AMEN / News: Recent posts

Dear User,
IMPORTANT: The AMEN installer for windows is no more available. See the installation procedure in the README.txt file for more details on how to download, install and run AMEN. Moreover, the GraphViz program was replaced by the "igraph" R library" to draw network into AMEN.

Several changes including probably the most important one since the AMEN creation: Annotation and Network data files are now automatically generated! There's no more need to download different databases and convert them! Just use the "Menu>Options>Download databases" module.
Other changes:
- "Main entries" are now called "Reference entries".
- Annotation and interaction data files could now include "multi-reference entries" (separated by semi-colon ';') as "reference entries" (1rst column)
- "Upload data" was removed and associated modules were moved into either "Expression" or "Options" menu... read more

Dear User,
Two major bugs were fixed.
Enjoy AMEN!!!
Fred

Dear User,
IMPORTANT: The AMEN installer for windows is no more available. See the installation procedure in the README.txt file for more details on how to download, install and run AMEN. Moreover, the GraphViz program was replaced by the "igraph" R library" to draw network into AMEN.
One minor bug was fixed: Impossible to execute the "quantile-quantile" normalization module properly.
Enjoy AMEN!!!
Fred

Dear User,
IMPORTANT: The AMEN installer for windows is no more available. See the installation procedure in the README.txt file for more details on how to download, install and run AMEN. Moreover, the GraphViz program was replaced by the "igraph" R library" to draw network into AMEN.
One major bug was fixed: Due to a recent change, AMEN was enable to start correctly. Sorry about that...
Enjoy AMEN!!!
Fred1.3.0

Dear User,
IMPORTANT: The AMEN installer for windows is no more available. See the installation procedure in the README.txt file for more details on how to download, install and run AMEN. Moreover, the GraphViz program was replaced by the "igraph" R library" to draw network into AMEN.
Several changes and modules were added into AMEN.
One major change:
- The GraphViz program is now replace by the "igraph" R library. So now, no need to
install GraphViz prior to execute AMEN.
One minor change:
- The "interaction" panel into the AMEN GUI was renamed by "network".... read more

Dear User,
IMPORTANT: The AMEN installer for windows is no more available. See the installation procedure in the README.txt file for more details on how to download, install and run AMEN.
Several changes and modules were added into AMEN. Users can now import interaction databases such as IntAct, BioGRID, MINT as well as NCBI 'interactions' file, DIP, HPRD, MPPI, CORUM and MatrixDB.
Enjoy AMEN!!!
Fred

Dear User,
IMPORTANT: The AMEN installer for windows is no more available. See the installation procedure in the README.txt file for more details on how to download, install and run AMEN.
One minor bug into the AMEN GUI was fixed.
Enjoy AMEN!!!
Fred

Dear User,
IMPORTANT: The AMEN installer for windows is no more available. See the installation procedure in the README.txt file for more details on how to download, install and run AMEN.
Three changes:
- A brand new AMEN Graphical user Interface.
- No more restrictions on length names in the interface.
- When importing EBI proteome file (.dat), ORFNames and Synonyms are also extracted.

Enjoy AMEN!!!
Fred

Dear User,
IMPORTANT: The AMEN installer for windows is no more available. See the installation procedure in the README.txt file for more details on how to download, install and run AMEN.
Two changes:
- A module is now available to pre-process the Affymetrix Exon Array as
well as Affymetrix Gene Array CEL files. Users should download the CDF file available
for each microarray in the "library files" section (into the support menu)
- A module is now available to import the Affymetrix Exon Array as
well as Affymetrix Gene Annotation files (CSV files). Users should download the CSV file available
for each microarray in the "annotation data" section (into the support menu)... read more

Dear User,
IMPORTANT: The AMEN installer for windows is no more available. See the installation procedure in the README.txt file for more details on how to download, install and run AMEN.
1 bug fixed (thanks Fred):
- AMEN was enable to install the required R packages if the path to the AMEN folder contained space characters.

Enjoy AMEN!!!
Fred

Dear User,
IMPORTANT: The AMEN installer for windows is no more available. See the installation procedure in the README.txt file for more details on how to download, install and run AMEN.
1 change:
- The missing files (deleted or moved or renamed) in the current project will not be loaded into the AMEN interface.

2 minor bugs fixed:
- Impossible to display KEGG pathways anymore.
- Impossible to select a pathway indicated into the displayed KEGG pathway. This bug is due to a change into the KEGG web site. ... read more

Dear User,
IMPORTANT: The AMEN installer for windows is no more available. See the installation procedure in the README.txt file for more details on how to download, install and execute AMEN.
3 new modules:
- A Quality-control module after normalization is now available for intensity signal data directly added to the 'Expression' panel. This module includes boxplot, scatterplot and correlation matrix pictures saved into pdf files.
- A log2-/unlog2-transformation module was added.
- A new visualization module allows user to display the expression signals using a radar view.... read more

