The association ARMGHM

The association ARMGHM - Atlas Génétique des Cancers - is a non-profit association (french law 1901), whose goal is to host and handle the Atlas of Genetics and Cytogenetics in Oncology and Haematology (AtlasGeneticsOncology.org), to facilitate the editorial process and to permit the circulation of its content.

Built up in 1993 by Doctor Jean-Loup Huret, founder of the Atlas, the association has been chaired by Doctor Franck Viguié, and, later on, by Jean Loup Huret; Jesús María Hernández Rivas is now the chairman, from the 1st of January, 2020. The association has also a Scientific Board and the Atlas an Editorial Bard of more than 40 high level researchers and clnincians from various countries over the world.

Executive Board

Bureau of the Executive Board

	Jesús María Hernández Rivas (Salamanca, Spain) President of the association, Professor of Hematology Co-Editor in Chief of the Atlas
	Jean-Loup Huret (Quinçay, France) Past President of the association, Honorary Associate Professor and Consultant of the French Universities Co-Editor in Chief of the Atlas This email address is being protected from spambots. You need JavaScript enabled to view it. and This email address is being protected from spambots. You need JavaScript enabled to view it.
	Ana Eugenia Rodriguez Vicente (Salamanca, Spain) Secretary of the association Researcher Section Editor in the Atlas This email address is being protected from spambots. You need JavaScript enabled to view it.

Members of the Executive Board

 
Philippe Dessen,
Jean Loup Huret,
Marina Lafage,
Philippe Misserey ,
Hossein Mossafa,
Jean-Marie Nicolas,
Jesús María Hernández Rivas,
Franck Viguié,
Ana Eugenia Rodriguez Vicente,
Lucienne Michaux, représentant la Belgian Society of Human Genetics (BeSHG), Présidente du Belgian Cytogenetics Group in Haematology and Oncology (BCGHO)
Dominique Penther, représentant l'Association des Cytogénéticiens de Langue Française (ACLF), membre du bureau du Groupe Francophone de Cytogénétique Hématologique (GFCH),
Fléchère Fortin représentant l'Association de Cytogénétique du Québec

Editorial Team

The association has employed 5 collaborators full time, each holder of a MSc or a PhD, who have managed the Atlas for years with the Editor, who acknowledge their excellent work: Mohammad Ahmad, Mélanie Arsaban, Anne Malo, Carol Moreau, Vanessa Le Berre

ARMGHM

Official declaration in prefecture : 15-06-1993
n° Siret : 392 427 381 00018
n° Siren : 392 427 381
n° URSSAF : 860 200 231151
n° ASSEDIC : 39133439X8602
code NAF ("code APE"): 7219Z

Addresses of the ARMGHM

ARMGHM, at Dr Ana E. Rodríguez, Instituto de Investigación Biomédica de Salamanca, Paseo de San Vicente, 58-182, 37007 Salamanca (Spain)

Donate now

• by credit card, on our platform for secure online payment using PayPal :

Program

Enrichment with more cards

Development of the research side

- The Atlas participates in research on cancer epidemiology.

- The Atlas is part of the genome project. It is orientated towards the genome and may serve as a portal for many applications, from probes resources to genome sequences. At a time where maturation therapies and other oncogene-targeted therapies are being developed, the Atlas and its links make sense in the bioinformatics field.

Diagnostic and therapeutic decision aid

The Atlas helps the clinician in the diagnostic and in the patient treatment process: the iconography of chromosome anomalies can be compared by the cytogeneticist with his findings in a given patient, guiding his diagnosis. Next step, the clinician with a cytogenetic diagnosis may be helped by the description of the associated disease. In any case, the clinician ignores the prognostic associated with the chromosome findings in many cases (there are more than 600 leukemias!), and the Atlas would guide his treatment decision: a bone marrow graft may kill, it should be reserved for highly aggressive leukemias, and that risk must not be taken when the leukaemia would be cured in any case. The Atlas is indispensable in particular in rare diseases (and rare diseases, because they are numerous, are frequent). We must continue to develop this part.

Informatics developments

Atlas web site becoming a true database - from old html to xml: the Atlas is supported by an ancient html system, made in 1997, at a time where Internet was a starting technology (we were one of the pioneers !). Systems have evolved, since. A modern data base will soon replace our old html.

Enhancement of the Atlas position in the scientific literature world:

We have therefore developed an 'electronic journal' version of the Atlas, comprising 2 154 articles in 87 issues from 1998 making 7 169 pages. See: http://documents.irevues.inist.fr/handle/2042/15655 .

# ##################################################
# A. General pipeline for updating the Atlas #
# ##################################################
# 2017-07-29 Dessen Philippe ( This email address is being protected from spambots. You need JavaScript enabled to view it. )
#
# all scripts are running in $CYT_DIR/Scripts directory
#
#!/usr/bin/bash
# ===============================================================
# AUTHOR : P. DESSEN
# DATE : Mon Aug 2 18:27:27 MET DST 1999
# FILE : maj_full.sh
# GOAL : Automatic updating of html files from txt files
# RUN : ./maj_full.sh 2>/dev/null > indexation.log &
# ===============================================================
cd $CYT_DIR/Scripts
date1=`date`
echo "start " $date1
# I. Generation of Genes links from Anomalies, Tumors, Kprones
# =============================================================
# Identification of all links (CC: TXT: ID: > in all txt files

./ident_hyper.pl

# Generation of several files
# hyper_Genes0.txt
# hyper_Anomalies.txt
# hyper_Tumors.txt
# hyper_Kprones.txt
# followed by concatenation in ./Scripts/Data/hyper_All.txt
# creation of Data if does exist

