Need a help

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Need a help

swetha
Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.

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Re: Need a help

Scott Cain
Hi Swetha,

The only way I can think of to do that is with separate configuration files for GBrowse unfortunately.  The "data source" drop down was originally conceived of to allow selecting different "species", but that concept doesn't map very well to strains of a virus.  There are two approaches I could see using:

1. Revamp the way you're using GBrowse data sources altogether, so that each data source represents one type of virus, so in the drop down you'd have two entries, one for H. influenzae and one for the other virus.  Each strain would then be analogous a chromosome. One advantage to this approach is that when/if you have hundreds of strains of a virus the drop down will still be useable (that is, a drop down menu with a more than 20-30 entries is very unwieldy).  Users would be able to use the search box to find strains they are interested in.  A potential downside is that searching for a particular gene would yield results for that gene in every strain.

2. Create separate gbrowse2 config directories for each virus.  Then you need to edit gbrowse2.conf file that lives in the apache configuration; where that is varies depending on your OS; on Ubuntu 12.04 it's in /etc/apache2/conf.d/.  You'll need separate cgi-bin directories too, for example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and /usr/lib/cgi-bin/Segb2 for the Something else virus :-)  In the apache gbrowse.conf file you need separate entries for the different cgi-bin directores that have different "SetEnv GBROWSE_CONF" entries to point at the separate gbrowse config directories.

Obviously, it's up to you to decide which is better; there will be work either way.  I suggest that if you choose the second path that you make very incremental changes and test that GBrowse still works all along the way, because there are several moving parts that could break GBrowse and with the changes required, it might be difficult to sort out what happened if something goes wrong.

Scott


On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <[hidden email]> wrote:
Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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Fwd: Need a help

swetha

Dear Sir,

Tons of thanks. I followed your suggestion, option 2. Now it works well. You helped me a lot in GBrowse (Starting from installation to till now). Thank you so much. I used GBrowse in two databases and both are published. One in Genomics and other in Computers in Biology and Medicine. This publication is not possible without your guidance.

Thank you.

Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.

On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

Thank you so much for your quick reply. Let me work according to your suggestion and If I stuck at any point, Please help me.

Yours sincerely,
Swetha R G.

On Wed, Nov 26, 2014 at 9:53 PM, Scott Cain <[hidden email]> wrote:
Hi Swetha,

The only way I can think of to do that is with separate configuration files for GBrowse unfortunately.  The "data source" drop down was originally conceived of to allow selecting different "species", but that concept doesn't map very well to strains of a virus.  There are two approaches I could see using:

1. Revamp the way you're using GBrowse data sources altogether, so that each data source represents one type of virus, so in the drop down you'd have two entries, one for H. influenzae and one for the other virus.  Each strain would then be analogous a chromosome. One advantage to this approach is that when/if you have hundreds of strains of a virus the drop down will still be useable (that is, a drop down menu with a more than 20-30 entries is very unwieldy).  Users would be able to use the search box to find strains they are interested in.  A potential downside is that searching for a particular gene would yield results for that gene in every strain.

2. Create separate gbrowse2 config directories for each virus.  Then you need to edit gbrowse2.conf file that lives in the apache configuration; where that is varies depending on your OS; on Ubuntu 12.04 it's in /etc/apache2/conf.d/.  You'll need separate cgi-bin directories too, for example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and /usr/lib/cgi-bin/Segb2 for the Something else virus :-)  In the apache gbrowse.conf file you need separate entries for the different cgi-bin directores that have different "SetEnv GBROWSE_CONF" entries to point at the separate gbrowse config directories.

Obviously, it's up to you to decide which is better; there will be work either way.  I suggest that if you choose the second path that you make very incremental changes and test that GBrowse still works all along the way, because there are several moving parts that could break GBrowse and with the changes required, it might be difficult to sort out what happened if something goes wrong.

Scott


On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <[hidden email]> wrote:
Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research




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by Intel and developed in partnership with Slashdot Media, is your hub for all
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news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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Re: Need a help

Scott Cain
In reply to this post by Scott Cain
Hi Swetha,

Please always ask questions on the mailing list (cc'ed here).

If you are using fastcgi, you may need to restart apache to recognize the change you made in your config file.  The other possibility is that you didn't really edit the config file that GBrowse is using (believe me, I've done that many times, where I edit a copy of the config file and can't understand why it isn't having any effect).

Scott


On Wed, Mar 4, 2015 at 6:58 AM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

I have a doubt in Gbrowse. Can you please help me sir?

Herewith, I have attached the conf file.


