Recent changes to Home

Home modified by Asher

Asher — Mon, 27 Jun 2016 15:38:16 -0000

--- v21
+++ v22
@@ -1,22 +1,22 @@
-Gene Slider is a data visualization tool that helps visualize conservation and entropy of orthologous DNA and protein sequences. Alignments can be loaded into Gene Slider and displayed as one long sequence logo that can be zoomed in and out. It also displays transcription factor binding sites.
+Gene Slider is a data visualization tool that helps visualize conservation and entropy of aligned DNA and protein sequences. Alignments can be loaded into Gene Slider and displayed as one long sequence logo that can be zoomed in and out of. It also displays transcription factor binding sites, mapped by FIMO (Grant et al, 2011)

 [TOC]

 # How Gene Slider Works
-Gene Slider uses HTML, CSS, and JavaScript for front-end web page. The Gene Slider program is written in Processing.js programming language. It GETs data from REST API using AJAX request from JavaScript. The Gene Slider REST API consists of two web services: one returns data given an AGI ID and the other returns data given a chromosomal region. A MySQL database stores gene annotations and locations of alignment files. This information is used to get alignment files from the file system. The Gene Slider architecture is summarized in the figure below:
+Gene Slider uses HTML, CSS, and JavaScript for the front-end web page. The Gene Slider program is written in the Processing.js programming language. It GETs data from a REST API using an AJAX request from JavaScript. The Gene Slider REST API consists of two web services: one returns data given an AGI ID and the other returns data given a chromosomal region. A MySQL database stores gene annotations and locations of alignment files. This information is used to get alignment files from the file system. The Gene Slider architecture is summarized in the figure below:
 [[img src=architecture.png alt="Gene Slider Architecture" width="100%"]]
 # How to Use Gene Slider
 There are two ways to visualize data in Gene Slider. You can use an existing alignment, or you can upload your own alignments.
 ## Using Existing Alignments
 There are Arabidopsis thaliana alignments on the Bio-Analytic Resource from Haudry, A. et al. (2013).  These alignments have pre-mapped data from JASPAR (Mathelier, A. et al., 2014) and Weirauch, M.T. et al. (2014). Data from these sources can be visualized in two different ways:

-1. Data could be loaded using Arabidopsis AGI ID:
+1. Data, mapped using FIMO (Grant et al.,, 2011) with a p-value cutoff of 1e^-4, may be loaded using an Arabidopsis AGI ID:
     * Visit [Gene Slider](http://bar.utoronto.ca/geneslider/)
-    * In "Locus" text box, type in AGI or locus name such as ABI3
+    * In the "Locus" text box, type in the AGI ID (E.g. At3g24650) or locus name such as ABI3
     * Input desired numbers in "Bases Upstream" and "Bases Downstream." For example, "100" and "100" respectively
     * Click "Go"

-2. Data could also be loaded using Arabidopsis chromosomal region:
+2. Data may also be loaded for an Arabidopsis chromosomal region:
     * Visit [Gene Slider](http://bar.utoronto.ca/geneslider/)
     * From "Chromosome" drop down box, choose a chromosome, for example, "1".
     * Enter the start and the end of the region in the respective text boxes, for example, "1" and "7000".
@@ -24,17 +24,17 @@
     * To upload additional motifs, download this [example file](http://bar.utoronto.ca/geneslider/Documentation/example_motifs_only.gff), which has sample mappings between 1 and 7000 base pairs. Then, upload this file into Gene Slider by clicking "Select file" in the top right. 