./otheranom_gene2.pl

# otheranom_gene2.pl in Scripts
# creation of an html bloc in Genes html_files
# with relation with Anomalies files
# Generation of id.html files in the directory
# ../Genes/AnomLinks/1.html
# 2 distinct extracts
# 1. genes associated with a FUSION_GENE in Anom files
# 2. genes associated with Anom in hyperlinks <CC: TXT: ID:>
# use the file ./Data/hyper_All.txt
# and the file ./genes_gc.txt (indexation of filename with NAME)

./othertumor_gene2.pl

# othertumor_gene.pl dans Scripts
# creation of an html bloc in Genes html_files
# with relation with Tumors files
# Generation of id.html files in the directory
# ../Genes/TumorsLinks/1.html
# 2 distinct extracts
# 1. genes associated with FUSION_GENE in the Tumors files
# 2. genes associated with Tumors in hyperlinks <CC: TXT: ID:>

./otherkprone_gene2.pl

# otherkprone_gene2.pl in Scripts
# creation of an html bloc in Genes html_files
# Generation of id.html files in the directory
# ../Genes/KpronesLinks/10001.html
# 2 distinct extractions
# 1. genes associated with SYMBOL dans les fiches Kprones
# 2. genes associated with Kprones in hyperlinks <CC: TXT: ID:>

./othergene_anom.pl
# othergene_anom.pl id_chrom_clin in Scripts
# creation of a html bloc html for Anomalies
# in the directory
# ../Anomalies/GeneLinks/1001.html

./othertransloc_anom.pl

# othertransloc_anom.pl in Scripts
# creation of a transloc html bloc for Anomalies
# Validation in first the creation of the fil
# ./Data/hyper_translocAll.txt
# with the script extract_transloc_name.pl
#
# Generation of links files of transloc files with Anomalies
# File created by extract_transloc_name.pl from
# ./Data/hyper_translocAll.txt

./othergene_tumor.pl

# othergene_tumor.pl dans Scripts
# uses the file ./Data/hyper_All.txt
# creation of an html bloc for Tumors in
# ../Tumors/GeneLinks/5001.html
# Generation of links of Genes files with Tumors
# File created by extract_gene_name.pl from
# ./Data/hyper_All.txt
#
require "./miscfct.pl"; # fonctions diverses
require "gereDbid.pl"; # -- pour l'id des genes




./cytatlas
$ ls -ld */*Links
drwxrwxr-x+ 1 phd None 0 1 juil. 09:28 Anomalies/GeneLinks
drwxrwxr-x+ 1 phd None 0 1 juil. 09:24 Genes/AnomLinks
drwxrwxr-x+ 1 phd None 0 1 juil. 09:27 Genes/KproneLinks
drwxrwxr-x+ 1 phd None 0 1 juil. 09:27 Genes/TumorLinks
drwxrwxr-x+ 1 phd None 0 1 juil. 09:28 Tumors/GeneLinks


#
# II. Generation of Genes txt and html files
# ==========================================
rm ../Genes/GC_*.txt
rm -f ../../chromcancer/Genes/GC_*.html

# for the 2 sets of non annotated genes
./gen_genes_gn.sh
./gen_genes_gc.sh
# for the set of experted genes (Genes0)

./gen_gene2.sh

# creation of links from GC_annot_genes to AtlasFilename
# This permits to address url either bt AtlasFilename or by
# symolic url "GC_<symbol>.html"

./gen_genes_link.sh
#
# III. indexation
# ===============
./indexation.sh
#
# IV. Generation of all html files
# ================================
# preliminary
# generation of preliminary files LK_xxx.html , TU_xxx.html ..
# for forsale files

./maj_prelim.sh
#
# generation of html cards files
./gen_anom.sh
./gen_kprone.sh
./gen_tumor.sh
./gen_report.sh
./gen_educ.sh
./gen_deep.sh
#./gen_study.sh

# chromosome pages indexation
./index_bychrom3.pl

# reindexation (second round : not mandatory ?)
./indexation.sh
# regeneration of html cards (after reindexation)
./gen_gene2.sh
./gen_anom.sh
./gen_kprone.sh
./gen_tumor.sh
./gen.educ.sh
./gen_deep.sh
./gen_report.sh

# Management of images
cp_anom_img.sh
cp_deep_img.sh
cp_educ_img.sh
cp_genes_img.sh
cp_kpr_img.sh
cp_report_img.sh
cp_tum_img.sh
date2=`date`
echo "end " $date2
echo "maj_full.sh " $date1 $date2
echo "==================================="
#
mail -s "Atlas_IGR__maj_full " This email address is being protected from spambots. You need JavaScript enabled to view it. < nohup.out
mail -s "Atlas_IGR__maj_full " This email address is being protected from spambots. You need JavaScript enabled to view it. < indexation.log