It works well in Browser. In file, suppose, If I change initial landmark = NC_022659.1:1..10000 to initial landmark = NC_022659.1:20639..15623, the browser displays the old landmark itself (i.e 1..10000). I know its because of some cache problem. If I delete the browser history, then the browser displays the new landmark. Can you please solve this issue?

Yours sincerely,
Swetha R G,
Senior Research Fellow (ICMR),
VIT University,
Vellore,
India.








On Thu, Nov 27, 2014 at 8:21 PM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

Tons of thanks. I followed your suggestion, option 2. Now it works well. You helped me a lot in GBrowse (Starting from installation to till now). Thank you so much. I used GBrowse in two databases and both are published. One in Genomics and other in Computers in Biology and Medicine. This publication is not possible without your guidance.

Thank you.

Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.

On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

Thank you so much for your quick reply. Let me work according to your suggestion and If I stuck at any point, Please help me.

Yours sincerely,
Swetha R G.

On Wed, Nov 26, 2014 at 9:53 PM, Scott Cain <[hidden email]> wrote:
Hi Swetha,

The only way I can think of to do that is with separate configuration files for GBrowse unfortunately.  The "data source" drop down was originally conceived of to allow selecting different "species", but that concept doesn't map very well to strains of a virus.  There are two approaches I could see using:

1. Revamp the way you're using GBrowse data sources altogether, so that each data source represents one type of virus, so in the drop down you'd have two entries, one for H. influenzae and one for the other virus.  Each strain would then be analogous a chromosome. One advantage to this approach is that when/if you have hundreds of strains of a virus the drop down will still be useable (that is, a drop down menu with a more than 20-30 entries is very unwieldy).  Users would be able to use the search box to find strains they are interested in.  A potential downside is that searching for a particular gene would yield results for that gene in every strain.

2. Create separate gbrowse2 config directories for each virus.  Then you need to edit gbrowse2.conf file that lives in the apache configuration; where that is varies depending on your OS; on Ubuntu 12.04 it's in /etc/apache2/conf.d/.  You'll need separate cgi-bin directories too, for example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and /usr/lib/cgi-bin/Segb2 for the Something else virus :-)  In the apache gbrowse.conf file you need separate entries for the different cgi-bin directores that have different "SetEnv GBROWSE_CONF" entries to point at the separate gbrowse config directories.

Obviously, it's up to you to decide which is better; there will be work either way.  I suggest that if you choose the second path that you make very incremental changes and test that GBrowse still works all along the way, because there are several moving parts that could break GBrowse and with the changes required, it might be difficult to sort out what happened if something goes wrong.

Scott


On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <[hidden email]> wrote:
Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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Re: Need a help

swetha

Dear sir,

I edited in the config file where GBrowse is using.

If I delete the browsing history, then its show the new landmark. Is there any possibility without deleting the browser history? Kindly let me know

On Mar 4, 2015 7:44 PM, "Scott Cain" <[hidden email]> wrote:
Hi Swetha,

Please always ask questions on the mailing list (cc'ed here).

If you are using fastcgi, you may need to restart apache to recognize the change you made in your config file.  The other possibility is that you didn't really edit the config file that GBrowse is using (believe me, I've done that many times, where I edit a copy of the config file and can't understand why it isn't having any effect).

Scott


On Wed, Mar 4, 2015 at 6:58 AM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

I have a doubt in Gbrowse. Can you please help me sir?

Herewith, I have attached the conf file.


It works well in Browser. In file, suppose, If I change initial landmark = NC_022659.1:1..10000 to initial landmark = NC_022659.1:20639..15623, the browser displays the old landmark itself (i.e 1..10000). I know its because of some cache problem. If I delete the browser history, then the browser displays the new landmark. Can you please solve this issue?

Yours sincerely,
Swetha R G,
Senior Research Fellow (ICMR),
VIT University,
Vellore,
India.








On Thu, Nov 27, 2014 at 8:21 PM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

Tons of thanks. I followed your suggestion, option 2. Now it works well. You helped me a lot in GBrowse (Starting from installation to till now). Thank you so much. I used GBrowse in two databases and both are published. One in Genomics and other in Computers in Biology and Medicine. This publication is not possible without your guidance.

Thank you.

Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.

On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

Thank you so much for your quick reply. Let me work according to your suggestion and If I stuck at any point, Please help me.

Yours sincerely,
Swetha R G.

On Wed, Nov 26, 2014 at 9:53 PM, Scott Cain <[hidden email]> wrote:
Hi Swetha,

The only way I can think of to do that is with separate configuration files for GBrowse unfortunately.  The "data source" drop down was originally conceived of to allow selecting different "species", but that concept doesn't map very well to strains of a virus.  There are two approaches I could see using:

1. Revamp the way you're using GBrowse data sources altogether, so that each data source represents one type of virus, so in the drop down you'd have two entries, one for H. influenzae and one for the other virus.  Each strain would then be analogous a chromosome. One advantage to this approach is that when/if you have hundreds of strains of a virus the drop down will still be useable (that is, a drop down menu with a more than 20-30 entries is very unwieldy).  Users would be able to use the search box to find strains they are interested in.  A potential downside is that searching for a particular gene would yield results for that gene in every strain.

