[BioMart Users] a few questions about Biomart

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[BioMart Users] a few questions about Biomart

Brenden Chen
To whom it may concern,

My name is Brenden Chen, a postdoc fellow at Mount Sinai in New York (US).
I have a few questions regarding Biomart and hope that someone could help clarify them.

Q1. Regarding ID converter, I was converting UCSC IDs to HGNC IDs a few days ago. The return at the time included several blank HGNC IDs, which is fine as, I was told later,
UCSC updates their database daily whereas HGNC/Ensemble database does not. However, earlier today (Mar. 26, 2013) when I was trying with the same ID converter, while the
result in the pop-up window still included blank HGNC IDs, the download file actually removed those that did not have a matching HGNC IDs. Is this "removal" functionality a revised version of Biomart ID converter or a glitch? From a user's standpoint, it's still useful to have unmatched blank IDs listed, at least we could manually fill in the blank. Now we need to manually add those UCSC IDs that do not have a matching HGNC IDs.

Q2. The website seems to be maintained by several groups around the globe. One of my prior communication with Biomart mentioned that I could have further inquiries emailed to
[hidden email]. What is the "correct" corresponding emails for any similar question like the one above.

Please advise. Thank you

Brenden

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[BioMart Users] openID issues

Nabihoudine Ibou
Dear all,

I'm trying to manage users with the openID system. I'm using the default
msd protein structure configuration as described in the documentation.
The documentation also says that the openID system support gmail
addresses, so I've added a new user group (named secure) and one user
with an associated Gmail account. I've also activated all acces points
and tabulation for the new user group.
The login with the gmail account works perfectly. The problem is that
the martform is empty (the attribute and the filters blocs are empty).
With the default user (anonymous) everything works perfectly.

Did you have any issue with this and a solution ?

Thanks in advance and best regards,

Ibou
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Re: [BioMart Users] openID issues

Das, Ujjwal
Hi Ibou,

Good that you brought up this issue. I had the same problem. I thought it was something to do with java version.
But that is not the case. Hopefully there will be a solution soon.
Cheers
ujjwal


Ujjwal Das, PhD
NIHR Biomedical Research Centre for Mental Health
South London and Maudsley NHS Foundation Trust &
Institute of Psychiatry, Kings College London
Box P092
De Crespigny Park
London SE5 8AF
020 7848 0473

________________________________________
From: [hidden email] [[hidden email]] on behalf of Nabihoudine Ibou [[hidden email]]
Sent: 27 March 2013 14:10
To: [hidden email]
Subject: [BioMart Users]  openID issues

Dear all,

I'm trying to manage users with the openID system. I'm using the default
msd protein structure configuration as described in the documentation.
The documentation also says that the openID system support gmail
addresses, so I've added a new user group (named secure) and one user
with an associated Gmail account. I've also activated all acces points
and tabulation for the new user group.
The login with the gmail account works perfectly. The problem is that
the martform is empty (the attribute and the filters blocs are empty).
With the default user (anonymous) everything works perfectly.

Did you have any issue with this and a solution ?

Thanks in advance and best regards,

Ibou
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users


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[hidden email]
https://lists.biomart.org/mailman/listinfo/users
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[BioMart Users] how to change the maximum upload file size ?

Nabihoudine Ibou
Hi,

I would like to upload an identifier file larger than 100k in a local
instance of biomart 0.8.
The system answer is : 'File must be less than 100000 bytes'
Where do I set the file size limit in the parameter file?

