scores in Bio::DB::BigBed

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scores in Bio::DB::BigBed

Daniel Lang
Hi,

quick question about the BigBed adaptor: Is it correct that the bin and
summary functions only return statistics about the number of features in
the defined intervals?
I was expecting them to deliver statistics about the score if the
respective bb file has a defined score field.
If this is true, does this also mean that I cannot plot the distribution
of scores in BigBed files in gbrowse?

This is the first time I'm using BigBed, maybe I'm doing something wrong...

I had some trouble formatting the bed files correctly in order to see
the score in the features returned by the Bio::DB::BigBed::features()
routine. It seems the bigbed entries will only have a correctly assigned
score field if you also provide a non-empty name field. Initially I
thought that the order of columns is irrelevant if you use an .as file
in the bedToBigBed call, but that doesn't seem to be the case.

Best,
Daniel
--

Dr. Daniel Lang
University of Freiburg, Plant Biotechnology
Schaenzlestr. 1, D-79104 Freiburg
fax:        +49 761 203 6945
phone:      +49 761 203 6989
homepage:   http://www.plant-biotech.net/
            http://www.cosmoss.org/
e-mail:     [hidden email]

#################################################
My software never has bugs.
It just develops random features.
#################################################




------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
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Re: scores in Bio::DB::BigBed

Timothy Parnell
Hi Daniel,

You are correct about the bin and summary function of the BigBed adaptor
working only with the number of features and not the individual scores.

There is a workaround, albeit not as efficient as the statistical method.
In the conf stanza, you'll need to use the region feature, and then use
the older xyplot glyph. This glyph will iterate through all the bed
features, calling the score method on each, and then draw an xyplot with
those collected scores. Be sure to set the group_on function to tie them
all into one graph. Here is an example.

[bigbed_score_graph]
database     = bigbed_db
feature      = region
glyph        = xyplot
graph_type   = line
group_on     = type

As for the BED format, per the format definition from UCSC, the first
three columns (chromosome, start, stop) are required, and any additional
higher number columns must have the lower columns filled. So to include a
score (5th column), you need to also fill the name (4th) column.

If your features don't have names, then I would recommend using the BigWig
format instead. You can load a bedgraph file (chromosome, start, stop,
score) into a BigWig database. You'll also have access to the fast summary
statistical functions that work on the scores.

Hope that helps.
Tim



On 7/3/11 3:48 AM, "Daniel Lang" <[hidden email]>
wrote:

>Hi,
>
>quick question about the BigBed adaptor: Is it correct that the bin and
>summary functions only return statistics about the number of features in
>the defined intervals?
>I was expecting them to deliver statistics about the score if the
>respective bb file has a defined score field.
>If this is true, does this also mean that I cannot plot the distribution
>of scores in BigBed files in gbrowse?
>
>This is the first time I'm using BigBed, maybe I'm doing something
>wrong...
>
>I had some trouble formatting the bed files correctly in order to see
>the score in the features returned by the Bio::DB::BigBed::features()
>routine. It seems the bigbed entries will only have a correctly assigned
>score field if you also provide a non-empty name field. Initially I
>thought that the order of columns is irrelevant if you use an .as file
>in the bedToBigBed call, but that doesn't seem to be the case.
>
>Best,
>Daniel
>--
>
>Dr. Daniel Lang
>University of Freiburg, Plant Biotechnology
>Schaenzlestr. 1, D-79104 Freiburg
>fax:        +49 761 203 6945
>phone:      +49 761 203 6989
>homepage:   http://www.plant-biotech.net/
>            http://www.cosmoss.org/
>e-mail:     [hidden email]
>
>#################################################
>My software never has bugs.
>It just develops random features.
>#################################################
>
>
>
>
>--------------------------------------------------------------------------
>----
>All of the data generated in your IT infrastructure is seriously valuable.
>Why? It contains a definitive record of application performance, security
>threats, fraudulent activity, and more. Splunk takes this data and makes
>sense of it. IT sense. And common sense.
>http://p.sf.net/sfu/splunk-d2d-c2
>_______________________________________________
>Gmod-gbrowse mailing list
>[hidden email]
>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Gmod-gbrowse mailing list
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Re: scores in Bio::DB::BigBed

Daniel Lang
Hi Timothy,

thanks for your immediate and thorough response! That helps me a lot!
I'll try it out directly.