2. Create separate gbrowse2 config directories for each virus.  Then you need to edit gbrowse2.conf file that lives in the apache configuration; where that is varies depending on your OS; on Ubuntu 12.04 it's in /etc/apache2/conf.d/.  You'll need separate cgi-bin directories too, for example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and /usr/lib/cgi-bin/Segb2 for the Something else virus :-)  In the apache gbrowse.conf file you need separate entries for the different cgi-bin directores that have different "SetEnv GBROWSE_CONF" entries to point at the separate gbrowse config directories.

Obviously, it's up to you to decide which is better; there will be work either way.  I suggest that if you choose the second path that you make very incremental changes and test that GBrowse still works all along the way, because there are several moving parts that could break GBrowse and with the changes required, it might be difficult to sort out what happened if something goes wrong.

Scott


On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <[hidden email]> wrote:
Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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Re: Need a help

Scott Cain
Hi Swetha,

I assume you mean you delete the browser's cache and then the changes show up, right?  There is not much GBrowse can do to force a browser to refresh its cache, but it generally happens on its own in a relatively short period of time.  I would guess that your users won't even notice.

Scott


On Wed, Mar 4, 2015 at 11:15 AM, Rayapadi Swetha <[hidden email]> wrote:

Dear sir,

I edited in the config file where GBrowse is using.

If I delete the browsing history, then its show the new landmark. Is there any possibility without deleting the browser history? Kindly let me know

On Mar 4, 2015 7:44 PM, "Scott Cain" <[hidden email]> wrote:
Hi Swetha,

Please always ask questions on the mailing list (cc'ed here).

If you are using fastcgi, you may need to restart apache to recognize the change you made in your config file.  The other possibility is that you didn't really edit the config file that GBrowse is using (believe me, I've done that many times, where I edit a copy of the config file and can't understand why it isn't having any effect).

Scott


On Wed, Mar 4, 2015 at 6:58 AM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

I have a doubt in Gbrowse. Can you please help me sir?

Herewith, I have attached the conf file.


It works well in Browser. In file, suppose, If I change initial landmark = NC_022659.1:1..10000 to initial landmark = NC_022659.1:20639..15623, the browser displays the old landmark itself (i.e 1..10000). I know its because of some cache problem. If I delete the browser history, then the browser displays the new landmark. Can you please solve this issue?

Yours sincerely,
Swetha R G,
Senior Research Fellow (ICMR),
VIT University,
Vellore,
India.








On Thu, Nov 27, 2014 at 8:21 PM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

Tons of thanks. I followed your suggestion, option 2. Now it works well. You helped me a lot in GBrowse (Starting from installation to till now). Thank you so much. I used GBrowse in two databases and both are published. One in Genomics and other in Computers in Biology and Medicine. This publication is not possible without your guidance.

Thank you.

Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.

On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

Thank you so much for your quick reply. Let me work according to your suggestion and If I stuck at any point, Please help me.

Yours sincerely,
Swetha R G.

On Wed, Nov 26, 2014 at 9:53 PM, Scott Cain <[hidden email]> wrote:
Hi Swetha,

The only way I can think of to do that is with separate configuration files for GBrowse unfortunately.  The "data source" drop down was originally conceived of to allow selecting different "species", but that concept doesn't map very well to strains of a virus.  There are two approaches I could see using:

1. Revamp the way you're using GBrowse data sources altogether, so that each data source represents one type of virus, so in the drop down you'd have two entries, one for H. influenzae and one for the other virus.  Each strain would then be analogous a chromosome. One advantage to this approach is that when/if you have hundreds of strains of a virus the drop down will still be useable (that is, a drop down menu with a more than 20-30 entries is very unwieldy).  Users would be able to use the search box to find strains they are interested in.  A potential downside is that searching for a particular gene would yield results for that gene in every strain.

2. Create separate gbrowse2 config directories for each virus.  Then you need to edit gbrowse2.conf file that lives in the apache configuration; where that is varies depending on your OS; on Ubuntu 12.04 it's in /etc/apache2/conf.d/.  You'll need separate cgi-bin directories too, for example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and /usr/lib/cgi-bin/Segb2 for the Something else virus :-)  In the apache gbrowse.conf file you need separate entries for the different cgi-bin directores that have different "SetEnv GBROWSE_CONF" entries to point at the separate gbrowse config directories.

