Difference between revisions of "WBConfCall 2016.01.07-Agenda and Minutes"

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(Created page with "=Agenda= ==1. SAB schedule== Submitted by Kevin<br> http://wiki.wormbase.org/index.php/2016_Advisory_Board_Meeting#Organisation_of_SAB_talks ==2. WormBase exhibit at the Dev...")
 
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==2. WormBase exhibit at the Dev., Cell Bio and Gene Expression Meeting==
 
==2. WormBase exhibit at the Dev., Cell Bio and Gene Expression Meeting==
Submitted by Chris<br>
+
Submitted by Chris
 
<pre>
 
<pre>
 
Anne Marie Mahoney wants to know if we're interested in having a booth at
 
Anne Marie Mahoney wants to know if we're interested in having a booth at
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I know I'd be happy if you help organize the WormBase contingent.
 
I know I'd be happy if you help organize the WormBase contingent.
 
</pre>
 
</pre>
==3. Discussion topic about data submission forms==
+
 
Submitted by Paul D.<br>
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==3. Data submission forms==
 +
Submitted by Paul D.
 
<pre>
 
<pre>
 
Should we have a more centralised place or have some form of webforwarding for the user submission forms rather than exposing the machine and username of one of the WormBase Caltech staff?
 
Should we have a more centralised place or have some form of webforwarding for the user submission forms rather than exposing the machine and username of one of the WormBase Caltech staff?
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http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/
 
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/
 
</pre>
 
</pre>
Reply from Jauncarlos<br>
+
 
 +
Reply from Juancarlos
 
<pre>
 
<pre>
 
We've had the forms on tazendra ~azurebrd since 2001 (tazendra was minerva at the time, until 03 or 04) and haven't had any problems, so I'm okay with leaving things as they are (if the issue is the safety and privacy of my account and machine).
 
We've had the forms on tazendra ~azurebrd since 2001 (tazendra was minerva at the time, until 03 or 04) and haven't had any problems, so I'm okay with leaving things as they are (if the issue is the safety and privacy of my account and machine).
 
A lot of the forms interact with the local postgreSQL server directly, and for speed and potential network issues, it's nice that they're in the same machine. If we wanted to move things to a different centralised place for user submission, we could, but I don't know where it would be, and how much benefit we'd get from it. If someone wants to pilot that, I could move some non-postgreSQL forms and see how that works.
 
A lot of the forms interact with the local postgreSQL server directly, and for speed and potential network issues, it's nice that they're in the same machine. If we wanted to move things to a different centralised place for user submission, we could, but I don't know where it would be, and how much benefit we'd get from it. If someone wants to pilot that, I could move some non-postgreSQL forms and see how that works.
 
</pre>
 
</pre>
 +
 +
Reply from Todd
 +
<pre>
 +
Personally, I think it looks more professional to have everything hosted from the same domain.
 +
</pre>
 +
 +
Reply from Kevin
 +
<pre>
 +
The service could still be physically hosted on tazendra (and maintained by @azurebrd ), but have a WormBase domain URL root, right? e.g. www.wormbase.org/submissions, or even submissions.wormbase.org.
 +
</pre>
 +
 +
Reply from Todd
 +
<pre>
 +
Yep! It could be configured either way. The first would require a transparent reverse proxy, the second either proxy or direct traffic to host.
 +
</pre>
 +
 
==4. WS252 on staging==
 
==4. WS252 on staging==
 
Submitted by Todd
 
Submitted by Todd
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http://staging.wormbase.org/
 
http://staging.wormbase.org/
 
</pre>
 
</pre>
 +
 +
==5. WS253 model call==
 +
Submitted by Paul
 +
<pre>
 +
As the SAB has a major impact on the WS253 build schedule could I get an idea of what models are going to be touched and how complicated a change they are likely to be. A brief summary that would be great.
 +
I am aware that Mary Ann is in the process of preparing a simple change to the Transcription_factor::Feature connections but I believe that is the only one.
 +
</pre>
 +
 +
=Outstanding helpdesk issues=
 +
*ticket #4463 user is trying to find all genes encoding the proline tRNA that recognizes "CCC" codon
 +
<pre>
 +
I am trying to find the gene (or genes) that encodes the Proline tRNA that recognizes the "CCC" codon. I know previous versions of Wormbase annotation (for example, WS230) used tRNAscan-SE as the source for defining tRNA genes. However, the currently published versions of the tRNAscans for WS220 show no tRNAs that recognize the CCC codon. C. elegans clearly uses this codon for Proline, so there must be a tRNA for it. Can you tell me whether there is now a known Proline tRNA (CCC), and if not, how I might go about identifying it? (I will soon try to run tRNAscan on the latest genome release, but I'm guessing that's already been done).
 +
</pre>
 +
 +
*ticket #4455
 +
<pre>
 +
I sent a message a while ago. Apparently the problem is that your Blat only works with short input sequences? With 400 bases it wotked,but BLAT is supposed toaccept up to 20000 bases.
 +
Please advise
 +
</pre>
 +
 +
* Bug Report: Server Error: 500 <br>
 +
should people who report these be responded to, if so
 +
*#4467
 +
*#4452
 +
*#4458
 +
*#4454
 +
 +
 +
 