I didn't correctly connect the dots with BigWig vs BigBed. So if I don't
want to identify individual features, I should better use that...

Best,
Daniel


Am 03.07.2011 22:10, schrieb Timothy Parnell:

> Hi Daniel,
>
> You are correct about the bin and summary function of the BigBed adaptor
> working only with the number of features and not the individual scores.
>
> There is a workaround, albeit not as efficient as the statistical method.
> In the conf stanza, you'll need to use the region feature, and then use
> the older xyplot glyph. This glyph will iterate through all the bed
> features, calling the score method on each, and then draw an xyplot with
> those collected scores. Be sure to set the group_on function to tie them
> all into one graph. Here is an example.
>
> [bigbed_score_graph]
> database     = bigbed_db
> feature      = region
> glyph        = xyplot
> graph_type   = line
> group_on     = type
>
> As for the BED format, per the format definition from UCSC, the first
> three columns (chromosome, start, stop) are required, and any additional
> higher number columns must have the lower columns filled. So to include a
> score (5th column), you need to also fill the name (4th) column.
>
> If your features don't have names, then I would recommend using the BigWig
> format instead. You can load a bedgraph file (chromosome, start, stop,
> score) into a BigWig database. You'll also have access to the fast summary
> statistical functions that work on the scores.
>
> Hope that helps.
> Tim
>
>
>
> On 7/3/11 3:48 AM, "Daniel Lang" <[hidden email]>
> wrote:
>
>> Hi,
>>
>> quick question about the BigBed adaptor: Is it correct that the bin and
>> summary functions only return statistics about the number of features in
>> the defined intervals?
>> I was expecting them to deliver statistics about the score if the
>> respective bb file has a defined score field.
>> If this is true, does this also mean that I cannot plot the distribution
>> of scores in BigBed files in gbrowse?
>>
>> This is the first time I'm using BigBed, maybe I'm doing something
>> wrong...
>>
>> I had some trouble formatting the bed files correctly in order to see
>> the score in the features returned by the Bio::DB::BigBed::features()
>> routine. It seems the bigbed entries will only have a correctly assigned
>> score field if you also provide a non-empty name field. Initially I
>> thought that the order of columns is irrelevant if you use an .as file
>> in the bedToBigBed call, but that doesn't seem to be the case.
>>
>> Best,
>> Daniel
>> --
>>
>> Dr. Daniel Lang
>> University of Freiburg, Plant Biotechnology
>> Schaenzlestr. 1, D-79104 Freiburg
>> fax:        +49 761 203 6945
>> phone:      +49 761 203 6989
>> homepage:   http://www.plant-biotech.net/
>>            http://www.cosmoss.org/
>> e-mail:     [hidden email]
>>
>> #################################################
>> My software never has bugs.
>> It just develops random features.
>> #################################################
>>
>>
>>
>>
>> --------------------------------------------------------------------------
>> ----
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--

Dr. Daniel Lang
University of Freiburg, Plant Biotechnology
Schaenzlestr. 1, D-79104 Freiburg
fax:        +49 761 203 6945
phone:      +49 761 203 6989
homepage:   http://www.plant-biotech.net/
            http://www.cosmoss.org/
e-mail:     [hidden email]

#################################################
My software never has bugs.
It just develops random features.
#################################################




------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: scores in Bio::DB::BigBed

Lincoln Stein
In reply to this post by Daniel Lang
Hi Dan,

The documentation for BigBed is scanty; all I know about it is what is provided by the bigbed library is in Jim Kent's bigbed.h include file. I had thought that the scores in BED files would come through into the summary statistics like those in BigWig, but now I'm looking at the example data provided in Jim's source code, and see that the BigBed example source file has scores of "0".