# ##################################
# B. Indexation procedure #
# ##################################

# Use indexation.sh after any modifications on cards to maintain
# updated indexes and links

# indexation.sh

#!/bin/bash
# ==============================================================
# AUTHOR : P.DESSEN
# DATE : 11.12.99
# FILE :./indexation.sh
# GOAL : automatic generation of indexes and catalogs
# ex: ./indexation.sh 2 >/dev/null > indexation_20160306.log &
# to be run in $CYT_DIR/Scripts
# ==============================================================
# ------------------------------------------------
# ATLAS environnement variables
# ------------------------------------------------
# CYT_DIR needs to be defined (in $HOME/cytatlas.sh)
# CYT_DIR='..'
source $HOME/cytatlas.sh
GENE_DIR=$CYT_DIR/Genes
ANOM_DIR=$CYT_DIR/Anomalies
TUMOR_DIR=$CYT_DIR/Tumors
KPRON_DIR=$CYT_DIR/Kprones
REPORT_DIR=$CYT_DIR/Reports
STUDY_DIR=$CYT_DIR/StudyGroup
DEEP_DIR=$CYT_DIR/Deep
EDUC_DIR=$CYT_DIR/Educ
WGENE_DIR=$CYTW_DIR/Genes
WANOM_DIR=$CYTW_DIR/Anomalies
WTUMOR_DIR=$CYTW_DIR/Tumors
WKPRON_DIR=$CYTW_DIR/Kprones
WREPORT_DIR=$CYTW_DIR/Reports
WDEEP_DIR=$CYTW_DIR/Deep
WEDUC_DIR=$CYTW_DIR/Educ
WCOLLAB_DIR=$CYTW_DIR/Collab
SCRIPT_DIR=$CYT_DIR/Scripts
export GENE_DIR ANOM_DIR TUMOR_DIR KPRON_DIR SCRIPT_DIR
export REPORT_DIR STUDY_DIR DEEP_DIR EDUC_DIR
export WGENE_DIR WANOM_DIR WTUMOR_DIR WKPRON_DIR
export WREPORT_DIR WDEEP_DIR WEDUC_DIR WCOLLAB_DIR
# ----------------------------------------------
echo "--------------------------------------------------------"
echo " Atlas indexation
echo "`date`
echo "--------------------------------------------------------"
DATEIN=`date`
# pretraitment
# Regeneration of GC.txt files_
echo "Generation of GC_xxx.txt files "
echo "the genes_gc.txt and genes_gn.txt files need to be updated\n"
perl $CYT_DIR/Scripts/gener_gc.pl genes_gc.txt 2>/dev/null
perl $CYT_DIR/Scripts/gener_gc.pl genes_gn.txt 2>/dev/null
ls -l genes_gc.txt
ls -l genes_gn.txt
# ----------------------------------------------------------
# Build of the database of all objects of Atlas
# ObjDB.txt contains the list
# ----------------------------------------------------------
echo "Build of the database ObjDB.txt"
echo "`date`";
perl $CYT_DIR/Scripts/x_id.pl # build if ObjDB.txt
ls -l ObjDB.txt
# ----------------------------------------------------------
# Build of the Genes : file ObjDB0.txt
perl $CYT_DIR/Scripts/majgene.pl 2>/dev/null #
ls -l ObjDB0.txt
# ----------------------------------------------------------
# catalog maintains several features of each card
echo "Creation of a catalog"
perl $CYT_DIR/Scripts/catalog.pl 2>/dev/null #
ls -l catalog
# ----------------------------------------------------------
# reconstruction des index divers
echo "Build of ObjDB1.txt and ObjDB2.txt"
perl $CYT_DIR/Scripts/majfich.pl 2>/dev/null #
ls -l ObjDB1.txt
ls -l ObjDB2.txt
echo "Build of ObjDB1.html"
perl $CYT_DIR/Scripts/majfich2.pl 2>/dev/null #
echo "Build of ObjDB3.txt and ObjDB4.txt"
perl $CYT_DIR/Scripts/majfich3.pl 2>/dev/null #
ls -l ObjDB3.txt
ls -l ObjDB4.txt
echo "Build of ObjDB5.txt (correlation anom tumor genes) and ObjDB7.txt"
perl $CYT_DIR/Scripts/majfich5.pl 2>/dev/null
ls -l ObjDB5.txt
# ----------------------------------------------------------
# Generation of tabulated files for catalog and forsale
# catalog_out.txt and forsale_out.txt
perl $CYT_DIR/Scripts/forsale_out.pl forsale 2>/dev/null # perl $CYT_DIR/Scripts/forsale_out.pl catalog 2>/dev/null #
ls -l forsale_out.txt
ls -l catalog_out.txt
# ----------------------------------------------------------
# modification of catalog_out.txt depending of the reserved file
perl $CYT_DIR/Scripts/reserved.pl
# ----------------------------------------------------------
# concatenation of catalogs (catalog + forsale)
cat $CYT_DIR/Scripts/catalog_out.txt > catalog_full.txt
cat $CYT_DIR/Scripts/forsale_out.txt >> catalog_full.txt
ls -l catalog_full.txt
# Generation of a expertized Gene file
grep GENE ../../chromcancer/Collab/catalog_out.txt | awk -F\t '{print $3,"\t",$5} ' |grep -v GC_ > gce.txt
# ----------------------------------------------------------
#
echo "============= End of rebuild ================"
# ----------------------------------------------------------
# --- Indexations -----
# creation of several indexes for Genes
# index of genes by symbol
# index of objects by chromosome.
# ----------------------------------------------------------
echo " "
echo " --- Indexation des genes ---"
cd $GENE_DIR
$CYT_DIR/Scripts/index_gene2.pl 2>/dev/null > $WGENE_DIR/Geneliste.html
ls -l $WGENE_DIR/Geneliste.html
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/index_genes_red.pl
echo " "
echo " --- Indexation of Anomalies ---"
$CYT_DIR/Scripts/index_anom2.pl 2>/dev/null > $WANOM_DIR/Anomliste.html
$CYT_DIR/Scripts/index_lymphoma.pl 2>/dev/null > $WANOM_DIR/Lymphomaliste.html
$CYT_DIR/Scripts/index_myeloid.pl 2>/dev/null > $WANOM_DIR/Myeloidliste.html
ls -l $WANOM_DIR/Anomliste.html
ls -l $WANOM_DIR/Lymphomaliste.html
ls -l $WANOM_DIR/Myeloidliste.html
echo " "
echo " --- Indexation of Tumors ---"
cd $TUMOR_DIR
$CYT_DIR/Scripts/index_tumor2.pl 2>/dev/null > $WTUMOR_DIR/Tumorliste.html
ls -l $WTUMOR_DIR/Tumorliste.html
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/solid_section.pl 2>/dev/null
echo " "
