-
-* GenePrioritization : for gene-based prioritization methods
-* ProteinPrioritization : for protein-based prioritization methods
-
-inherit from Prioritization which should not be directly implemented.
-
-####jBPM Task####
-
-* ModuleWorkItemHandler : to be used as a jBPM service task
-
-####Features manipulated####
-
-* Feature : the general implemtantion of objects like Gene or Protein.
-* Protein : the protein object
-* Gene : the gene object
-
-####Exceptions####
-
-* DependenciesNotFoundException : when dependencies are not satisfied
-* GEPETTOModuleException : when a _general_ exception occured
+####Local prioritization module####
+
+#####Module definition#####
+
+* ___GEPETTOModule___ : local prioritization module, uncoupled from the jBPM workflow engine
+* ___ModuleWorkItemHandler___ : to use as a jBPM service task
+* ___GEPETTOLocal___ : results of local prioritization (scores and annotations)
+* ___LocalPrioritization___ : result of local prioritization for one feature.
+
+#####Dataset#####
+
+* ___DatasetLoader___ : to load data sets (training / test)
+
+#####Scoring methods#####
+
+* ___GenePrioritization___ : for gene-based prioritization method
+* ___ProteinPrioritization___ : for protein-based prioritization method
+
+inherit from ___Prioritization___ which should not be directly implemented.
+
+#####Annotations#####
+
+* ___AbstractAnnotationFeature___ : annotations for test set 
+* ___AbstractAnnotationFeatureElement___ : annotation for a test element
+* ___AbstractAnnotationTraining___ : annotations for the training set
+* ___AbstractAnnotationTrainingElement___ : annotation for a training element
+
+inherit from ___Annotation___ which should not be directly implemented.
+
+####Others####
+
+#####Logging#####
+
+* ___GEPETTOLogger___ : to log informations, errors, etc.
+
+#####Exceptions#####
+
+* ___DependenciesNotFoundException___ : when dependencies are not satisfied
+* ___GEPETTOModuleException___ : when a _general_ exception occured
+
+#####Manipulated features#####
+
+* ___GEPETTOSet___ : set of genes / proteins and the correspondence between them
+
+* ___Protein___ : to identify a protein object
+* ___Gene___: to identify a gene ibject
+
+inherit from ___Feature___ which must be used preferably.
+
+#####Manipulated Results#####
+
+* ___ModuleQuery___ ; intermediate form for data processing in local prioritization methods
+* ___Score___ : for the score
+* ___Rank___ : for the rank
+
+#####Global prioritization#####
+
+
+* ___GEPETTOGlobal___ : results of global prioritization (scores and annotations)
+* ___GlobalPrioritization___ : result of global prioritization for one feature.

 ###MANIFEST file###

WikiPage Modules modified by Vincent WALTER

Vincent WALTER — Thu, 28 Feb 2013 22:55:33 -0000

--- v28
+++ v29
@@ -151,6 +151,28 @@
 * __organisation.module.scoring__ : for the scoring methods

 ###GEPETTOModel-based classes implementations###
+
+####Prioritization class####
+
+* GenePrioritization : for gene-based prioritization methods
+* ProteinPrioritization : for protein-based prioritization methods
+
+inherit from Prioritization which should not be directly implemented.
+
+####jBPM Task####
+
+* ModuleWorkItemHandler : to be used as a jBPM service task
+
+####Features manipulated####
+
+* Feature : the general implemtantion of objects like Gene or Protein.
+* Protein : the protein object
+* Gene : the gene object
+
+####Exceptions####
+
+* DependenciesNotFoundException : when dependencies are not satisfied
+* GEPETTOModuleException : when a _general_ exception occured

 ###MANIFEST file###

WikiPage Modules modified by Vincent WALTER

Vincent WALTER — Thu, 28 Feb 2013 22:33:11 -0000

--- v27
+++ v28
@@ -139,11 +139,18 @@

 The default modules comply with a particular structure. You can reproduce it in your module to satisfy a particular standard but it is not required.

-==>...packages...<==
+The packages names are based on :
+
+* your organisation _organisation_ (_eg. org.igbmc.lbgi_)
+* the name of your module _modulename_ (eg. modulename)
+
+So you will have, at least :
+
+* __organisation.module.modulename__ : specfic of the module
+* __organisation.module.modulename.annotate__ : for the annotations of training/test sets
+* __organisation.module.scoring__ : for the scoring methods

 ###GEPETTOModel-based classes implementations###
-
-

 ###MANIFEST file###

@@ -161,7 +168,7 @@

 * __Name__ : the name of the module
 * __JBPM-Main-Class__ : the class that extends _org.igbmc.lbgi.gepetto.model.module.ModuleWorkItemHandler_
-* __JBPM-Task-Name__ : tje name used in the jBPM workflow definition file
+* __JBPM-Task-Name__ : the name used in the jBPM workflow definition file

 ###Module registration###

WikiPage Modules modified by Vincent WALTER

Vincent WALTER — Thu, 28 Feb 2013 22:26:03 -0000

--- v26
+++ v27
@@ -149,7 +149,19 @@

 You need to edit the MANIFEST file to add some required fields to be compatible with the [GEPETTO] core.

