[Gmod-ajax] RNA bam track problem

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[Gmod-ajax] RNA bam track problem

Keiran Raine
Hi,

We have RNA data with large spans in BAM format.  What I'm finding is that it works when zoomed in at ~2kb but as I zoom out above this I get 'Too much data to show; zoom in to see detail'.

I assumed this was 'chunkSizeLimit' but that has no effect (tried 100MB), I've also tried setting 'maxFeatureScreenDensity' to high values (100).

Any ideas?  Config at end of email.

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


{
  "maxFeatureScreenDensity": 4,
  "glyph": "JBrowse/View/FeatureGlyph/Alignment",
  "maxFeatureGlyphExpansion": 0,
  "maxHeight": 600,
  "histograms": {
    "description": "coverage depth",
    "min": 0
  },
  "style": {
    "_defaultHistScale": 4,
    "_defaultLabelScale": 30,
    "_defaultDescriptionScale": 120,
    "showLabels": false,
    "showTooltips": true,
    "featureScale": 1,
    "height": 7
  },
  "displayMode": "normal",
  "events": {},
  "menuTemplate": [
    {
      "label": "View details",
      "title": "{type} {name}",
      "action": "contentDialog",
      "iconClass": "dijitIconTask"
    },
    {
      "iconClass": "dijitIconFilter"
    }
  ],
  "hideDuplicateReads": true,
  "hideQCFailingReads": true,
  "hideSecondary": true,
  "hideSupplementary": true,
  "hideMissingMatepairs": false,
  "hideForwardStrand": false,
  "hideReverseStrand": false,
  "key": "TopHat BAM HCC1187_RNA",
  "storeClass": "JBrowse/Store/SeqFeature/BAM",
  "urlTemplate": "../nfs/cancer_trk-dev03/00000011/11253.tophat.nodup.bam",
  "metadata": {
    "TYPE": "TopHat BAM",
    "SAMPLE": "HCC1187_RNA",
    "category": "HCC1187_RNA",
    "Description": "Results from TopHat BAM"
  },
  "type": "JBrowse/View/Track/Alignments2",
  "label": "HCC1187_RNA-TopHat BAM",
  "baiUrlTemplate": "../nfs/cancer_trk-dev02/00000003/11254.tophat.nodup.bai",
  "chunkSizeLimit": 500000,
}

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: RNA bam track problem

Robert Buels-2
You've got style.featureScale set, which overrides
maxFeatureScreenDensity.  You'll want to either delete that, or tweak
its value.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/03/2014 11:48 AM, Keiran Raine wrote:

> Hi,
>
> We have RNA data with large spans in BAM format.  What I'm finding is
> that it works when zoomed in at ~2kb but as I zoom out above this I get
> 'Too much data to show; zoom in to see detail'.
>
> I assumed this was 'chunkSizeLimit' but that has no effect (tried
> 100MB), I've also tried setting 'maxFeatureScreenDensity' to high values
> (100).
>
> Any ideas?  Config at end of email.
>
> Thanks,
>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
>
> [hidden email] <mailto:[hidden email]>
> Tel:+44 (0)1223 834244 Ext: 7703
> Office: H104
>
>
> {
>    "maxFeatureScreenDensity": 4,
>    "glyph": "JBrowse/View/FeatureGlyph/Alignment",
>    "maxFeatureGlyphExpansion": 0,
>    "maxHeight": 600,
>    "histograms": {
>      "description": "coverage depth",
>      "min": 0
>    },
>    "style": {
>      "_defaultHistScale": 4,
>      "_defaultLabelScale": 30,
>      "_defaultDescriptionScale": 120,
>      "showLabels": false,
>      "showTooltips": true,
>      "featureScale": 1,
>      "height": 7
>    },
>    "displayMode": "normal",
>    "events": {},
>    "menuTemplate": [
>      {
>        "label": "View details",
>        "title": "{type} {name}",
>        "action": "contentDialog",
>        "iconClass": "dijitIconTask"
>      },
>      {
>        "iconClass": "dijitIconFilter"
>      }
>    ],
>    "hideDuplicateReads": true,
>    "hideQCFailingReads": true,
>    "hideSecondary": true,
>    "hideSupplementary": true,
>    "hideMissingMatepairs": false,
>    "hideForwardStrand": false,
>    "hideReverseStrand": false,
>    "key": "TopHat BAM HCC1187_RNA",
>    "storeClass": "JBrowse/Store/SeqFeature/BAM",
>    "urlTemplate": "../nfs/cancer_trk-dev03/00000011/11253.tophat.nodup.bam",
>    "metadata": {
>      "TYPE": "TopHat BAM",
>      "SAMPLE": "HCC1187_RNA",
>      "category": "HCC1187_RNA",
>      "Description": "Results from TopHat BAM"
>    },
>    "type": "JBrowse/View/Track/Alignments2",
>    "label": "HCC1187_RNA-TopHat BAM",
>    "baiUrlTemplate":
> "../nfs/cancer_trk-dev02/00000003/11254.tophat.nodup.bai",
>    "chunkSizeLimit": 500000,
>    "baseUrl":
> "http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/autoconf/t712/"
> }
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: RNA bam track problem