 ## Using Your Own Data
-You can also use your FASTA alignments as follows:
+You can also use your own FASTA alignments as follows:

 * Visit [Gene Slider](http://bar.utoronto.ca/geneslider/)
 * Download an [example file](http://bar.utoronto.ca/geneslider/Documentation/example.fa) and upload it into Gene Slider by clicking "Select file" button in top right.
-* GFF data can also be visualized. For example, this [GFF file](http://bar.utoronto.ca/geneslider/Documentation/example.gff) and be uploaded after loading the alignment into Gene Slider.
-* Addition motif files, such as [this file](http://bar.utoronto.ca/geneslider/Documentation/example_motifs_only.gff) could also be uploaded.
+* GFF data can also be visualized. For example, this [GFF file](http://bar.utoronto.ca/geneslider/Documentation/example.gff) may be uploaded after loading the alignment into Gene Slider.
+* Additional motif files, such as [this file](http://bar.utoronto.ca/geneslider/Documentation/example_motifs_only.gff) could also be uploaded.

-# How to Implement Gene Slider on Your Server
+# How to Implement Gene Slider on Your Own Server
 Gene Slider runs on Apache HTTPD and MySQL on Linux. You can implement Gene Slider on your server as follows:

-1. Install web servers software such as Apache HTTPD and enable CGI support following documentation for your web server and operating system.
+1. Install web server software, such as Apache HTTPD, and enable CGI support following documentation for your web server and operating system.
 2. Install database management software such as MySQL and Perl DBI.
 3. Download Gene Slider and uncompress file geneslider_v1.tar.gz by using the command `tar -xvzf geneslider_v1.tar.gz`.
 4. Uploading databases:
@@ -43,22 +43,23 @@
         * create database cistome;
         * create database eplant2;
         * create database geneslider;
-    * Exit from MySQL and load the data into the databases. The database dumps are in databases directory of Gene Slider (Please note that these are not complete BAR database dumps. There are only tables that are needed by Gene Slider and only have data up to 100k base pairs): Run the following command in the terminal:
+    * Exit from MySQL and load the data into the databases. The database dumps are in the databases directory of the Gene Slider tarball (Please note that these are not complete BAR database dumps. There are only tables that are needed by Gene Slider and only have data up to 100k base pairs): Run the following command in the terminal:
         * mysql -u root -p annotations_lookup < annotations_lookup.sql
         * mysql -u root -p cistome < cistome.sql
         * mysql -u root -p eplant2 < eplant2.sql
         * mysql -u root -p geneslider < geneslider.sql
-    * Log into MySQL and create a user account for Gene Slider and grant select privilege to the user on all four of these databases. 
-5. Create a directories for data ('/DATA/GeneSlider/') and recursively copy contents of data directory into /DATA/GeneSlider/.
+    * Log into MySQL and create a user account for Gene Slider and grant select privilege to the user on all four of these databases and flush privileges.  
+5. Create a directory for data ('/DATA/GeneSlider/') and recursively copy contents of data directory into /DATA/GeneSlider/.
 6. Copy and paste geneslider directory into your web root directory or public_html directory.
 7. In geneslider/cgi-bin directory, we use USERNAME and PASSWORD as place holder for username and password repectively. Please chages these to your MySQL database username and database password. 
 8. Final checks:
-    * Visit index.html page in geneslider directory to check if the page load. If not, please check your server settings.
-    * Enter a gene alias (ABI3) to check Perl CGI and database connectivity. If AGI ID is not displayed in a dropdown box, please check if CGI is enabled for geneslider/cgi-bin dirctory, and also Perl DBI libraries are installed for your operating system.
-    * Click 'GO' and Gene Slider should load alignment. If not, please make sure /DATA/GeneSlider/ directory is readable by HTTP server's user.
-    * If it still doesn't work, we can help.
-9. Gene Slider can also be modified for use with other species. 
+    * Visit index.html page in geneslider directory to check if the page loads. If not, please check your server settings.
+    * Enter a gene alias (ABI3) to check Perl CGI and database connectivity. If AGI ID is not displayed in a dropdown box, please check if CGI is enabled for geneslider/cgi-bin dirctory with appropriate permission (`chmod 755 *`), and also Perl DBI libraries are installed for your operating system.
+    * Click 'GO' and Gene Slider should load the alignment. If not, please make sure /DATA/GeneSlider/ directory is readable by HTTP server's user (`chmod 744 *`).
+    * If it still doesn't work, we can help. 
+9. Gene Slider can also be modified for use with other species. (There are some regexes that are specific for AGI IDs).
 # References
-* Haudry, A. et al. (2013). An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45, 891–898.
-* Mathelier, A. et al. (2014). JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 42, D142–D147.
-* Weirauch, M.T. et al. (2014). Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158, 1431–1443.
+* Grant, C. E. et al. 2011. FIMO: Scanning for occurrences of a given motif. Bioinformatics, 27(7):1017-1018.
+* Haudry, A. et al. (2013). An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45, 891–898.
+* Mathelier, A. et al. (2014). JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 42, D142–D147.
+* Weirauch, M.T. et al. (2014). Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158, 1431–1443.