-==>...fields...<==
+~~~~~~
+Manifest-Version: 1.0
+Name: Alignment
+JBPM-Main-Class: org.igbmc.lbgi.gepetto.module.alignment.AlignmentWorkItemHandler
+JBPM-Task-Name: alignment
+X-COMMENT: Main-Class will be added automatically by build
+~~~~~~
+
+with the flowwoing required fields :
+
+* __Name__ : the name of the module
+* __JBPM-Main-Class__ : the class that extends _org.igbmc.lbgi.gepetto.model.module.ModuleWorkItemHandler_
+* __JBPM-Task-Name__ : tje name used in the jBPM workflow definition file

 ###Module registration###

WikiPage Modules modified by Vincent WALTER

Vincent WALTER — Tue, 26 Feb 2013 18:27:03 -0000

--- v25
+++ v26
@@ -139,14 +139,17 @@

 The default modules comply with a particular structure. You can reproduce it in your module to satisfy a particular standard but it is not required.

-
 ==>...packages...<==

 ###GEPETTOModel-based classes implementations###

+
+
 ###MANIFEST file###

 You need to edit the MANIFEST file to add some required fields to be compatible with the [GEPETTO] core.
+
+==>...fields...<==

 ###Module registration###

@@ -155,7 +158,9 @@
 * Copy the project/module JAR file into the __module__ directory
 * Copy the dependencies (libraries) into the __lib__ directory
 * Copy data into the __data__ directory
-* Run the following command
+* Register it.
+
+To register it, run the following command

 ~~~~~~
 gepettoupdate
@@ -168,3 +173,7 @@
 ~~~~~~

 ###Community###
+
+In order to advance the project and allow other community members to take advantage of your developments, think to share it. Please contact us to add it to the default modules, add it to the GEPETTO SVN and add it to our Debian repository.
+
+Together we are strength!

WikiPage Modules modified by Vincent WALTER

Vincent WALTER — Tue, 26 Feb 2013 18:21:11 -0000

--- v24
+++ v25
@@ -129,12 +129,42 @@

 ###Create a new jar project###

+Any new module should be distributed as a new JAR library. If you want to create a new module, you have to create a new Java Application project. You can use an IDE (Integrated Development Environment) like JDevelopper, Netbeans, Eclipse, IntelliJ,...
+
+If you need a Java library (eg. Apache Commons), take the version used by [GEPETTO] if it is already imported into the ___lib___ folder, or a later version to avoid compatibility problems with other modules.
+
+You need to import the __Spring Framework__, __jBPM__, __GEPETTOModel__ libraries.
+
 ###Architecture of packages###
+
+The default modules comply with a particular structure. You can reproduce it in your module to satisfy a particular standard but it is not required.
+
+
+==>...packages...<==

 ###GEPETTOModel-based classes implementations###

 ###MANIFEST file###

+You need to edit the MANIFEST file to add some required fields to be compatible with the [GEPETTO] core.
+
 ###Module registration###

+To use your module, you must register it by the [GEPETTO] core. To do this, you have to :
+
+* Copy the project/module JAR file into the __module__ directory
+* Copy the dependencies (libraries) into the __lib__ directory
+* Copy data into the __data__ directory
+* Run the following command
+
+~~~~~~
+gepettoupdate
+~~~~~~
+
+To verify that the module is registered and usable, run the following command and look if it appears in the list returned :
+
+~~~~~~
+gepettomodule 
+~~~~~~
+
 ###Community###

WikiPage Modules modified by Vincent WALTER

Vincent WALTER — Tue, 26 Feb 2013 16:38:34 -0000

--- v23
+++ v24
@@ -5,6 +5,8 @@

 Current modules
 ---------------
+
+Currently, several modules use R/RJava to perform clustering and statistics computations. In the future, we want to break those dependencies to facilitate the portability on other operating system (Windows). To do that, we want to integrate the methods provided by [Weka 3: Data Mining Software in Java](www.cs.waikato.ac.nz/ml/weka/ "Weka 3: Data Mining Software in Java") and the [Apache Commons Math](http://commons.apache.org/proper/commons-math//userguide/stat.html "Apache Commons Math").

 ###Alignment###