Obviously, it's up to you to decide which is better; there will be work either way.  I suggest that if you choose the second path that you make very incremental changes and test that GBrowse still works all along the way, because there are several moving parts that could break GBrowse and with the changes required, it might be difficult to sort out what happened if something goes wrong.

Scott


On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <[hidden email]> wrote:
Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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Re: Need a help

swetha
Hi Sir,

Yes, When I delete the browser's cache, it shows up the new initial landmark.

Whenever, I am changing the initial land mark, I need to delete the browsers' cache to display the changed initial land mark. How to solve this issue sir? Is there anything I can change in GBrowse files to resolve this?

Yours sincerely,
Swetha R G.



On Thu, Mar 5, 2015 at 12:48 AM, Scott Cain <[hidden email]> wrote:
Hi Swetha,

I assume you mean you delete the browser's cache and then the changes show up, right?  There is not much GBrowse can do to force a browser to refresh its cache, but it generally happens on its own in a relatively short period of time.  I would guess that your users won't even notice.

Scott


On Wed, Mar 4, 2015 at 11:15 AM, Rayapadi Swetha <[hidden email]> wrote:

Dear sir,

I edited in the config file where GBrowse is using.

If I delete the browsing history, then its show the new landmark. Is there any possibility without deleting the browser history? Kindly let me know

On Mar 4, 2015 7:44 PM, "Scott Cain" <[hidden email]> wrote:
Hi Swetha,

Please always ask questions on the mailing list (cc'ed here).

If you are using fastcgi, you may need to restart apache to recognize the change you made in your config file.  The other possibility is that you didn't really edit the config file that GBrowse is using (believe me, I've done that many times, where I edit a copy of the config file and can't understand why it isn't having any effect).

Scott


On Wed, Mar 4, 2015 at 6:58 AM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

I have a doubt in Gbrowse. Can you please help me sir?

Herewith, I have attached the conf file.


It works well in Browser. In file, suppose, If I change initial landmark = NC_022659.1:1..10000 to initial landmark = NC_022659.1:20639..15623, the browser displays the old landmark itself (i.e 1..10000). I know its because of some cache problem. If I delete the browser history, then the browser displays the new landmark. Can you please solve this issue?

Yours sincerely,
Swetha R G,
Senior Research Fellow (ICMR),
VIT University,
Vellore,
India.








On Thu, Nov 27, 2014 at 8:21 PM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

Tons of thanks. I followed your suggestion, option 2. Now it works well. You helped me a lot in GBrowse (Starting from installation to till now). Thank you so much. I used GBrowse in two databases and both are published. One in Genomics and other in Computers in Biology and Medicine. This publication is not possible without your guidance.

Thank you.

Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.

On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <[hidden email]> wrote:
Dear Sir,

Thank you so much for your quick reply. Let me work according to your suggestion and If I stuck at any point, Please help me.

Yours sincerely,
Swetha R G.

On Wed, Nov 26, 2014 at 9:53 PM, Scott Cain <[hidden email]> wrote:
Hi Swetha,

The only way I can think of to do that is with separate configuration files for GBrowse unfortunately.  The "data source" drop down was originally conceived of to allow selecting different "species", but that concept doesn't map very well to strains of a virus.  There are two approaches I could see using:

1. Revamp the way you're using GBrowse data sources altogether, so that each data source represents one type of virus, so in the drop down you'd have two entries, one for H. influenzae and one for the other virus.  Each strain would then be analogous a chromosome. One advantage to this approach is that when/if you have hundreds of strains of a virus the drop down will still be useable (that is, a drop down menu with a more than 20-30 entries is very unwieldy).  Users would be able to use the search box to find strains they are interested in.  A potential downside is that searching for a particular gene would yield results for that gene in every strain.

2. Create separate gbrowse2 config directories for each virus.  Then you need to edit gbrowse2.conf file that lives in the apache configuration; where that is varies depending on your OS; on Ubuntu 12.04 it's in /etc/apache2/conf.d/.  You'll need separate cgi-bin directories too, for example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and /usr/lib/cgi-bin/Segb2 for the Something else virus :-)  In the apache gbrowse.conf file you need separate entries for the different cgi-bin directores that have different "SetEnv GBROWSE_CONF" entries to point at the separate gbrowse config directories.

Obviously, it's up to you to decide which is better; there will be work either way.  I suggest that if you choose the second path that you make very incremental changes and test that GBrowse still works all along the way, because there are several moving parts that could break GBrowse and with the changes required, it might be difficult to sort out what happened if something goes wrong.

Scott


On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <[hidden email]> wrote:
Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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