=Minutes=
 
=Minutes=

Revision as of 16:15, 7 January 2016

Agenda

1. SAB schedule

Submitted by Kevin
http://wiki.wormbase.org/index.php/2016_Advisory_Board_Meeting#Organisation_of_SAB_talks

2. WormBase exhibit at the Dev., Cell Bio and Gene Expression Meeting

Submitted by Chris

Anne Marie Mahoney wants to know if we're interested in having a booth at
the Orlando meeting in July:
http://www.genetics2016.org/exhibits/exhibits
It looks like the cost is $3,000 USD for an 8'x10' non-profit exhibit
space. Do we have any definitive plans for attending this conference? I
would like to attend and am happy to represent WormBase.

Reply from Todd

We should certainly have people attending and presenting at this meeting.
Various Intermine groups (probably including WormMine) will be presenting as a consortia. It makes sense for WormBase to be there, too. Whether or not we need an exhibit space probably hinges on what we will present and how many are attending.
We could always be creative and organize things like WormBase breakfast/lunch/dinner meet ups although it is hard gather too many people around a lap top.
I know I'd be happy if you help organize the WormBase contingent.

3. Data submission forms

Submitted by Paul D.

Should we have a more centralised place or have some form of webforwarding for the user submission forms rather than exposing the machine and username of one of the WormBase Caltech staff?
The following is used as the root of most/all user submission forms.
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/

Reply from Juancarlos

We've had the forms on tazendra ~azurebrd since 2001 (tazendra was minerva at the time, until 03 or 04) and haven't had any problems, so I'm okay with leaving things as they are (if the issue is the safety and privacy of my account and machine).
A lot of the forms interact with the local postgreSQL server directly, and for speed and potential network issues, it's nice that they're in the same machine. If we wanted to move things to a different centralised place for user submission, we could, but I don't know where it would be, and how much benefit we'd get from it. If someone wants to pilot that, I could move some non-postgreSQL forms and see how that works.

Reply from Todd

Personally, I think it looks more professional to have everything hosted from the same domain.

Reply from Kevin

The service could still be physically hosted on tazendra (and maintained by @azurebrd ), but have a WormBase domain URL root, right? e.g. www.wormbase.org/submissions, or even submissions.wormbase.org.

Reply from Todd

Yep! It could be configured either way. The first would require a transparent reverse proxy, the second either proxy or direct traffic to host.

4. WS252 on staging

Submitted by Todd

WS252 is now available (again) on staging.wormbase.org for testing.
http://staging.wormbase.org/

5. WS253 model call

Submitted by Paul

As the SAB has a major impact on the WS253 build schedule could I get an idea of what models are going to be touched and how complicated a change they are likely to be. A brief summary that would be great.
I am aware that Mary Ann is in the process of preparing a simple change to the Transcription_factor::Feature connections but I believe that is the only one.

Outstanding helpdesk issues

  • ticket #4463 user is trying to find all genes encoding the proline tRNA that recognizes "CCC" codon
I am trying to find the gene (or genes) that encodes the Proline tRNA that recognizes the "CCC" codon. I know previous versions of Wormbase annotation (for example, WS230) used tRNAscan-SE as the source for defining tRNA genes. However, the currently published versions of the tRNAscans for WS220 show no tRNAs that recognize the CCC codon. C. elegans clearly uses this codon for Proline, so there must be a tRNA for it. Can you tell me whether there is now a known Proline tRNA (CCC), and if not, how I might go about identifying it? (I will soon try to run tRNAscan on the latest genome release, but I'm guessing that's already been done).
  • ticket #4455
I sent a message a while ago. Apparently the problem is that your Blat only works with short input sequences? With 400 bases it wotked,but BLAT is supposed toaccept up to 20000 bases.
Please advise
  • Bug Report: Server Error: 500

should people who report these be responded to, if so

    1. 4467
    2. 4452
    3. 4458
    4. 4454


Minutes