Added procedures to generate NaviCell maps

README.md

@@ -1,5 +1,7 @@
 # NaviCell
 
+Here is the [procedure for construction of maps](map_construction_procedures/NaviCell_Maps_Preparation_Procedure.pdf) in CellDesigner and preparation of modular hierarchical map structure. The procedure contains instructions for generation of semantic zoom levels for maps using a [set of scripts](map_construction_procedures/procedure_scripts).
+
 This is a <b>NaviCell Factory</b> package allowing to convert a <a href="http://celldesigner.org">CellDesigner</a> map into <a href="http://navicell.curie.fr">NaviCell</a> 
 Google Maps-based enviroment, allowing to explore the map online and visualize high-throughput data on top of it with <a href="https://navicell.curie.fr/pages/nav_web_service.html">NaviCell Web Service</a>.
 

map_construction_procedures/procedure_scripts/make_zoom_2.sh

@@ -0,0 +1,2 @@
+#!/bin/bash 
+java -Xmx3000M -cp .:BiNoM_all.jar fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures --makezoomlevel2 --xml rcd_master.xml --xmlout rcd_master-2_noscaling.xml --fontsize 20

map_construction_procedures/procedure_scripts/merge_level_2.sh

@@ -0,0 +1,2 @@
+#!/bin/bash 
+java -Xmx3000M -cp .:BiNoM_all.jar  fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures --mergepngs --png1 rcd_master-2_noscaling.png  --png2 rcd_master-2_noscaling_noreactions.png --transparency2 0.7  --pngout rcd_master-2_merged.png

map_construction_procedures/procedure_scripts/merge_level_3.sh

@@ -0,0 +1,2 @@
+#!/bin/bash 
+java -Xmx3000M -cp .:BiNoM_all.jar  fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures --mergepngs --png1 rcd_master.png  --png2 rcd_master_noreactions.png --transparency2 0.7  --pngout rcd_master-3.png

map_construction_procedures/procedure_scripts/remove_reactions.sh

@@ -0,0 +1,2 @@
+#!/bin/bash 
+java -Xmx3000M -cp .:BiNoM_all.jar fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures --removereactions --xml rcd_master.xml

map_construction_procedures/procedure_scripts/remove_reactions_level_2.sh

@@ -0,0 +1,2 @@
+#!/bin/bash 
+java -Xmx3000M -cp .:BiNoM_all.jar fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures --removereactions --xml rcd_master-2_noscaling.xml

map_construction_procedures/procedure_scripts/scale_1_to_0.sh

@@ -0,0 +1,2 @@
+#!/bin/bash 
+java -Xmx3000M -cp .:BiNoM_all.jar fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures --scalepng --png1 rcd_master-1.png --pngout rcd_master-0.png

map_construction_procedures/procedure_scripts/scale_2_merged_to_2.sh

@@ -0,0 +1,2 @@
+#!/bin/bash 
+java -Xmx3000M -cp .:BiNoM_all.jar fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures --scalepng --png1 rcd_master-2_merged.png --pngout rcd_master-2.png

map_construction_procedures/procedure_scripts/scale_2_to_1.sh

@@ -0,0 +1,2 @@
+#!/bin/bash 
+java -Xmx3000M -cp .:BiNoM_all.jar fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures --scalepng --png1 rcd_master-2.png --pngout rcd_master-1.png