In web/etc/webdefault.xml I already have :

     <init-param>
       <param-name>maxCacheSize</param-name>
       <param-value>256000000</param-value>
     </init-param>
     <init-param>
       <param-name>maxCachedFileSize</param-name>
       <param-value>10000000</param-value>
     </init-param>
     <init-param>
       <param-name>maxCachedFiles</param-name>
       <param-value>1000</param-value>
     </init-param>

Cheers,

Ibou
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Re: [BioMart Users] a few questions about Biomart

Rhoda Kinsella
In reply to this post by Brenden Chen
Hi Brenden
Here are my responses to Q1 and Q2:

Q1: I tried to replicate your issue using the Ensembl biomart databases at www.ensembl.org, for which my team are responsible for creating and maintaining. I clicked on UCSC ID and HGNC ID attributes (no filters selected) and downloaded the results in TSV format. Here is a sample of what I got:

HGNC ID(s) UCSC ID
uc022acc.1
32652 uc003eoi.2
38207
uc021rcb.1
41892 uc003imv.3
33192
uc021vrp.1
32622 uc009ywe.3
43036
38305
32982 uc021sci.1
uc021zag.1
uc021tlh.1
uc021xuv.1

You will see that for some lines there is a UCSC ID but no HGNC ID and vice versa. For these instances there is a blank space for the missing ID. This is the expected BioMart behaviour. If I understand you correctly, you have input UCSC IDs and in the interface you see that input ID with a corresponding blank space if there is no HGNC ID. I think that if the database does not contain the UCSC ID that you have input, it should not report back anything on the interface or on the output file. This may be a new feature of the BioMart 0.8 interface, so I would be grateful if you could provide some example IDs for which this is occurring so that I can investigate further.

Q2: As I mentioned in my previous emails to you, I work for the Ensembl project and we create the Ensembl BioMart databases that are added to the BioMart central portal along with many other databases from different projects. If you have a query about the data in the Ensembl BioMart databases, please do email [hidden email]. For any BioMart central portal issues, please email this [hidden email] mailing list.

I hope that helps,
Regards
Rhoda




On 26 Mar 2013, at 20:48, Brenden Chen <[hidden email]> wrote:

To whom it may concern,

My name is Brenden Chen, a postdoc fellow at Mount Sinai in New York (US).
I have a few questions regarding Biomart and hope that someone could help clarify them.

Q1. Regarding ID converter, I was converting UCSC IDs to HGNC IDs a few days ago. The return at the time included several blank HGNC IDs, which is fine as, I was told later,
UCSC updates their database daily whereas HGNC/Ensemble database does not. However, earlier today (Mar. 26, 2013) when I was trying with the same ID converter, while the
result in the pop-up window still included blank HGNC IDs, the download file actually removed those that did not have a matching HGNC IDs. Is this "removal" functionality a revised version of Biomart ID converter or a glitch? From a user's standpoint, it's still useful to have unmatched blank IDs listed, at least we could manually fill in the blank. Now we need to manually add those UCSC IDs that do not have a matching HGNC IDs.

Q2. The website seems to be maintained by several groups around the globe. One of my prior communication with Biomart mentioned that I could have further inquiries emailed to
[hidden email]. What is the "correct" corresponding emails for any similar question like the one above.

Please advise. Thank you

Brenden
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD




_______________________________________________
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https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] a few questions about Biomart

Brenden Chen
Hi, Rhoda

Thank you very much for getting back to me.
I just re-tested the IDs and as I alluded to in the last email, perhaps it was just an one-time glitch.
Today's re-testing yielded the expected result as yours (and as one of my earlier attempts). Attached is the screenshot and the download txt file I had for today's re-test. I also am attaching a "made-up" result that is similar to what I encountered last time. In the made-up result, the unmatched HGNC symbols were automatically removed (i.e. NO blank space), even though I still saw them in pop-up result box, as shown in the "screenshot" attachment. For my purpose, I manually added those unmatched HGNS symbols, and identified the corresponding UCSC IDs (that have not yet been updated in ENSEMBLE).

So the upshot is Biomart is doing what it's supposed to, as we speak. But in contrast to what you mentioned about Biomart 0.8 version, I think the output SHOULD report the blank (to me, blank data simply implies the two databases are not synced yet).

