Recent changes to Gen3D Walkthrough

Gen3D Walkthrough modified by Lingfei

Lingfei — Thu, 14 May 2015 01:25:01 -0000

--- v36
+++ v37
@@ -52,7 +52,7 @@
 ls -art 21pF*\* | awk -F_ 'BEGIN{my2=0;my3=0;my4=0;my5=0} {if(2*$2 + 2*$3 + 3*$5 + $4> 2*my2 + 2*my3 + 3*my5 + my4){my2=$2;my3=$3;my4=$4;my5=$5;my=$0} } END{print my}'
 For normal chromosomes, replace 19 with corresponding chromosome number; for cancerous ones, replace 19 with corresponding chromosome number + "p", like "19p".

-*\*NOTE: In the source code, there are two parameters CON and NON (line #34 and # 35) control the minimum contact and non-contact score of the models generated. Given greater parameters, the program can generate higher quality but lower number of models. Given smaller parameters, the program can generate lower quality but larger number of models. \**
+*\*NOTE: In the source code, there are two parameters CON and NON (line #26 and # 27) control the minimum contact and non-contact score of the models generated. Given greater parameters, the program can generate higher quality but lower number of models. Given smaller parameters, the program can generate lower quality but larger number of models. \**

 #Viewing Genome Models

Gen3D Walkthrough modified by Lingfei

Lingfei — Tue, 12 May 2015 21:14:28 -0000

--- v35
+++ v36
@@ -49,7 +49,7 @@
 Pif: number of the satisfied interaction frequency

 To pick the best model, we can run a command to get the highest score model from ensemble of models. 
-ls -art 21pF** | awk -F_ 'BEGIN{my2=0;my3=0;my4=0;my5=0} {if(2*$2 + 2*$3 + 3*$5 + $4> 2*my2 + 2*my3 + 3*my5 + my4){my2=$2;my3=$3;my4=$4;my5=$5;my=$0} } END{print my}'
+ls -art 21pF*\* | awk -F_ 'BEGIN{my2=0;my3=0;my4=0;my5=0} {if(2*$2 + 2*$3 + 3*$5 + $4> 2*my2 + 2*my3 + 3*my5 + my4){my2=$2;my3=$3;my4=$4;my5=$5;my=$0} } END{print my}'
 For normal chromosomes, replace 19 with corresponding chromosome number; for cancerous ones, replace 19 with corresponding chromosome number + "p", like "19p".

 *\*NOTE: In the source code, there are two parameters CON and NON (line #34 and # 35) control the minimum contact and non-contact score of the models generated. Given greater parameters, the program can generate higher quality but lower number of models. Given smaller parameters, the program can generate lower quality but larger number of models. \**

Gen3D Walkthrough modified by Lingfei

Lingfei — Tue, 12 May 2015 21:13:55 -0000

--- v34
+++ v35
@@ -49,7 +49,7 @@
 Pif: number of the satisfied interaction frequency

 To pick the best model, we can run a command to get the highest score model from ensemble of models. 
-ls -art 21pF* | awk -F_ 'BEGIN{my2=0;my3=0;my4=0;my5=0} {if(2*$2 + 2*$3 + 3*$5 + $4> 2*my2 + 2*my3 + 3*my5 + my4){my2=$2;my3=$3;my4=$4;my5=$5;my=$0} } END{print my}'
+ls -art 21pF** | awk -F_ 'BEGIN{my2=0;my3=0;my4=0;my5=0} {if(2*$2 + 2*$3 + 3*$5 + $4> 2*my2 + 2*my3 + 3*my5 + my4){my2=$2;my3=$3;my4=$4;my5=$5;my=$0} } END{print my}'
 For normal chromosomes, replace 19 with corresponding chromosome number; for cancerous ones, replace 19 with corresponding chromosome number + "p", like "19p".

 *\*NOTE: In the source code, there are two parameters CON and NON (line #34 and # 35) control the minimum contact and non-contact score of the models generated. Given greater parameters, the program can generate higher quality but lower number of models. Given smaller parameters, the program can generate lower quality but larger number of models. \**

Gen3D Walkthrough modified by Lingfei

Lingfei — Tue, 12 May 2015 17:04:06 -0000

--- v33
+++ v34
@@ -49,7 +49,7 @@
 Pif: number of the satisfied interaction frequency

 To pick the best model, we can run a command to get the highest score model from ensemble of models. 
-ls -art 19F* | awk -F_ 'BEGIN{my2=0;my3=0;} {if($2>my2 && $3>my3){my2=$2;my3=$3;my=$0} } END{print my}'
+ls -art 21pF* | awk -F_ 'BEGIN{my2=0;my3=0;my4=0;my5=0} {if(2*$2 + 2*$3 + 3*$5 + $4> 2*my2 + 2*my3 + 3*my5 + my4){my2=$2;my3=$3;my4=$4;my5=$5;my=$0} } END{print my}'
 For normal chromosomes, replace 19 with corresponding chromosome number; for cancerous ones, replace 19 with corresponding chromosome number + "p", like "19p".