echo " --- Indexation of Kprones ---"
cd $KPRON_DIR
$CYT_DIR/Scripts/index_kprone.pl 2>/dev/null > $WKPRON_DIR/Kproneliste.html
ls -l $WKPRON_DIR/Kproneliste.html
echo " "
echo " --- Indexation of Reports ---"
cd $REPORT_DIR
$CYT_DIR/Scripts/index_report.pl 2>/dev/null > $WREPORT_DIR/Reportliste.html
ls -l $WREPORT_DIR/Reportliste.html
echo " --- Indexation of Deep ---"
cd $DEEP_DIR
$CYT_DIR/Scripts/index_deep.pl 2>/dev/null > $WDEEP_DIR/deeplist.html
ls -l $WDEEP_DIR/deeplist.html
cd $CYT_DIR/Scripts
chmod a+r $CYTW_DIR/Genes/Geneliste.html
chmod a+r $CYTW_DIR/Anomalies/Anomliste.html
chmod a+r $CYTW_DIR/Tumors/Tumorliste.html
chmod a+r $CYTW_DIR/Kprones/Kproneliste.html
chmod a+r $CYTW_DIR/Reports/Reportliste.html
chmod a+r $CYTW_DIR/Deep/deeplist.html
# ----------------------------------------------------------
#
## echo " "
## echo "--- Indexation of GeneLink ---"
#### Normally done in maj_full.sh #####
#### $CYT_DIR/Scripts/ident_hyper.pl
#### $CYT_DIR/Scripts/othergene_anom.pl
#### $CYT_DIR/Scripts/othergene_tumor.pl
#### $CYT_DIR/Scripts/othergene_kprone.pl
#### $CYT_DIR/Scripts/otheranom_gene2.pl
#### $CYT_DIR/Scripts/othertransloc_anom.pl
#### $CYT_DIR/Scripts/othertumor_gene2.pl
#### $CYT_DIR/Scripts/otherkprone_gene2.pl
# ----------------------------------------------------------
#
echo " "
echo " --- Mitelman Files ---"
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/report2mitelman.pl 2> /dev/null
$CYT_DIR/Scripts/report2mitelman2.pl2> /dev/null
$CYT_DIR/Scripts/a0_mitel2jlh.pl > ../../chromcancer/Collab/mitelman_anom.txt
echo ""
# ----------------------------------------------------------
#
#echo " ----- Indexation of Genes GC --- "
#cd $CYT_DIR/Scripts
#perl $CYT_DIR/Scripts/index_genes_gc.sh
# ----------------------------------------------------------
#
echo " "
echo " --- Indexation by chrom ---"
cd $CYT_DIR/Scripts
perl $CYT_DIR/Scripts/index_bychrom3.pl 2> /dev/null
perl $CYT_DIR/Scripts/index_genes_chromg.pl 2>/dev/null
echo " "
echo " --- Creation of th file cytoentities.html ---"
perl $CYT_DIR/Scripts/cytoentities.pl 2> /dev/null
perl $CYT_DIR/Scripts/cytoentities2.pl 2> /dev/null
# ----------------------------------------------------------
### echo " --- Indexation of the file hugo2url.dat ---"
### perl $CYT_DIR/Scripts/hugo2url.pl
# ----------------------------------------------------------
echo " "
echo " --- Creation of file GeneExtlnk.txt ---"
perl $CYT_DIR/Scripts/extlnk2.pl Genes 2>/dev/null
echo " "
echo " --- Creation of file GeneExtlnk.html ---"
perl $CYT_DIR/Scripts/extlnk3.pl Genes 2>/dev/null
echo " "
echo " --- Creation of file GeneLink.txt ---"
perl $CYT_DIR/Scripts/extlnk4.pl Genes
# ----------------------------------------------------------
## indexation des authors
cd $CYT_DIR/Scripts
perl indxauth.pl 2>/dev/null
ls -l IndxAuth.txt
perl indxauth2.pl 2>/dev/null
ls -l indxauth2.pl
ls -l IndxAuth.html
ls -l IndxAuth2.txt
echo "Be careful : the key_date_pays.txt file may be updated...."
ls -l key_date_pays.txt
echo "Indexation IndxAuth3.txt "
perl indxauth3.pl 2>/dev/null
ls -l IndxAuth3.txt
echo "Indexation IndxAuth4.txt "
perl traitauth.pl 2>/dev/null > ./IndxAuth4.txt
ls -l IndxAuth4.txt
echo "Indexation IndxAuth5.txt "
perl indxauth5.pl 2>/dev/null
ls -l IndxAuth5.txt
echo "Indexation IndxAuth6.txt "
perl indxauth6.pl 2>/dev/null
ls -l IndxAuth6.txt
echo "Indexation IndxAuth1.txt "
perl indxauth1.pl 2>/dev/null
ls -l IndxAuth1.txt
## copies of authors indexes in Collab (Archive)
echo "mv to ../../chromcancer/Collab "
mv IndxAuth.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth.txt
mv IndxAuth.html $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth.html
mv IndxAuth2.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth2.txt
mv IndxAuth2.html $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth.html
mv IndxAuth3.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth3.txt
mv IndxAuth4.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth4.txt
mv IndxAuth5.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth5.txt
mv IndxAuth6.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth6.txt
mv IndxAuth1.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth1.txt
mv IndxAuth1.html $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth1.html
cp -p key_date_pays.txt $CYTW_DIR/Collab
# ----------------------------------------------------------
# Generation of Nosology
echo "Reconsruction des Nosology"
perl $CYT_DIR/Scripts/solid_nosology2.pl 2>/dev/null
ls -l $CYTW_DIR/Tumors/Solid_Nosol*.html
# ----------------------------------------------------------
## indexation des images
echo "Indexation of images"
perl $CYT_DIR/Scripts/indximg.pl 2>/dev/null
cp -p $CYT_DIR/Scripts/IndxImg.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxImg.txt
# ----------------------------------------------------------
### indexation of PMID
echo "Indexation of PMID"
perl $CYT_DIR/Scripts/parsing_med.pl 2>/dev/null
## indexation of bibliographic references
echo "indexation of bibliographic references"
perl $CYT_DIR/Scripts/parsing_ref.pl 2/dev/null > ../../chromcancer/Collab/url_ref.txt
ls -l ../../chromcancer/Collab/url_ref.txt
## indexation of bibliographic references
echo "indexation of bibliographic references"
perl $CYT_DIR/Scripts/parsing_biblio.pl 2>/dev/null > ../../chromcancer/Collab/parsing_biblio.txt