I will include similar attachments to facilitate the discussion in the future, if I should encounter any other aberrations in Biomart,

Thank you again (for both getting back to me and helping maintain the useful online tools)

On Fri, Apr 5, 2013 at 4:42 AM, Rhoda Kinsella <[hidden email]> wrote:
Hi Brenden
Here are my responses to Q1 and Q2:

Q1: I tried to replicate your issue using the Ensembl biomart databases at www.ensembl.org, for which my team are responsible for creating and maintaining. I clicked on UCSC ID and HGNC ID attributes (no filters selected) and downloaded the results in TSV format. Here is a sample of what I got:

HGNC ID(s) UCSC ID
uc022acc.1
32652 uc003eoi.2
38207
uc021rcb.1
41892 uc003imv.3
33192
uc021vrp.1
32622 uc009ywe.3
43036
38305
32982 uc021sci.1
uc021zag.1
uc021tlh.1
uc021xuv.1

You will see that for some lines there is a UCSC ID but no HGNC ID and vice versa. For these instances there is a blank space for the missing ID. This is the expected BioMart behaviour. If I understand you correctly, you have input UCSC IDs and in the interface you see that input ID with a corresponding blank space if there is no HGNC ID. I think that if the database does not contain the UCSC ID that you have input, it should not report back anything on the interface or on the output file. This may be a new feature of the BioMart 0.8 interface, so I would be grateful if you could provide some example IDs for which this is occurring so that I can investigate further.

Q2: As I mentioned in my previous emails to you, I work for the Ensembl project and we create the Ensembl BioMart databases that are added to the BioMart central portal along with many other databases from different projects. If you have a query about the data in the Ensembl BioMart databases, please do email [hidden email]. For any BioMart central portal issues, please email this [hidden email] mailing list.

I hope that helps,
Regards
Rhoda




On 26 Mar 2013, at 20:48, Brenden Chen <[hidden email]> wrote:

To whom it may concern,

My name is Brenden Chen, a postdoc fellow at Mount Sinai in New York (US).
I have a few questions regarding Biomart and hope that someone could help clarify them.

Q1. Regarding ID converter, I was converting UCSC IDs to HGNC IDs a few days ago. The return at the time included several blank HGNC IDs, which is fine as, I was told later,
UCSC updates their database daily whereas HGNC/Ensemble database does not. However, earlier today (Mar. 26, 2013) when I was trying with the same ID converter, while the
result in the pop-up window still included blank HGNC IDs, the download file actually removed those that did not have a matching HGNC IDs. Is this "removal" functionality a revised version of Biomart ID converter or a glitch? From a user's standpoint, it's still useful to have unmatched blank IDs listed, at least we could manually fill in the blank. Now we need to manually add those UCSC IDs that do not have a matching HGNC IDs.

Q2. The website seems to be maintained by several groups around the globe. One of my prior communication with Biomart mentioned that I could have further inquiries emailed to
[hidden email]. What is the "correct" corresponding emails for any similar question like the one above.

Please advise. Thank you

Brenden
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD





_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

results.txt (5K) Download Attachment
screenshot.docx (381K) Download Attachment
made-up results.docx (18K) Download Attachment
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Re: [BioMart Users] a few questions about Biomart

Brenden Chen
In reply to this post by Rhoda Kinsella
Hi, Rhonda

Today (Apr 9th, 2013), the same phenomenon (as described in our prior correspondence, see below) occurred again. Please see attachments for the details.
As you could see in the screenshot.docx, several UCSC IDs have no matching HGNC symbols.
However, in the downloaded file - result040913.txt - all unmatched UCSC IDs were removed.
I am not clear if you meant a new version of ID converter will remove the unmatched IDs (or not remove?).
But as of today, it looks like the program chooses to remove them, even though the unmatched UCSC IDs are true transcripts of respective genes.
I do hope the program would keep all unmatched IDs, as long as they are legitimate transcripts.

Could you confirm if a new version of ID converter has been implemented ?

