Merge remote-tracking branch 'origin/master'

+
+python3 training_validation_v11.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70.txt --testFile test-data-set-30.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run1 --version _v11 > ../outputs/Run1_v11.txt
+python3 training_validation_v11.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70.txt --testFile test-data-set-30.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run2 --version _v11 --S1 > ../outputs/Run2_v11.txt
+python3 training_validation_v11.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70.txt --testFile test-data-set-30.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run3 --version _v11 --S2 > ../outputs/Run3_v11.txt
+python3 training_validation_v11.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70.txt --testFile test-data-set-30.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run4 --version _v11 --S1 --S2 > ../outputs/Run4_v11.txt
+python3 training_validation_v11.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70.txt --testFile test-data-set-30.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run5 --version _v11 --S3 > ../outputs/Run5_v11.txt
+python3 training_validation_v11.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70.txt --testFile test-data-set-30.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run6 --version _v11 --S1 --S3 > ../outputs/Run6_v11.txt
+python3 training_validation_v11.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70.txt --testFile test-data-set-30.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run7 --version _v11 --S2 --S3 > ../outputs/Run7_v11.txt
+python3 training_validation_v11.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70.txt --testFile test-data-set-30.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run8 --version _v11 --S1 --S2 --S3 > ../outputs/Run8_v11.txt
+
+

-python3 training_validation_v9.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70_v4.txt --testFile test-data-set-30_v4.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run1 --version _v1
-python3 training_validation_v9.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70_v4.txt --testFile test-data-set-30_v4.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run2 --version _v1 --S1
-python3 training_validation_v9.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70_v4.txt --testFile test-data-set-30_v4.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run3 --version _v1 --S2
-python3 training_validation_v9.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70_v4.txt --testFile test-data-set-30_v4.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run4 --version _v1 --S1 --S2
-python3 training_validation_v9.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70_v4.txt --testFile test-data-set-30_v4.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run5 --version _v1 --S3
-python3 training_validation_v9.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70_v4.txt --testFile test-data-set-30_v4.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run6 --version _v1 --S1 --S3
-python3 training_validation_v9.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70_v4.txt --testFile test-data-set-30_v4.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run7 --version _v1 --S2 --S3
-python3 training_validation_v9.py --inputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/data-sets --trainingFile training-data-set-70_v4.txt --testFile test-data-set-30_v4.txt --outputPath /home/egaytan/automatic-extraction-growth-conditions/CRF/ --Gridname Run8 --version _v1 --S1 --S2 --S3

@@ -24,9 +24,9 @@ echo
 echo
 echo
 echo "Filter all paragraphs with tags..."
 echo "Filter all paragraphs with tags..."
 echo "Add sentence-end-tag PGCGROWTHCONDITIONS..."
 echo "Add sentence-end-tag PGCGROWTHCONDITIONS..."
-grep -E "<[^<]*>"  * | grep -E  '!'| cut -f2 -d'='|sort|uniq|awk '{ print $_" PGCGROWTHCONDITIONS"; }'  > /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt
+grep -E "<[^<]*>"  * | grep -E  '!'| cut -f2-5 -d'='|sort|uniq|awk '{ print $_" PGCGROWTHCONDITIONS"; }'  > /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces.txt
 echo
 echo
-echo "Number of total tag sentences: "$(wc /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt -l);
+echo "Number of total tag sentences: "$(wc /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces.txt -l);
 echo
 echo
 echo
 echo
-echo "Saving file: /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt";
+echo "Saving file: /home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces.txt";

@@ -4,7 +4,7 @@ echo "==============================Run CoreNLP=================================
 echo
 echo
 echo
 echo
 
 
-input="/home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces_v2.txt";
+input="/home/egaytan/automatic-extraction-growth-conditions/CoreNLP/input/raw-metadata-senteneces.txt";
 output="/home/egaytan/automatic-extraction-growth-conditions/CoreNLP/output/";
 output="/home/egaytan/automatic-extraction-growth-conditions/CoreNLP/output/";
 echo "input file: "$input;
 echo "input file: "$input;
 echo
 echo