Home modified by Asher

Asher — Mon, 27 Jun 2016 03:34:50 -0000

--- v20
+++ v21
@@ -3,39 +3,39 @@
 [TOC]

 # How Gene Slider Works
-Gene Slider uses HTML, CSS, and JavaScript for front-end web page. The Gene Slider program is written in Processing programming language. It gets data from REST API using AJAX request from JavaScript. Gene Slider REST API consists of two web services: one returns data given an AGI ID and the other returns data given a chromosomal region. MySQL database stores gene annotations and location of alignment files. This information is used the get alignment files from the file system. The Gene Slider architecture is summarized in the figure below:
+Gene Slider uses HTML, CSS, and JavaScript for front-end web page. The Gene Slider program is written in Processing.js programming language. It GETs data from REST API using AJAX request from JavaScript. The Gene Slider REST API consists of two web services: one returns data given an AGI ID and the other returns data given a chromosomal region. A MySQL database stores gene annotations and locations of alignment files. This information is used to get alignment files from the file system. The Gene Slider architecture is summarized in the figure below:
 [[img src=architecture.png alt="Gene Slider Architecture" width="100%"]]
 # How to Use Gene Slider
-There are two ways to visualize data in Gene Slider. You can use an existing alignment, or you can upload your alignments.
+There are two ways to visualize data in Gene Slider. You can use an existing alignment, or you can upload your own alignments.
 ## Using Existing Alignments
-There are Arabidopsis thaliana alignments on the Bio-Analytic Resource from Haudry, A. et al. (2013).  These alignments have mapped data from JASPAR (Mathelier, A. et al., 2014) and Weirauch, M.T. et al. (2014). Data from these sources can be visualized in two different ways:
+There are Arabidopsis thaliana alignments on the Bio-Analytic Resource from Haudry, A. et al. (2013).  These alignments have pre-mapped data from JASPAR (Mathelier, A. et al., 2014) and Weirauch, M.T. et al. (2014). Data from these sources can be visualized in two different ways:

 1. Data could be loaded using Arabidopsis AGI ID:
     * Visit [Gene Slider](http://bar.utoronto.ca/geneslider/)
-    * In Locus text box, type in AGI or locus name such as ABI3
+    * In "Locus" text box, type in AGI or locus name such as ABI3
     * Input desired numbers in "Bases Upstream" and "Bases Downstream." For example, "100" and "100" respectively
     * Click "Go"

 2. Data could also be loaded using Arabidopsis chromosomal region:
     * Visit [Gene Slider](http://bar.utoronto.ca/geneslider/)
-    * From "Chromosome" drop down box, choose chromosome, for example, "1".
-    * Enter start and end of the region in the respective text boxes, for example, "1" and "7000".
+    * From "Chromosome" drop down box, choose a chromosome, for example, "1".
+    * Enter the start and the end of the region in the respective text boxes, for example, "1" and "7000".
     * Click "Go"
-    * To upload additional motifs, download this [example file](http://bar.utoronto.ca/geneslider/Documentation/example_motifs_only.gff), which had sample mappings between 1 and 7000 base pairs. Then, upload this file into Gene Slider by clicking "Select file" in the top right. 
+    * To upload additional motifs, download this [example file](http://bar.utoronto.ca/geneslider/Documentation/example_motifs_only.gff), which has sample mappings between 1 and 7000 base pairs. Then, upload this file into Gene Slider by clicking "Select file" in the top right. 