ls -l ../../chromcancer/Collab/parsing_biblio.txt
# ----------------------------------------------------------
cd $CYT_DIR/Scripts
echo "copies dans ../../chromcancer/Collab"
# copies in ../../chromcancer/Collab
## copy des ObjDB.txt dans $CYTW_DIR/Collab/
cp -p ObjDB*.txt $CYTW_DIR/Collab
## copy of ObjDB1.html in $CYTW_DIR/Collab/
mv ObjDB*.html $CYTW_DIR/Collab
## copy of GeneExtlnk.txt in $CYTW_DIR/Collab/
mv GeneExtlnk.txt $CYTW_DIR/Collab
mv GeneExtlnk.html $CYTW_DIR/Collab
##mv $CYT_DIR/Scripts/GeneLink.txt $CYTW_DIR/Collab
## copy of cytoentities.html
## copie of tabulated files : forsale et catalog
cp forsale_out.txt $CYTW_DIR/Collab
cp catalog_out.txt $CYTW_DIR/Collab
cp forsale $CYTW_DIR/Collab
cp catalog $CYTW_DIR/Collab
cp catalog_full.txt $CYTW_DIR/Collab
## copie du fichier genes_cancer.txt
cp -p genes_gc.txt $CYTW_DIR/Collab
cp -p genes_gn.txt $CYTW_DIR/Collab
cp -p genes_gcr.txt $CYTW_DIR/Collab
## copy of genes non_cancer
cp -p genes_gn.txt $CYTW_DIR/Collab
# copy of parsing_med
cp -p list_refmedline.txt $CYTW_DIR/Collab
#
chmod 664 $CYTW_DIR/Collab/*.txt
chmod 664 $CYTW_DIR/Collab/*.html
# ----------------------------------------------------------
# generation of the genes atlas file
echo "Generation du fichier gene_atlas.txt "
filtcol genes_gc.txt 45 "<>" "-" > $CYTW_DIR/Collab/genes_atlas.txt
ls -l $CYTW_DIR/Collab/genes_atlas.txt
# ----------------------------------------------------------
# generation of the humprot_atlas.txt file
prtab $CYTW_DIR/Collab/genes_atlas.txt 1 2 10-12 22-23 46 > $CYTW_DIR/Collab/humprot_atlas.txt
echo "generation of the humprot_atlas.txt file"
ls -l $CYTW_DIR/Collab/humprot_atlas.txt
# ----------------------------------------------------------
## copy of Amplicons
echo "copy of amplicons"
cp -p $CYT_DIR/Ampl/*.html $CYTW_DIR/Ampl
cp -p $CYT_DIR/Ampl/Images/*.jpg $CYTW_DIR/Ampl/Images
# ----------------------------------------------------------
# Categories
# indexation of images
cd $CYT_DIR/Scripts
echo "indexation of categories "
cd $CYT_DIR/Scripts/Data/Category_editor
./prepcat2.sh
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/indximgcategory.pl 2>/dev/null
$CYT_DIR/Scripts/index_category2.pl 2>/dev/null
ls -l Categories_img.txt
ls -l category_img.txt
ls -l category_lst.txt
cp -p catdeepgene.txt $CYTW_DIR/Collab/catdeepgene.txt
cp -p Categories_img.txt $CYTW_DIR/Collab/Categories_img.txt
cp -p category_img.txt $CYTW_DIR/Collab/
cp -p category_lst.txt $CYTW_DIR/Collab/
# ----------------------------------------------------------
# generation of atlas_statuts
perl $CYT_DIR/Scripts/atlas_status.pl 2> /dev/null
echo "rebuild of Status directories"
ls -l $CYTW_DIR/Status/Status_*html
# ----------------------------------------------------------
# Indexation of ICD
perl $CYT_DIR/Scripts/index_icd_topo.pl 2> /dev/null
perl $CYT_DIR/Scripts/index_icd_morph.pl 2> /dev/null
# ----------------------------------------------------------
# Update of recents files (2 years)
echo "Update of recents files (2 years) "
# lastfiles : Report.html
$CYT_DIR/Scripts/lastfile.pl 2>/dev/null
ls -l $CYTW_DIR/Recent.html
# ----------------------------------------------------------
# Statfiches
echo "statfiches "
$CYT_DIR/Scripts/statfiches.pl 2>/dev/null
ls -l $CYTW_DIR/Collab/StatFiches.html
# ----------------------------------------------------------
# Update of Backpage
# modifBackpage creates a Backpage2.html file
# the addlist file contains new authors
#$CYT_DIR/Scripts/modifBackpage addlist
#cp $CYTW_DIR/BackpageAbout.html $CYTW_DIR/BackpageAbout0.html #mv $CYTW_DIR/BackpageAbout2.html $CYTW_DIR/BackpageAbout.html
cp $CYT_DIR/Scripts/listeAuthBPage.txt $CYTW_DIR/Collab/
# ----------------------------------------------------------
# creation of a synthesis file JLH ObjDB6.txt
echo "creation of ObjDB6.txt "
majfich4.pl 2>/dev/null
ls -l $CYTW_DIR/Collab/ObjDB6.txt
# ----------------------------------------------------------
# List of regular updates (depending of releases)
# creation of chromcancer/cosmic_study.html
# read of ../Standards/COSMIC/cosmic_study.txt
./cosmic2html.pl
#
# ICGC : list of projects
# creation of ../../chromcancer/icgc_projects.html
# Lecture de ../TCGA_ICGC/ICGC/cgc_projects.txt
./icgc2html.pl
#
# copies of the Band files
cp $CYT_DIR/Scripts/tmp_allgenes.txt $CYTW_DIR/Collab
cp $CYT_DIR/Scripts/tmp_allanom.txt $CYTW_DIR/Collab
cp $CYT_DIR/Scripts/anom_bandall.txt $CYTW_DIR/Collab
cp $CYT_DIR/Scripts/gene_bandall.txt $CYTW_DIR/Collab
# list of files on archive ( Collab )
echo "list of files on archive $CYTW/Collab "
ls -lt $CYTW_DIR/Collab
# Update of the data on index.html
# Sun Aug 12 12:09:46 MEST 2007
# Sat Nov 21 10:28:10 MET 2009
# Thu Jul 9 15:36:42 MEST 2015
DATEOUT=`date`
# to be adapted to time/date format (depending of UNIX)
perl -pi.bak -ne 's@\S+ \S+ \d+ \d+:\d+:\d+ MEST 20\d\d@$DATEOUT@' $CYTW_DIR/index.html
rm $CYTW_DIR/index.html.bak
echo "start of indexation $DATEIN"
echo "end of indexation $DATEOUT"
# ----------------------------------------------------------
# statistics
$CYT_DIR/Scripts/stat_atlas.pl > $CYTW_DIR/stat_atlas.html
#
echo "Do not forgot to update the key_date_pays.txt file"
ls -l key_date_pays.txt
# Update of the MySQL indexation (only on INIST)
# ----------------------------------------------------------
############################################################