Best,
Brenden


On Fri, Apr 5, 2013 at 4:42 AM, Rhoda Kinsella <[hidden email]> wrote:
Hi Brenden
Here are my responses to Q1 and Q2:

Q1: I tried to replicate your issue using the Ensembl biomart databases at www.ensembl.org, for which my team are responsible for creating and maintaining. I clicked on UCSC ID and HGNC ID attributes (no filters selected) and downloaded the results in TSV format. Here is a sample of what I got:

HGNC ID(s) UCSC ID
uc022acc.1
32652 uc003eoi.2
38207
uc021rcb.1
41892 uc003imv.3
33192
uc021vrp.1
32622 uc009ywe.3
43036
38305
32982 uc021sci.1
uc021zag.1
uc021tlh.1
uc021xuv.1

You will see that for some lines there is a UCSC ID but no HGNC ID and vice versa. For these instances there is a blank space for the missing ID. This is the expected BioMart behaviour. If I understand you correctly, you have input UCSC IDs and in the interface you see that input ID with a corresponding blank space if there is no HGNC ID. I think that if the database does not contain the UCSC ID that you have input, it should not report back anything on the interface or on the output file. This may be a new feature of the BioMart 0.8 interface, so I would be grateful if you could provide some example IDs for which this is occurring so that I can investigate further.

Q2: As I mentioned in my previous emails to you, I work for the Ensembl project and we create the Ensembl BioMart databases that are added to the BioMart central portal along with many other databases from different projects. If you have a query about the data in the Ensembl BioMart databases, please do email [hidden email]. For any BioMart central portal issues, please email this [hidden email] mailing list.

I hope that helps,
Regards
Rhoda




On 26 Mar 2013, at 20:48, Brenden Chen <[hidden email]> wrote:

To whom it may concern,

My name is Brenden Chen, a postdoc fellow at Mount Sinai in New York (US).
I have a few questions regarding Biomart and hope that someone could help clarify them.

Q1. Regarding ID converter, I was converting UCSC IDs to HGNC IDs a few days ago. The return at the time included several blank HGNC IDs, which is fine as, I was told later,
UCSC updates their database daily whereas HGNC/Ensemble database does not. However, earlier today (Mar. 26, 2013) when I was trying with the same ID converter, while the
result in the pop-up window still included blank HGNC IDs, the download file actually removed those that did not have a matching HGNC IDs. Is this "removal" functionality a revised version of Biomart ID converter or a glitch? From a user's standpoint, it's still useful to have unmatched blank IDs listed, at least we could manually fill in the blank. Now we need to manually add those UCSC IDs that do not have a matching HGNC IDs.

Q2. The website seems to be maintained by several groups around the globe. One of my prior communication with Biomart mentioned that I could have further inquiries emailed to
[hidden email]. What is the "correct" corresponding emails for any similar question like the one above.

Please advise. Thank you

Brenden
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD





_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

results040913.txt (1K) Download Attachment
screenshot.docx (392K) Download Attachment
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Re: [BioMart Users] a few questions about Biomart

Rhoda Kinsella
Hi Brenden
As I mentioned in previous emails, I don't work for the BioMart project so I cannot comment on whether anything has changed with the ID converter on the BioMart Central portal. I have cc'd Arek who might be able to help you.
Regards
Rhoda

On 9 Apr 2013, at 20:12, Brenden Chen <[hidden email]> wrote:

Hi, Rhonda

Today (Apr 9th, 2013), the same phenomenon (as described in our prior correspondence, see below) occurred again. Please see attachments for the details.
As you could see in the screenshot.docx, several UCSC IDs have no matching HGNC symbols.
However, in the downloaded file - result040913.txt - all unmatched UCSC IDs were removed.
I am not clear if you meant a new version of ID converter will remove the unmatched IDs (or not remove?).
But as of today, it looks like the program chooses to remove them, even though the unmatched UCSC IDs are true transcripts of respective genes.
I do hope the program would keep all unmatched IDs, as long as they are legitimate transcripts.

Could you confirm if a new version of ID converter has been implemented ?