 ## Using Your Own Data
 You can also use your FASTA alignments as follows:

 * Visit [Gene Slider](http://bar.utoronto.ca/geneslider/)
-* Download an [example file](http://bar.utoronto.ca/geneslider/Documentation/example.fa) and load it in Gene Slider by clicking "Select file" button in top right.
-* GFF data can also be visualized. For example, this [GFF file](http://bar.utoronto.ca/geneslider/Documentation/example.gff) and be uploaded after loading alignment into Gene Slider.
+* Download an [example file](http://bar.utoronto.ca/geneslider/Documentation/example.fa) and upload it into Gene Slider by clicking "Select file" button in top right.
+* GFF data can also be visualized. For example, this [GFF file](http://bar.utoronto.ca/geneslider/Documentation/example.gff) and be uploaded after loading the alignment into Gene Slider.
 * Addition motif files, such as [this file](http://bar.utoronto.ca/geneslider/Documentation/example_motifs_only.gff) could also be uploaded.

 # How to Implement Gene Slider on Your Server
 Gene Slider runs on Apache HTTPD and MySQL on Linux. You can implement Gene Slider on your server as follows:

 1. Install web servers software such as Apache HTTPD and enable CGI support following documentation for your web server and operating system.
-2. Install database management software such as MySQL.
+2. Install database management software such as MySQL and Perl DBI.
 3. Download Gene Slider and uncompress file geneslider_v1.tar.gz by using the command `tar -xvzf geneslider_v1.tar.gz`.
 4. Uploading databases:
     * Log into MySQL, and create databases using the following commands as root user:
@@ -43,7 +43,7 @@
         * create database cistome;
         * create database eplant2;
         * create database geneslider;
-    * Exit from MySQL and load data into databases. The database dumps are in databases directory of Gene Slider (Please note that these are not complete BAR database dumps. There are only tables that are needed by Gene Slider and only have data up to 100k base pairs): Run the following command in the terminal:
+    * Exit from MySQL and load the data into the databases. The database dumps are in databases directory of Gene Slider (Please note that these are not complete BAR database dumps. There are only tables that are needed by Gene Slider and only have data up to 100k base pairs): Run the following command in the terminal:
         * mysql -u root -p annotations_lookup < annotations_lookup.sql
         * mysql -u root -p cistome < cistome.sql
         * mysql -u root -p eplant2 < eplant2.sql
@@ -51,12 +51,13 @@
     * Log into MySQL and create a user account for Gene Slider and grant select privilege to the user on all four of these databases. 
 5. Create a directories for data ('/DATA/GeneSlider/') and recursively copy contents of data directory into /DATA/GeneSlider/.
 6. Copy and paste geneslider directory into your web root directory or public_html directory.
-7. Final checks:
-    * Visit index.html page in geneslider directory to check if page load. If not, please check your server settings.
-    * Enter a gene alias (ABI3) to check Perl CGI and database connectivity. If AGI ID is not displayed in a dropdown box, check if CGI is enabled for geneslider/cgi-bin dirctory, and also Perl DBI libraries are installed for your operating system.
+7. In geneslider/cgi-bin directory, we use USERNAME and PASSWORD as place holder for username and password repectively. Please chages these to your MySQL database username and database password. 
+8. Final checks:
+    * Visit index.html page in geneslider directory to check if the page load. If not, please check your server settings.
+    * Enter a gene alias (ABI3) to check Perl CGI and database connectivity. If AGI ID is not displayed in a dropdown box, please check if CGI is enabled for geneslider/cgi-bin dirctory, and also Perl DBI libraries are installed for your operating system.
     * Click 'GO' and Gene Slider should load alignment. If not, please make sure /DATA/GeneSlider/ directory is readable by HTTP server's user.
     * If it still doesn't work, we can help.
-8. Gene Slider can also be modified for use with other species. 
+9. Gene Slider can also be modified for use with other species. 
 # References
 * Haudry, A. et al. (2013). An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45, 891–898.
 * Mathelier, A. et al. (2014). JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 42, D142–D147.