TEMPLATES

TEMPLATE for GENES

II- TEMPLATE for LEUKEMIAS

III- TEMPLATE for SOLID TUMORS

IV- TEMPLATE for CANCER-PRONE DISEASES

Editorial workflow in the Atlas

The Atlas editorial team stands in need of Section Editors (see http://atlasgeneticsoncology.org/BackpageAbout.html#EDITORIAL ) devoting 10% of their time for the Atlas.

The workflow detailed herein below applies when MSc students/workers are involved in the process. Indeed, a senior researcher will skim through the various steps described below. However a secretary's active watch on forthcoming papers from the various authors is needed (like an appointment calendar). Moreover, when the Atlas has evolved into a true database with an automated editorial process, many of these time consuming tasks will vanish.

For each of the themes included in the atlas (genes, leukemias, solid tumors, hereditary diseases involving increased risk of cancer, "deep insight" …), the editorial team is tasked with appraising the subjects (or "items") lending themselves to publication on the site.

As regards genes, for instance, usinga predefined list of the genes potentially implicated in cancer (a list determined by algorithms for different data bases by Philippe Dessen, the data base manager), the editorial team is initially tasked with verifying the implication (or non-implication) of these genes in carcinogenesis. With this in mind, they study the existing bibliography, primarily on the basis of the information contained in PubMed. They then endeavor to determine whether or not the published data suffice to justify a detailed written review.

As regards the other themes (leukemias, solid tumors, hereditary diseases involving increased risk of cancer...), the bibliographic research is also carried out from PubMed, and also on specialized sites (Mitelman, Orphanet, OMIM, WHO, …). This research phase favors subjects for which enough recent publications are available to allow for high-quality reviews.

Finally, the editorial team decides whether or not a given subject will constitute an item justifying publication. After that, it is a matter of searching for and selecting the author in the best position to write this review.

Once a subject has been determined, the editorial team conducts a search of recent publications in view of choosing the author/the team in the best position to write something for the Atlas: their second appraisal. Concerning their choice, the following factors have got to be taken into account: number of publications by the author, the impact factor of his or her publications, and the author's status: clinician, hospital-based biologist, researcher. The author's disciplines are likewise taken into consideration: oncology, a specific organ, cytogenetic biology, molecular biology, cellular biology, physiopathology, etc. As regards teams, a multidisciplinary team will be preferred.

This is a highly sensitive step. According to the author chosen, the quality of the review is likely to vary, and its scientific orientation will be more or less fundamental or clinical.

Other selection criteria include: qualities of clarity in data presentation, synthesis and the use of schemas or medical imagery (in the broad sense of the word, including anatomopathology and chromosomes).

Along with the different items (genes, leukemias, solid tumors...), all important data on the authors are conserved in dedicated files.

And for each gene, the spreadsheets inventory information on its implication, as well as all other information deemed useful for future research (authors to be contacted, their contact information, e-mail exchanges, agreement to write an article, speed in production, and subjects to be reserved for a given author...). Totally indispensable, the spreadsheets are of concrete use during each phase of the work. They need to be ergonomic, and evolve according to changing needs.

For each theme in the Atlas (Genes, Leukemias, Solid Tumors, Hereditary Diseases involving increased risk of cancer, "deep Insights", Teaching Chapters), there exists a dedicated spreadsheet.