Best,
Brenden


On Fri, Apr 5, 2013 at 4:42 AM, Rhoda Kinsella <[hidden email]> wrote:
Hi Brenden
Here are my responses to Q1 and Q2:

Q1: I tried to replicate your issue using the Ensembl biomart databases at www.ensembl.org, for which my team are responsible for creating and maintaining. I clicked on UCSC ID and HGNC ID attributes (no filters selected) and downloaded the results in TSV format. Here is a sample of what I got:

HGNC ID(s) UCSC ID
uc022acc.1
32652 uc003eoi.2
38207
uc021rcb.1
41892 uc003imv.3
33192
uc021vrp.1
32622 uc009ywe.3
43036
38305
32982 uc021sci.1
uc021zag.1
uc021tlh.1
uc021xuv.1

You will see that for some lines there is a UCSC ID but no HGNC ID and vice versa. For these instances there is a blank space for the missing ID. This is the expected BioMart behaviour. If I understand you correctly, you have input UCSC IDs and in the interface you see that input ID with a corresponding blank space if there is no HGNC ID. I think that if the database does not contain the UCSC ID that you have input, it should not report back anything on the interface or on the output file. This may be a new feature of the BioMart 0.8 interface, so I would be grateful if you could provide some example IDs for which this is occurring so that I can investigate further.

Q2: As I mentioned in my previous emails to you, I work for the Ensembl project and we create the Ensembl BioMart databases that are added to the BioMart central portal along with many other databases from different projects. If you have a query about the data in the Ensembl BioMart databases, please do email [hidden email]. For any BioMart central portal issues, please email this [hidden email] mailing list.

I hope that helps,
Regards
Rhoda




On 26 Mar 2013, at 20:48, Brenden Chen <[hidden email]> wrote:

To whom it may concern,

My name is Brenden Chen, a postdoc fellow at Mount Sinai in New York (US).
I have a few questions regarding Biomart and hope that someone could help clarify them.

Q1. Regarding ID converter, I was converting UCSC IDs to HGNC IDs a few days ago. The return at the time included several blank HGNC IDs, which is fine as, I was told later,
UCSC updates their database daily whereas HGNC/Ensemble database does not. However, earlier today (Mar. 26, 2013) when I was trying with the same ID converter, while the
result in the pop-up window still included blank HGNC IDs, the download file actually removed those that did not have a matching HGNC IDs. Is this "removal" functionality a revised version of Biomart ID converter or a glitch? From a user's standpoint, it's still useful to have unmatched blank IDs listed, at least we could manually fill in the blank. Now we need to manually add those UCSC IDs that do not have a matching HGNC IDs.

Q2. The website seems to be maintained by several groups around the globe. One of my prior communication with Biomart mentioned that I could have further inquiries emailed to
[hidden email]. What is the "correct" corresponding emails for any similar question like the one above.

Please advise. Thank you

Brenden
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD




<results040913.txt><screenshot.docx>

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD




_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] a few questions about Biomart

Brenden Chen
Ah - sorry -
Didn't know the distinction between ENSEMBLE Biomart database and Biomart portal.
Understandably any database of this scale is likely maintained by multiple groups. unfortunately, a lot of us traditional biologists did not and still do not know it. 
Thank you for cc'ing my report to Arek, or whoever is involved in Biomart portal maintenance.
And I apologize again for troubling you with an inappropriate issue.




On Wed, Apr 10, 2013 at 5:00 AM, Rhoda Kinsella <[hidden email]> wrote:
Hi Brenden
As I mentioned in previous emails, I don't work for the BioMart project so I cannot comment on whether anything has changed with the ID converter on the BioMart Central portal. I have cc'd Arek who might be able to help you.
Regards
Rhoda

On 9 Apr 2013, at 20:12, Brenden Chen <[hidden email]> wrote:

Hi, Rhonda

Today (Apr 9th, 2013), the same phenomenon (as described in our prior correspondence, see below) occurred again. Please see attachments for the details.
As you could see in the screenshot.docx, several UCSC IDs have no matching HGNC symbols.
However, in the downloaded file - result040913.txt - all unmatched UCSC IDs were removed.
I am not clear if you meant a new version of ID converter will remove the unmatched IDs (or not remove?).
But as of today, it looks like the program chooses to remove them, even though the unmatched UCSC IDs are true transcripts of respective genes.
I do hope the program would keep all unmatched IDs, as long as they are legitimate transcripts.