@@ -35,7 +35,11 @@
  ArgR_<Supp>Arginine</Supp>_2 PGCGROWTHCONDITIONS
  ArgR_<Supp>Arginine</Supp>_2 PGCGROWTHCONDITIONS
  ArgR_<Supp>NH4Cl</Supp>_1 PGCGROWTHCONDITIONS
  ArgR_<Supp>NH4Cl</Supp>_1 PGCGROWTHCONDITIONS
  ArgR_<Supp>NH4Cl</Supp>_2 PGCGROWTHCONDITIONS
  ArgR_<Supp>NH4Cl</Supp>_2 PGCGROWTHCONDITIONS
- At <OD>OD450  PGCGROWTHCONDITIONS
+ At <OD>OD450 = 0.3</OD>, cultures induced with <Supp>1 mM IPTG</Supp>. Cells harvested 0 min after induction PGCGROWTHCONDITIONS
+ At <OD>OD450 = 0.3</OD>, cultures induced with <Supp>1 mM IPTG</Supp>. Cells harvested 10 min after induction PGCGROWTHCONDITIONS
+ At <OD>OD450 = 0.3</OD>, cultures induced with <Supp>1 mM IPTG</Supp>. Cells harvested 20 min after induction PGCGROWTHCONDITIONS
+ At <OD>OD450 = 0.3</OD>, cultures induced with <Supp>1 mM IPTG</Supp>. Cells harvested 2.5 min after induction PGCGROWTHCONDITIONS
+ At <OD>OD450 = 0.3</OD>, cultures induced with <Supp>1 mM IPTG</Supp>. Cells harvested 5 min after induction PGCGROWTHCONDITIONS
  A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS
  A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS
  A total of two samples were analyzed. ompR-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with <Supp>0.3 M of NaCl</Supp> at <Phase>mid-log pahse</Phase> for <Supp>30 min</Supp> with agitation. PGCGROWTHCONDITIONS
  A total of two samples were analyzed. ompR-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with <Supp>0.3 M of NaCl</Supp> at <Phase>mid-log pahse</Phase> for <Supp>30 min</Supp> with agitation. PGCGROWTHCONDITIONS
  carbon source: <Supp>acetate</Supp> PGCGROWTHCONDITIONS
  carbon source: <Supp>acetate</Supp> PGCGROWTHCONDITIONS
@@ -112,8 +116,8 @@
  E. coli K-12 MG1655 WT and Δfur were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS
  E. coli K-12 MG1655 WT and Δfur were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS
  E. coli K-12 MG1655 WT and Δfur were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For iron treated cells, <Supp>0.1mM of FeCl2</Supp> were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS
  E. coli K-12 MG1655 WT and Δfur were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For iron treated cells, <Supp>0.1mM of FeCl2</Supp> were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS
  E. coli K-12 MG1655 WT and ΔompR were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with <Supp>0.3 M of NaCl</Supp> at mid-log pahse for <Supp>30 min</Supp> with agitation. PGCGROWTHCONDITIONS
  E. coli K-12 MG1655 WT and ΔompR were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with <Supp>0.3 M of NaCl</Supp> at mid-log pahse for <Supp>30 min</Supp> with agitation. PGCGROWTHCONDITIONS
- E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> (<OD>OD600  PGCGROWTHCONDITIONS
- E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600  PGCGROWTHCONDITIONS
+ E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>. PGCGROWTHCONDITIONS
+ E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>. PGCGROWTHCONDITIONS
  E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS
  E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS
  E. coli strains harboring PurR-8myc were grown in minimal M9 medium supplemented with glucose (2 g/L) then inoculated into 100mL of fresh <Med>M9 minimal medium</Med>. PGCGROWTHCONDITIONS
  E. coli strains harboring PurR-8myc were grown in minimal M9 medium supplemented with glucose (2 g/L) then inoculated into 100mL of fresh <Med>M9 minimal medium</Med>. PGCGROWTHCONDITIONS
  E. coli strains harboring PurR-8myc were grown in minimal M9 medium supplemented with glucose (2 g/L) then inoculated into 100mL of fresh <Med>M9 minimal medium</Med> supplemented with <Supp>100ug/L adenine</Supp>. PGCGROWTHCONDITIONS
  E. coli strains harboring PurR-8myc were grown in minimal M9 medium supplemented with glucose (2 g/L) then inoculated into 100mL of fresh <Med>M9 minimal medium</Med> supplemented with <Supp>100ug/L adenine</Supp>. PGCGROWTHCONDITIONS
@@ -203,7 +207,7 @@
  growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>1 µM FeSO4</Supp> PGCGROWTHCONDITIONS
  growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>1 µM FeSO4</Supp> PGCGROWTHCONDITIONS
  growth phase: <Phase>exponential</Phase> PGCGROWTHCONDITIONS
  growth phase: <Phase>exponential</Phase> PGCGROWTHCONDITIONS
  growth phase: <Phase>mid-log</Phase> PGCGROWTHCONDITIONS
  growth phase: <Phase>mid-log</Phase> PGCGROWTHCONDITIONS
- growth phase: <Phase>mid-log phase</Phase> (<OD>OD600  PGCGROWTHCONDITIONS
+ growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>) PGCGROWTHCONDITIONS
  growth phase: <Phase>stationary</Phase> PGCGROWTHCONDITIONS
  growth phase: <Phase>stationary</Phase> PGCGROWTHCONDITIONS
  <Gtype>∆fnr</Gtype> - <Air>Anaeroibc</Air> PGCGROWTHCONDITIONS
  <Gtype>∆fnr</Gtype> - <Air>Anaeroibc</Air> PGCGROWTHCONDITIONS
  <Gtype>∆fnr</Gtype> ChIP DNA from <Gtype>PK4854</Gtype> PGCGROWTHCONDITIONS
  <Gtype>∆fnr</Gtype> ChIP DNA from <Gtype>PK4854</Gtype> PGCGROWTHCONDITIONS