Each spreadsheet provides a list of the subjects studied, the relevant dates, as well as the subjects to be studied, for which the right authors remain to be found.

The spreadsheets are updated daily, and new, potentially interesting subjects are added periodically. This supplementary material is enriched by readings of articles from the literature and by analysis of the articles received by the Atlas.

Each subject is designated by a specific and numbered identifier facilitating the establishment of internal links as the files are being edited.

Possible duplicate files are regularly sought out and subjected to analysis, and the spreadsheets are consequently "cleaned".

For an example, see below: Extracts from the "Genes" spreadsheet, which contains 9000 lines.

The authors are contacted through a common e-mail account using predetermined contact e-mail coordinates.

The e-mails are sent once a week, at the beginning of the week, as it has been observed that the highest response rate occurs at that time. On the same token, some times of the year are not conducive to soliciting authors who tend to be busy with applications for grants ... or on holiday. These periods are avoided as much as possible.

When an author fails to answer, he is re-contacted two or three times. If, after that, he still fails to answer, another author is sought out...

Author response statistics: 55% of the authors do not respond to the invitation; 25% of them refuse; 20% agree.

When authors refuse or do not respond, the process of searching for the right author is reinitiated. If no other author can or will write the requested review, the team will wait for new research to be published..

When, on the other hand, an author accepts, the team consults him on the time frame he thinks he shall need prior to sending his completed article. The publishing flow is thereby managed, both for the Internet site and the PDF journal. A model of writing for the review is given the author, who concomitantly receives relevant editorial information.

Quite frequently, articles fail to arrive within the allotted time. The status of ongoing articles has got to be regularly monitored, and reminder notes need to be sent.

It also often happens that notwithstanding an initially positive response, authors do not respond to reminder notes, or else they withdraw from the project. In those cases, search for the right author resumes.

Assistance for authors: Quite frequently, authors ask questions (deadlines , explanations pertaining to various details...) that call for timely responses.

Once the article has been received, the completed worksheet is registered on a common server.

The information is also recorded on common spreadsheets, in a common notebook dedicated to the editors' ongoing activities; it is also displayed on wall calendars providing overall perspective on publication flows.

With these calendars, the editorial team can rapidly apprise itself of a possible lack of articles for the PDF journals and try to optimally manage the flow of arriving articles. Unfortunately, given the fact that the authors are the ones who determine their sending dates, substantial variations in publication flow may come to exist, and not be easy to manage.

The articles received are reread by internal referees; 97% of them (in fact all the articles, except for clinical case reports) are reviews of the literature written at the request of the Atlas editorial board; they are known as "commissioned papers".It should be noted that the authors were preselected according to rigorously applied criteria preliminarily to their writing of an article. Following receipt, the process of rereading and assessment of articles is implemented by the Atlas editorial board. It should also be noted that as the process draws to a close, the board member having chosen the subject (and subsequently the author himself) possesses a precise overall vision as to what the article is supposed to produce (quantity of knowledge in molecular biology or clinical research on a given gene...).

Articles that do not correspond to the publication criteria or that do not provide a sufficiently detailed report on the knowledge available on the subject are sent back for revision. The editorial team remains vigilant, and about 20% of the articles submitted are indeed sent back for revision. It is often necessary to send reminders to the authors, before receiving the revised version (loss of time).

The clinical case studies in hematology (the remaining 3%) are subjected to an external assessment process involving 4 or 5 experts, while the final decision is made by the Atlas editor-in-chief. Practically all the clinical case studies are reviewed by the authors at least one time prior to publication; only 8% are immediately accepted, 68% are accepted following revision, and 24% of the articles having been submitted are finally refused.

Once the articles have been accepted, they are processed so that they can be placed on line by the data base manager.

The articles are to be formatted according to a strictly applied computational model in order to be properly handled by the scripts of the data base manager (see, as an example, the form below).

The text must be painstakingly reread so as to correct possible mistakes (typos, grammar, spelling...),and each bibliographical reference cited in the next has got to be verified and corrected (if need be).

The article header (the different tags or tracking devices allowing for indexing of the form in different parts of the data base in accordance with different criteria) must be carefully filled out, using the metadata contained in the article. The metadata will permit the data base manager to integrate the form within the site so that it can be inventoried with regard to the dedicated lists.

The articles in the Atlas must follow a predetermined model; each paragraph of the review must be included within the tags, and the text must be formatted according to a computer encoding system. Special characters (accent marks, Greek letters, symbols…ex: integrin &alpha;&nu;&beta;3) must be coded in the HTML format so that their posting on the website be correct.

In the text itself, all potential internal links to other items contained in the Atlas (genes, leukemias, solid tumors...) must be identified, and internal links created in such a way that readers are directed, if they wish, to other articles in the Atlas. New subjects for the Atlas are often found while the forms are being processed, and added to the shared spreadsheets.

Most often, the bibliography contains 50 to 100 references, and it has got to be processed in a predetermined format.

The articles also contain images, which are processed by Photoshop software. More often than not, the size of the images requires rectification, and the background of the image has got to be rendered transparent. Moreover, the text may need rewriting when it is too blurry or has been degraded due to the change in size.

Once processing of the worksheet has been completed, it is put through a simulator so as to verify the correctness of its formatting, and also so as to make sure that no component remains invisible, as happens when a closing tag such as > is forgotten.

The file and the attached images are then sent for validation to Jean-Loup Huret, the editor-in-chief, and subsequently to the data base manager for uploading or posting on line.

"Deep Insight" and "Educational items" constitute special cases. As these files are "free format" and do not correspond to a precise model, they are directly processed using specialized software (the Dreamweaver website-editing software) in the HTML format. For these files, it is necessary to carry out all coding and page layout in HTML.