Home modified by Asher

Asher — Mon, 27 Jun 2016 01:04:18 -0000

--- v19
+++ v20
@@ -56,6 +56,7 @@
     * Enter a gene alias (ABI3) to check Perl CGI and database connectivity. If AGI ID is not displayed in a dropdown box, check if CGI is enabled for geneslider/cgi-bin dirctory, and also Perl DBI libraries are installed for your operating system.
     * Click 'GO' and Gene Slider should load alignment. If not, please make sure /DATA/GeneSlider/ directory is readable by HTTP server's user.
     * If it still doesn't work, we can help.
+8. Gene Slider can also be modified for use with other species. 
 # References
 * Haudry, A. et al. (2013). An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45, 891–898.
 * Mathelier, A. et al. (2014). JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 42, D142–D147.

Home modified by Asher

Asher — Mon, 27 Jun 2016 00:44:07 -0000

--- v18
+++ v19
@@ -55,7 +55,7 @@
     * Visit index.html page in geneslider directory to check if page load. If not, please check your server settings.
     * Enter a gene alias (ABI3) to check Perl CGI and database connectivity. If AGI ID is not displayed in a dropdown box, check if CGI is enabled for geneslider/cgi-bin dirctory, and also Perl DBI libraries are installed for your operating system.
     * Click 'GO' and Gene Slider should load alignment. If not, please make sure /DATA/GeneSlider/ directory is readable by HTTP server's user.
-    * If it still does work, we can help.
+    * If it still doesn't work, we can help.
 # References
 * Haudry, A. et al. (2013). An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45, 891–898.
 * Mathelier, A. et al. (2014). JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 42, D142–D147.

Home modified by Asher

Asher — Mon, 27 Jun 2016 00:43:39 -0000

--- v17
+++ v18
@@ -49,7 +49,13 @@
         * mysql -u root -p eplant2 < eplant2.sql
         * mysql -u root -p geneslider < geneslider.sql
     * Log into MySQL and create a user account for Gene Slider and grant select privilege to the user on all four of these databases. 
-
+5. Create a directories for data ('/DATA/GeneSlider/') and recursively copy contents of data directory into /DATA/GeneSlider/.
+6. Copy and paste geneslider directory into your web root directory or public_html directory.
+7. Final checks:
+    * Visit index.html page in geneslider directory to check if page load. If not, please check your server settings.
+    * Enter a gene alias (ABI3) to check Perl CGI and database connectivity. If AGI ID is not displayed in a dropdown box, check if CGI is enabled for geneslider/cgi-bin dirctory, and also Perl DBI libraries are installed for your operating system.
+    * Click 'GO' and Gene Slider should load alignment. If not, please make sure /DATA/GeneSlider/ directory is readable by HTTP server's user.
+    * If it still does work, we can help.
 # References
 * Haudry, A. et al. (2013). An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45, 891–898.
 * Mathelier, A. et al. (2014). JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 42, D142–D147.