Keiran Raine
Ah thanks, the perils of auto generated config from a common method.

As a follow on how do I preserve the split read display as here:


When zooming out the linking line is lost and show like a contiguous read:


I thought it may be related to 'maxFeatureGlyphExpansion' but I can't find any reference to this in the docs.

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 3 Jan 2014, at 16:59, Robert Buels <[hidden email]> wrote:

You've got style.featureScale set, which overrides maxFeatureScreenDensity.  You'll want to either delete that, or tweak its value.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/03/2014 11:48 AM, Keiran Raine wrote:
Hi,

We have RNA data with large spans in BAM format.  What I'm finding is
that it works when zoomed in at ~2kb but as I zoom out above this I get
'Too much data to show; zoom in to see detail'.

I assumed this was 'chunkSizeLimit' but that has no effect (tried
100MB), I've also tried setting 'maxFeatureScreenDensity' to high values
(100).

Any ideas?  Config at end of email.

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

[hidden email] <[hidden email]>
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


{
  "maxFeatureScreenDensity": 4,
  "glyph": "JBrowse/View/FeatureGlyph/Alignment",
  "maxFeatureGlyphExpansion": 0,
  "maxHeight": 600,
  "histograms": {
    "description": "coverage depth",
    "min": 0
  },
  "style": {
    "_defaultHistScale": 4,
    "_defaultLabelScale": 30,
    "_defaultDescriptionScale": 120,
    "showLabels": false,
    "showTooltips": true,
    "featureScale": 1,
    "height": 7
  },
  "displayMode": "normal",
  "events": {},
  "menuTemplate": [
    {
      "label": "View details",
      "title": "{type} {name}",
      "action": "contentDialog",
      "iconClass": "dijitIconTask"
    },
    {
      "iconClass": "dijitIconFilter"
    }
  ],
  "hideDuplicateReads": true,
  "hideQCFailingReads": true,
  "hideSecondary": true,
  "hideSupplementary": true,
  "hideMissingMatepairs": false,
  "hideForwardStrand": false,
  "hideReverseStrand": false,
  "key": "TopHat BAM HCC1187_RNA",
  "storeClass": "JBrowse/Store/SeqFeature/BAM",
  "urlTemplate": "../nfs/cancer_trk-dev03/00000011/11253.tophat.nodup.bam",
  "metadata": {
    "TYPE": "TopHat BAM",
    "SAMPLE": "HCC1187_RNA",
    "category": "HCC1187_RNA",
    "Description": "Results from TopHat BAM"
  },
  "type": "JBrowse/View/Track/Alignments2",
  "label": "HCC1187_RNA-TopHat BAM",
  "baiUrlTemplate":
"../nfs/cancer_trk-dev02/00000003/11254.tophat.nodup.bai",
  "chunkSizeLimit": 500000,
  "baseUrl":
"http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/autoconf/t712/"
}

-- The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.


------------------------------------------------------------------------------
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organizations don't have a clear picture of how application performance
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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: RNA bam track problem

Robert Buels-2
When zoomed out past 0.2 pixels/bp, it stops trying to parse the reads'
MD and CIGAR fields for mismatches, because the thinking is that they
won't be visible anyway.

This works great for getting more performance when the mismatches are
all small, but it looks like it's causing problems when the reads have
big gaps like that one.  I'll try to find a better default behavior.
Could you send me a GFF3 export of that visible region?  I just want to
see the kind of MD and CIGAR tags those reads have.