 *\*NOTE: In the source code, there are two parameters CON and NON (line #34 and # 35) control the minimum contact and non-contact score of the models generated. Given greater parameters, the program can generate higher quality but lower number of models. Given smaller parameters, the program can generate lower quality but larger number of models. \**

Gen3D Walkthrough modified by Lingfei

Lingfei — Wed, 06 Aug 2014 20:36:39 -0000

--- v32
+++ v33
@@ -22,14 +22,14 @@

 For example:

-./model.out 22p
+./gen3d.out 22p

 This command will generate pdb files contain the malignant B-cell of an acute lymphoblastic leukemia patient's chromosome 22‘s prediction 3D structure and the score of these structure files.

 [[img src=22p_pdb2.PNG]]

-The picture above is one of the generated pdb files of chromosome 22. This file contains the 3D coordinate of each atom in the structure and contact information between two contact atoms. The pdb file is named like filename_ percentage of contact _percentage of non-contact_ maxdd_ percentage of satisfied interaction frequency.
+The picture above is one of the generated pdb files of chromosome 22. This file contains the 3D coordinate of each unit in the structure and contact information between two contact units. The pdb file is named like filename_ percentage of contact _percentage of non-contact_ maxdd_ percentage of satisfied interaction frequency.

 [[img src=22p_score.png]]

Gen3D Walkthrough modified by Lingfei

Lingfei — Fri, 01 Aug 2014 15:55:15 -0000

--- v31
+++ v32
@@ -16,7 +16,7 @@

 input_contact_data: genome contact data which contains only intra contacts information.

-output_pdb_file: pdbs file and the evaluation scores of all the generated structures
+output_pdb_file: generated models in pdb format and the evaluation scores of all the generated structures

 Result: a score.log file contains scores of the generated pdb files and generated pdb files

Gen3D Walkthrough modified by Lingfei

Lingfei — Fri, 01 Aug 2014 15:54:13 -0000

--- v30
+++ v31
@@ -9,6 +9,8 @@
 #Functions

 By using the gen3D you can generate 3D structured of the chromosome and learn evaluation the scores of these structures. The generated pdb file contains the 3D structure information of the genome. The generated score.log file contains the scores for the generated models.
+
+Command Format:

 Binary_program_file input_contact_data

Gen3D Walkthrough modified by Lingfei

Lingfei — Wed, 30 Jul 2014 16:58:57 -0000

--- v29
+++ v30
@@ -50,7 +50,7 @@
 ls -art 19F* | awk -F_ 'BEGIN{my2=0;my3=0;} {if($2>my2 && $3>my3){my2=$2;my3=$3;my=$0} } END{print my}'
 For normal chromosomes, replace 19 with corresponding chromosome number; for cancerous ones, replace 19 with corresponding chromosome number + "p", like "19p".

-*\*NOTE: In the source code, there are two parameters CON and NON control the minimum contact and non-contact score of the models generated. Given greater parameters, the program can generate higher quality but lower number of models. Given smaller parameters, the program can generate lower quality but larger number of models. \**
+*\*NOTE: In the source code, there are two parameters CON and NON (line #34 and # 35) control the minimum contact and non-contact score of the models generated. Given greater parameters, the program can generate higher quality but lower number of models. Given smaller parameters, the program can generate lower quality but larger number of models. \**

 #Viewing Genome Models

Gen3D Walkthrough modified by Lingfei

Lingfei — Wed, 30 Jul 2014 16:50:40 -0000

--- v28
+++ v29
@@ -48,7 +48,7 @@

 To pick the best model, we can run a command to get the highest score model from ensemble of models. 
 ls -art 19F* | awk -F_ 'BEGIN{my2=0;my3=0;} {if($2>my2 && $3>my3){my2=$2;my3=$3;my=$0} } END{print my}'
-//Replace 19 with corresponding chromosome number.
+For normal chromosomes, replace 19 with corresponding chromosome number; for cancerous ones, replace 19 with corresponding chromosome number + "p", like "19p".

 *\*NOTE: In the source code, there are two parameters CON and NON control the minimum contact and non-contact score of the models generated. Given greater parameters, the program can generate higher quality but lower number of models. Given smaller parameters, the program can generate lower quality but larger number of models. \**

Gen3D Walkthrough modified by Lingfei

Lingfei — Wed, 30 Jul 2014 16:46:05 -0000

--- v27
+++ v28
@@ -50,6 +50,8 @@
 ls -art 19F* | awk -F_ 'BEGIN{my2=0;my3=0;} {if($2>my2 && $3>my3){my2=$2;my3=$3;my=$0} } END{print my}'
 //Replace 19 with corresponding chromosome number.

+*\*NOTE: In the source code, there are two parameters CON and NON control the minimum contact and non-contact score of the models generated. Given greater parameters, the program can generate higher quality but lower number of models. Given smaller parameters, the program can generate lower quality but larger number of models. \**
+

 #Viewing Genome Models