Home modified by Asher

Asher — Mon, 27 Jun 2016 00:15:26 -0000

--- v16
+++ v17
@@ -37,7 +37,7 @@
 1. Install web servers software such as Apache HTTPD and enable CGI support following documentation for your web server and operating system.
 2. Install database management software such as MySQL.
 3. Download Gene Slider and uncompress file geneslider_v1.tar.gz by using the command `tar -xvzf geneslider_v1.tar.gz`.
-4. Uploading database:
+4. Uploading databases:
     * Log into MySQL, and create databases using the following commands as root user:
         * create database annotations_lookup;
         * create database cistome;

Home modified by Asher

Asher — Mon, 27 Jun 2016 00:14:38 -0000

--- v15
+++ v16
@@ -32,6 +32,24 @@
 * Addition motif files, such as [this file](http://bar.utoronto.ca/geneslider/Documentation/example_motifs_only.gff) could also be uploaded.

 # How to Implement Gene Slider on Your Server
+Gene Slider runs on Apache HTTPD and MySQL on Linux. You can implement Gene Slider on your server as follows:
+
+1. Install web servers software such as Apache HTTPD and enable CGI support following documentation for your web server and operating system.
+2. Install database management software such as MySQL.
+3. Download Gene Slider and uncompress file geneslider_v1.tar.gz by using the command `tar -xvzf geneslider_v1.tar.gz`.
+4. Uploading database:
+    * Log into MySQL, and create databases using the following commands as root user:
+        * create database annotations_lookup;
+        * create database cistome;
+        * create database eplant2;
+        * create database geneslider;
+    * Exit from MySQL and load data into databases. The database dumps are in databases directory of Gene Slider (Please note that these are not complete BAR database dumps. There are only tables that are needed by Gene Slider and only have data up to 100k base pairs): Run the following command in the terminal:
+        * mysql -u root -p annotations_lookup < annotations_lookup.sql
+        * mysql -u root -p cistome < cistome.sql
+        * mysql -u root -p eplant2 < eplant2.sql
+        * mysql -u root -p geneslider < geneslider.sql
+    * Log into MySQL and create a user account for Gene Slider and grant select privilege to the user on all four of these databases. 
+
 # References
 * Haudry, A. et al. (2013). An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45, 891–898.
 * Mathelier, A. et al. (2014). JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 42, D142–D147.

Home modified by Asher

Asher — Sun, 26 Jun 2016 05:07:50 -0000

--- v14
+++ v15
@@ -4,7 +4,7 @@

 # How Gene Slider Works
 Gene Slider uses HTML, CSS, and JavaScript for front-end web page. The Gene Slider program is written in Processing programming language. It gets data from REST API using AJAX request from JavaScript. Gene Slider REST API consists of two web services: one returns data given an AGI ID and the other returns data given a chromosomal region. MySQL database stores gene annotations and location of alignment files. This information is used the get alignment files from the file system. The Gene Slider architecture is summarized in the figure below:
-[[img src=architecture.png alt="Gene Slider Architecture"]]
+[[img src=architecture.png alt="Gene Slider Architecture" width="100%"]]
 # How to Use Gene Slider
 There are two ways to visualize data in Gene Slider. You can use an existing alignment, or you can upload your alignments.
 ## Using Existing Alignments

Home modified by Asher

Asher — Sun, 26 Jun 2016 05:06:46 -0000

Home modified by Asher

Asher — Sun, 26 Jun 2016 05:04:57 -0000

--- v12
+++ v13
@@ -4,7 +4,7 @@

 # How Gene Slider Works
 Gene Slider uses HTML, CSS, and JavaScript for front-end web page. The Gene Slider program is written in Processing programming language. It gets data from REST API using AJAX request from JavaScript. Gene Slider REST API consists of two web services: one returns data given an AGI ID and the other returns data given a chromosomal region. MySQL database stores gene annotations and location of alignment files. This information is used the get alignment files from the file system. The Gene Slider architecture is summarized in the figure below:
-[[img src=architecture.png alt="Gene Slider Architecture]]
+[[img src=architecture.png alt="Gene Slider Architecture"]]
 # How to Use Gene Slider
 There are two ways to visualize data in Gene Slider. You can use an existing alignment, or you can upload your alignments.
 ## Using Existing Alignments