There isn't a way to tweak it in the config right now, I'll add one in
1.11.1.  And I'll try to make better default behavior.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/03/2014 04:39 PM, Keiran Raine wrote:

> Ah thanks, the perils of auto generated config from a common method.
>
> As a follow on how do I preserve the split read display as here:
>
>
> When zooming out the linking line is lost and show like a contiguous read:
>
>
> I thought it may be related to 'maxFeatureGlyphExpansion' but I can't
> find any reference to this in the docs.
>
> Thanks,
>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
>
> [hidden email] <mailto:[hidden email]>
> Tel:+44 (0)1223 834244 Ext: 7703
> Office: H104
>
> On 3 Jan 2014, at 16:59, Robert Buels <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> You've got style.featureScale set, which overrides
>> maxFeatureScreenDensity.  You'll want to either delete that, or tweak
>> its value.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 01/03/2014 11:48 AM, Keiran Raine wrote:
>>> Hi,
>>>
>>> We have RNA data with large spans in BAM format.  What I'm finding is
>>> that it works when zoomed in at ~2kb but as I zoom out above this I get
>>> 'Too much data to show; zoom in to see detail'.
>>>
>>> I assumed this was 'chunkSizeLimit' but that has no effect (tried
>>> 100MB), I've also tried setting 'maxFeatureScreenDensity' to high values
>>> (100).
>>>
>>> Any ideas?  Config at end of email.
>>>
>>> Thanks,
>>>
>>> Keiran Raine
>>> Principal Bioinformatician
>>> Cancer Genome Project
>>> Wellcome Trust Sanger Institute
>>>
>>> [hidden email] <mailto:[hidden email]> <mailto:[hidden email]>
>>> Tel:+44 (0)1223 834244 Ext: 7703
>>> Office: H104
>>>
>>>
>>> {
>>>   "maxFeatureScreenDensity": 4,
>>>   "glyph": "JBrowse/View/FeatureGlyph/Alignment",
>>>   "maxFeatureGlyphExpansion": 0,
>>>   "maxHeight": 600,
>>>   "histograms": {
>>>     "description": "coverage depth",
>>>     "min": 0
>>>   },
>>>   "style": {
>>>     "_defaultHistScale": 4,
>>>     "_defaultLabelScale": 30,
>>>     "_defaultDescriptionScale": 120,
>>>     "showLabels": false,
>>>     "showTooltips": true,
>>>     "featureScale": 1,
>>>     "height": 7
>>>   },
>>>   "displayMode": "normal",
>>>   "events": {},
>>>   "menuTemplate": [
>>>     {
>>>       "label": "View details",
>>>       "title": "{type} {name}",
>>>       "action": "contentDialog",
>>>       "iconClass": "dijitIconTask"
>>>     },
>>>     {
>>>       "iconClass": "dijitIconFilter"
>>>     }
>>>   ],
>>>   "hideDuplicateReads": true,
>>>   "hideQCFailingReads": true,
>>>   "hideSecondary": true,
>>>   "hideSupplementary": true,
>>>   "hideMissingMatepairs": false,
>>>   "hideForwardStrand": false,
>>>   "hideReverseStrand": false,
>>>   "key": "TopHat BAM HCC1187_RNA",
>>>   "storeClass": "JBrowse/Store/SeqFeature/BAM",
>>>   "urlTemplate":
>>> "../nfs/cancer_trk-dev03/00000011/11253.tophat.nodup.bam",
>>>   "metadata": {
>>>     "TYPE": "TopHat BAM",
>>>     "SAMPLE": "HCC1187_RNA",
>>>     "category": "HCC1187_RNA",
>>>     "Description": "Results from TopHat BAM"
>>>   },
>>>   "type": "JBrowse/View/Track/Alignments2",
>>>   "label": "HCC1187_RNA-TopHat BAM",
>>>   "baiUrlTemplate":
>>> "../nfs/cancer_trk-dev02/00000003/11254.tophat.nodup.bai",
>>>   "chunkSizeLimit": 500000,
>>>   "baseUrl":
>>> "http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/autoconf/t712/"
>>> }
>>>
>>> -- The Wellcome Trust Sanger Institute is operated by Genome Research
>>> Limited, a charity registered in England with number 1021457 and a
>>> company registered in England with number 2742969, whose registered
>>> office is 215 Euston Road, London, NW1 2BE.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Rapidly troubleshoot problems before they affect your business. Most IT
>>> organizations don't have a clear picture of how application performance
>>> affects their revenue. With AppDynamics, you get 100% visibility into
>>> your
>>> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
>>> AppDynamics Pro!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.