Dear User,
IMPORTANT: User must install the 8.6beta version of Tcl/Tk (ActiveTcl) which already include the tkImg package. So user will not need to install this package.
One major change:
- During the installation process, the "TMP" folder is not required anymore. AMEN automatically creates this folder into its installation directory. Moreover AMEN automatically installs the required R packages into the "AMEN/RLIBRARIES" folder. This change should facilitate the installation for users which do not have administrator privileges. On the other hand, the user must be the owner of the installation folder ("AMEN" by default).
Apparently, there's still a problem to install automatically R packages on MAC OS. This beug should be fixed on the next version.... read more

Dear User,
IMPORTANT: User must install the 8.6beta version of Tcl/Tk (ActiveTcl) which already include the tkImg package. So user will not need to install this package.
3 beugs corrected:
- sometimes the "Profiles" module did not work depending on the signal distribution.
- better colors in KEGG pathways
- "Biological_process", "molecular_function", "cellular_component" were found always enriched in the over/under-representation module.... read more

Dear User!
AMEN v1.1.9 is released!
- IMPORTANT: User should now install the tkImg1.3 package available in sourceforge. This package will allow you to display KEGG metabolic pathways because they change their image format (GIF->PNG) and PNG format is not initially compatible in Tcl.
- One change in the hypergeometric p-value calculation.

Enjoy AMEN!
Fred

Dear all,
I'm pleased to announce a new module developer for AMEN: Aurélie Lardenois (post-doc in our lab). She is developping modules dedicated to regulatory and interaction network analysis and visualization.
Enjoy AMEN!

Deer all,
7 modules were added and twho changes occured.
Enjoy AMEN!

7 modules:
- Module to estimate if a biological entity (protein for exemple) interacts or regulates more genes/proteins in a cluster of genes as compared to whole genes (Enrichment on regulatory or interaction networks). Written by Aurélie Lardenois.
- Module to visualize these enrichments as a network. Written by Aurélie Lardenois.
- Two modules for semi-supervised k-means and PAM methods.
- Module to add gene set files (.gmt files from GSEA) into the annotation file.
- Module to normalize with positive or negative control genes.
- Module to reorganize the samples into an expression file... read more

Dear all,
Four bugs wre fixed!
Three bugs occured when expression data contained missing values in the following modules:
- Average/median expression calculation
- Standard deviation filtration
- Standardized normalization

The "affy" package does not provide the "normalize.quantiles" function anymore. AMEN now uses the "normalizeBetweenArrays" function from the "Limma" package into the quantile-quantile normalization module.
Enjoy AMEN!

Dear all,
Three bugs were fixed i the new AMEN version:
- the "DynamicTreeCut" R package was not automatically downloaded and installed into the R environment.
- there was an bug in the R script when using the "DynamicTreeCut" R package.
- Problems occured when space characters were present into the mapping or annotation filenames!
Enjoy AMEN!

Dear all,
The AMEN version 1.1.5 is out!
- one MAJOR bug was fixed and 4 changes were added

One major bug fixed:
- A problem when indexing expression data file (ExpressionPanel procedure) gave several problems in procedure using these expression data files and especially statistical modules (Standard deviation, Find similar patterns, Limma modules). These errors occured when not all the samples were selected.... read more

Dear All,
3 bugs were found and fixed in the last AMEN version 1.1.4.
Note that Statistical modules of AMEN seem not to be working when using Windows Vista. I will try to fix this problem as soon as possible.
Best regards
Fred

VERSION:1.1.3
- 19 changes and 4 bugs fixed

The AMEN_Windows_1.1.3.exe Windows 32-bit binary file automatically installs (user must have the administrative privileges) : ActiveTcl version 8.5.2.0 ; R version 2.7.1 ; GraphViz version 2.17. IMPORTANTLY, once AMEN has been successfully installed, user must directly "Launch AMEN" from the installation process to install the three integrated programs!... read more

AMEN (Annotation, Mapping, Expression and Network) is a stand-alone, unified suite of tools to manage, explore and combine biological multifaceted high-throughput data such as annotation, chromosomal location, expression and interaction data.

Dear users,
In the current version of AMEN, four changes were added and three bugs were fixed:
Four changes:
- A clustering module using the SOTA self-organizing map classification method was implemented.
- A clustering module using the dynamicTreeCut (Hybrid Adaptative Tree Cut For Hierarchical Clustering Dendograms) was implemented.
- A clustering validation module using the APN, AD, ADM, FOM, dunn, connectivity and silhouette width methods was implemented.
- Affymetrix changed its CSV annotation file format, I updated the AMEN importation module to take into account these changes.... read more

Dear users,
In the current version of AMEN, two changes were added and one minor bug was fixed
Two changes:
- The "two-class paired" SAM filtration module was added.
- The statistical filtration menu was changed. Statistical modules are now organized according to their type of filtration (time-course, two class unpaired, two class unpaired time course, ...)

One minor bug:
- Impossible to display under-representation terms.... read more

Dear All,
In the current version of AMEN, three major and one minor bugs were fixed
Three major bugs:
- the "CLARA" clustering module did not work anymore. It was just a typo mistake on a procedure name.
- the Heatmap and the Mapping modules did not work. I used "global" with a cell of a array instead of with the corresponding array.

One minor bug:
- In the new Tcl/Tk version (8.5.0) there is a bug using the "pow" option of the expr procedure. puts [expr pow(10,-1)] returns 0.10000000000001 instead of 0.1. I correct this error.... read more