Could you confirm if a new version of ID converter has been implemented ?

Best,
Brenden


On Fri, Apr 5, 2013 at 4:42 AM, Rhoda Kinsella <[hidden email]> wrote:
Hi Brenden
Here are my responses to Q1 and Q2:

Q1: I tried to replicate your issue using the Ensembl biomart databases at www.ensembl.org, for which my team are responsible for creating and maintaining. I clicked on UCSC ID and HGNC ID attributes (no filters selected) and downloaded the results in TSV format. Here is a sample of what I got:

HGNC ID(s) UCSC ID
uc022acc.1
32652 uc003eoi.2
38207
uc021rcb.1
41892 uc003imv.3
33192
uc021vrp.1
32622 uc009ywe.3
43036
38305
32982 uc021sci.1
uc021zag.1
uc021tlh.1
uc021xuv.1

You will see that for some lines there is a UCSC ID but no HGNC ID and vice versa. For these instances there is a blank space for the missing ID. This is the expected BioMart behaviour. If I understand you correctly, you have input UCSC IDs and in the interface you see that input ID with a corresponding blank space if there is no HGNC ID. I think that if the database does not contain the UCSC ID that you have input, it should not report back anything on the interface or on the output file. This may be a new feature of the BioMart 0.8 interface, so I would be grateful if you could provide some example IDs for which this is occurring so that I can investigate further.

Q2: As I mentioned in my previous emails to you, I work for the Ensembl project and we create the Ensembl BioMart databases that are added to the BioMart central portal along with many other databases from different projects. If you have a query about the data in the Ensembl BioMart databases, please do email [hidden email]. For any BioMart central portal issues, please email this [hidden email] mailing list.

I hope that helps,
Regards
Rhoda




On 26 Mar 2013, at 20:48, Brenden Chen <[hidden email]> wrote:

To whom it may concern,

My name is Brenden Chen, a postdoc fellow at Mount Sinai in New York (US).
I have a few questions regarding Biomart and hope that someone could help clarify them.

Q1. Regarding ID converter, I was converting UCSC IDs to HGNC IDs a few days ago. The return at the time included several blank HGNC IDs, which is fine as, I was told later,
UCSC updates their database daily whereas HGNC/Ensemble database does not. However, earlier today (Mar. 26, 2013) when I was trying with the same ID converter, while the
result in the pop-up window still included blank HGNC IDs, the download file actually removed those that did not have a matching HGNC IDs. Is this "removal" functionality a revised version of Biomart ID converter or a glitch? From a user's standpoint, it's still useful to have unmatched blank IDs listed, at least we could manually fill in the blank. Now we need to manually add those UCSC IDs that do not have a matching HGNC IDs.

Q2. The website seems to be maintained by several groups around the globe. One of my prior communication with Biomart mentioned that I could have further inquiries emailed to
[hidden email]. What is the "correct" corresponding emails for any similar question like the one above.

Please advise. Thank you

Brenden
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD




<results040913.txt><screenshot.docx>

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD





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Users mailing list
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https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] how to change the maximum upload file size ?

Syed Haider-4
In reply to this post by Nabihoudine Ibou
hi Ibou,

what happens when you do the above, recompile (ant) and restart jetty - does it not work ? Followiing recompile, the modified xml should make its way to dist/web/etc/ and hence restarting jetty should pick it up.

Syed


On 28 March 2013 14:56, Nabihoudine Ibou <[hidden email]> wrote:
Hi,

I would like to upload an identifier file larger than 100k in a local instance of biomart 0.8.
The system answer is : 'File must be less than 100000 bytes'
Where do I set the file size limit in the parameter file?

In web/etc/webdefault.xml I already have :

    <init-param>
      <param-name>maxCacheSize</param-name>
      <param-value>256000000</param-value>
    </init-param>
    <init-param>
      <param-name>maxCachedFileSize</param-name>
      <param-value>10000000</param-value>
    </init-param>
    <init-param>
      <param-name>maxCachedFiles</param-name>
      <param-value>1000</param-value>
    </init-param>

Cheers,

Ibou
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