Example below : Partial formatting of an article: In the example given below, any and all parts of the text in color are subjected to special processing.

BEGIN_HEADER

FILENAMESH3PXD2AID45995ch10q24.txt

CLASSE GENE

ID45995

LOCUSID

TRI_PAR_CHROMOSOME10

TRANSLOC t(10;10)(q24;q24) SH3PXD2A/OBFC1

TRANSLOC t(10;13)(q24;q14) SH3PXD2A/RB1

FUSION_GENESH3PXD2A/OBFC1

FUSION_GENESH3PXD2A/RB1

CATEGORYCytoskeleton

END_HEADER

etc..

etc...

FUNCTIONTKS5 was initially identified as a substrate for <CC: TXT:SRC ID: 448> (Lock et al., 1998), and was subsequently shown to play a critical role in invadosome formation in multiple cell types (Courtneidge, 2011; Murphy and Courtneidge, 2011; Paz et al., 2013). <BR>

FUNCTIONFull-length TKS5 functions as an adaptor for recruiting other proteins to the cell membrane for invadosome formation. The recruitment of TKS5 to the cell membrane depends on its PX domain and phosphorylation by Src (Abram et al., 2003). It has been proposed that phosphorylation of TKS5 releases its PX domain from intramolecular interaction and allows TKS5 to bind to cell membrane phosphatidylinositol lipids, such as phosphatidylinositol-3,4-bisphosphate (PI(3,4)P₂) (Abram et al., 2003; Oikawa et al., 2008). At the cell membrane, TKS5 is thought to interact with multiple components of invadosomes either directly or indirectly, and thereby mediates invadosome formation and maturation (Sharma et al., 2013). These interacting partners includes adaptor proteins and actin regulatory proteins, such as <CC: TXT:NCK1 ID:41505>, <CC: TXT:NCK2 ID:52582>, <CC: TXT:GRB2 ID: 386>, <CC: TXT: CTTN ID: 369> (Cortactin), <CC: TXT: WASL ID: 42803> (N-WASP), <CC: TXT: ACTR2ID: 49744<CC: TXT: ACTR3ID:46303> (Arp2/3) complex, and <CC: TXT: ARHGAP35 ID: 52237> (p190RhoGAP) (Crimaldi et al., 2009; Oikawa et al., 2008; Stylli et al., 2009).<BR>

FUNCTION TKS5 also interacts with <CC: TXT:NOXA1 ID:41563> and <CC: TXT: CYBA ID: 43882> (p22phox), which are components of the NADPH oxidase complex, and thereby promotes reactive oxygen species (ROS) production by NOX enzymes at invadosomes (Diaz et al., 2009; Gianni et al., 2010; 2009).ROS have been shown to facilitate invadosome formation by maintaining or amplifying the phosphorylation of TKS5. As such, TKS5 is thought to promote invadosome formation via ROS in a positive feedback loop.<BR>

FUNCTION Finally, TKS5 has also been shown to interact with members of the ADAM family metalloproteases, specifically <CC: TXT:ADAM12 ID:44084>, <CC: TXT:ADAM15 ID:46345>, <CC: TXT:ADAM19 ID:46837>(Abram et al., 2003). It is believed that Tks5 recruits theses proteases to the invadosome foci for processing growth factors and regulating cell motility. For example, ADAM12 has been shown to promote ectodomain shedding of <CC: TXT:HBEGF ID: 40369> (heparin-binding EGF-like growth factor) and enhance invadopodia formation in cancer cells (Diaz et al., 2013). <BR>

etc...

Article upload takes place virtually every week, and for each article, it has to be verified. Also to be verified: Has the article been correctly indexed inthe dedicated lists? Has the article been correctly displayed? .

Before a thank-you e-mail is sent to the authors of a review, their bibliographies are searched so as to see if they could possibly be tasked with another review. If this is the case, they are asked whether or not they would be interested in pursuing their collaboration.

The author is given the address at which he can find his review on the Atlas site.

Prior to each issue, the editor in charge of the journal is tasked with creating the table of contents and scrupulously selecting the articles to be published. This is because publishing workflow is highly fluctuating, and consequently demands "hands-on" management.

A tool for the future data base carrying out initial formatting of the articles and editing the table of contents provides assistance in the page layout of the PDF journal.

In each issue, page layout is a sensitive matter. It is performed article by article, and has got to be done in such a way that a given issue is harmonious and satisfactorily balanced; moreover, image management must ensure maximal quality.

Once the journal is formatted and paginated, it is validated by the editor-in-chief.

The issue is then sent to the INIST-CNRS for finalizing of the PDF. The INIST editors recover the meta-data for the articles and associate them with the issue. They are also tasked with assigning the DOI (digital object identifier) for each article that will serve as its single identification number.

For back-up purposes, this final PDF is registered on the future data base.

Once all of the above steps have been carried out, the authors are contacted anew and informed of the publication of their articles in the journal and the link to the latter in PDF with which they are being provided.

The above percentages are subject to modification according to editorial needs and the fluctuating importance of certain tasks.

Again, we want to make it clear that the workflow detailed herein applies when MSc students/workers are involved in the process. Indeed, a senior researcher will skim through the various steps. However a secretary's active watch on forcoming papers is needed. Moreover, when the Atlas has evolved into a true database with an automated editorial process, many of these time consuming tasks will vanish.

The Atlas can run with:

- an Editor in Chief (20% full-time) + secretary (2-5%).

- Section Editors (5- 10% full-time) + secretary (1%).

- a Bio-computer specialist (10% full time).

- .. and as many good authors as possible !