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Re: RNA bam track problem

Keiran Raine
Hi Robert,

I think the default is fine, we just need the ability to edit it for cases such as this.

I think you can probably get away with only checking the cigar for D/N events above that resolution.

$cigar =~ m/([[:digit:]]+)[DN]

Data as requested:


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.



Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 3 Jan 2014, at 21:53, Robert Buels <[hidden email]> wrote:

When zoomed out past 0.2 pixels/bp, it stops trying to parse the reads' MD and CIGAR fields for mismatches, because the thinking is that they won't be visible anyway.

This works great for getting more performance when the mismatches are all small, but it looks like it's causing problems when the reads have big gaps like that one.  I'll try to find a better default behavior. Could you send me a GFF3 export of that visible region?  I just want to see the kind of MD and CIGAR tags those reads have.

There isn't a way to tweak it in the config right now, I'll add one in 1.11.1.  And I'll try to make better default behavior.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/03/2014 04:39 PM, Keiran Raine wrote:
Ah thanks, the perils of auto generated config from a common method.

As a follow on how do I preserve the split read display as here:


When zooming out the linking line is lost and show like a contiguous read:


I thought it may be related to 'maxFeatureGlyphExpansion' but I can't
find any reference to this in the docs.

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

[hidden email] <[hidden email]>
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 3 Jan 2014, at 16:59, Robert Buels <[hidden email]
<[hidden email]>> wrote:

You've got style.featureScale set, which overrides
maxFeatureScreenDensity.  You'll want to either delete that, or tweak
its value.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/03/2014 11:48 AM, Keiran Raine wrote:
Hi,

We have RNA data with large spans in BAM format.  What I'm finding is
that it works when zoomed in at ~2kb but as I zoom out above this I get
'Too much data to show; zoom in to see detail'.

I assumed this was 'chunkSizeLimit' but that has no effect (tried
100MB), I've also tried setting 'maxFeatureScreenDensity' to high values
(100).

Any ideas?  Config at end of email.

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

[hidden email] <[hidden email]> <[hidden email]>
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


{
 "maxFeatureScreenDensity": 4,
 "glyph": "JBrowse/View/FeatureGlyph/Alignment",
 "maxFeatureGlyphExpansion": 0,
 "maxHeight": 600,
 "histograms": {
   "description": "coverage depth",
   "min": 0
 },
 "style": {
   "_defaultHistScale": 4,
   "_defaultLabelScale": 30,
   "_defaultDescriptionScale": 120,
   "showLabels": false,
   "showTooltips": true,
   "featureScale": 1,
   "height": 7
 },
 "displayMode": "normal",
 "events": {},
 "menuTemplate": [
   {
     "label": "View details",
     "title": "{type} {name}",
     "action": "contentDialog",
     "iconClass": "dijitIconTask"
   },
   {
     "iconClass": "dijitIconFilter"
   }
 ],
 "hideDuplicateReads": true,
 "hideQCFailingReads": true,
 "hideSecondary": true,
 "hideSupplementary": true,
 "hideMissingMatepairs": false,
 "hideForwardStrand": false,
 "hideReverseStrand": false,
 "key": "TopHat BAM HCC1187_RNA",
 "storeClass": "JBrowse/Store/SeqFeature/BAM",
 "urlTemplate":
"../nfs/cancer_trk-dev03/00000011/11253.tophat.nodup.bam",
 "metadata": {
   "TYPE": "TopHat BAM",
   "SAMPLE": "HCC1187_RNA",
   "category": "HCC1187_RNA",
   "Description": "Results from TopHat BAM"
 },
 "type": "JBrowse/View/Track/Alignments2",
 "label": "HCC1187_RNA-TopHat BAM",
 "baiUrlTemplate":
"../nfs/cancer_trk-dev02/00000003/11254.tophat.nodup.bai",
 "chunkSizeLimit": 500000,
 "baseUrl":
"http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/autoconf/t712/"
}

-- The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.


------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into
your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk



_______________________________________________
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-- The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.


------------------------------------------------------------------------------
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Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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RNA-12-21680614..21682025.gff3 (23K) Download Attachment