I'll investigate whether there is an issue in the Perl layer, but it could easily be a limitation in the library itself. Have you considered using a BedGraph file and indexing it with bedGraphToBigWig? I know that the Bio::DB::BigWig interface works perfectly to retrieve and summarize the scores.

Lincoln

On Sun, Jul 3, 2011 at 5:48 AM, Daniel Lang <[hidden email]> wrote:
Hi,

quick question about the BigBed adaptor: Is it correct that the bin and
summary functions only return statistics about the number of features in
the defined intervals?
I was expecting them to deliver statistics about the score if the
respective bb file has a defined score field.
If this is true, does this also mean that I cannot plot the distribution
of scores in BigBed files in gbrowse?

This is the first time I'm using BigBed, maybe I'm doing something wrong...

I had some trouble formatting the bed files correctly in order to see
the score in the features returned by the Bio::DB::BigBed::features()
routine. It seems the bigbed entries will only have a correctly assigned
score field if you also provide a non-empty name field. Initially I
thought that the order of columns is irrelevant if you use an .as file
in the bedToBigBed call, but that doesn't seem to be the case.

Best,
Daniel
--

Dr. Daniel Lang
University of Freiburg, Plant Biotechnology
Schaenzlestr. 1, D-79104 Freiburg
fax:        <a href="tel:%2B49%20761%20203%206945" value="+497612036945">+49 761 203 6945
phone:      <a href="tel:%2B49%20761%20203%206989" value="+497612036989">+49 761 203 6989
homepage:   http://www.plant-biotech.net/
           <a href="http://www.cosmoss.org/ e-mail" target="_blank">http://www.cosmoss.org/
e-mail:     [hidden email]

#################################################
My software never has bugs.
It just develops random features.
#################################################




------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: scores in Bio::DB::BigBed

Lincoln Stein
I had a look at the output of bigBedSummary, which is from Jim Kent's source tree (no Perl involved), and it appears that the statistics it provides are limited to coverage; so I don't think you can do anything with the scores if you're using BigBed indexing. Have a look at BedGraph=>BigWig and see if it meets your needs.

Lincoln

On Mon, Jul 4, 2011 at 9:04 AM, Lincoln Stein <[hidden email]> wrote:
Hi Dan,

The documentation for BigBed is scanty; all I know about it is what is provided by the bigbed library is in Jim Kent's bigbed.h include file. I had thought that the scores in BED files would come through into the summary statistics like those in BigWig, but now I'm looking at the example data provided in Jim's source code, and see that the BigBed example source file has scores of "0".

I'll investigate whether there is an issue in the Perl layer, but it could easily be a limitation in the library itself. Have you considered using a BedGraph file and indexing it with bedGraphToBigWig? I know that the Bio::DB::BigWig interface works perfectly to retrieve and summarize the scores.

Lincoln


On Sun, Jul 3, 2011 at 5:48 AM, Daniel Lang <[hidden email]> wrote:
Hi,

quick question about the BigBed adaptor: Is it correct that the bin and
summary functions only return statistics about the number of features in
the defined intervals?
I was expecting them to deliver statistics about the score if the
respective bb file has a defined score field.
If this is true, does this also mean that I cannot plot the distribution
of scores in BigBed files in gbrowse?

This is the first time I'm using BigBed, maybe I'm doing something wrong...

I had some trouble formatting the bed files correctly in order to see
the score in the features returned by the Bio::DB::BigBed::features()
routine. It seems the bigbed entries will only have a correctly assigned
score field if you also provide a non-empty name field. Initially I
thought that the order of columns is irrelevant if you use an .as file
in the bedToBigBed call, but that doesn't seem to be the case.

Best,
Daniel
--

Dr. Daniel Lang
University of Freiburg, Plant Biotechnology
Schaenzlestr. 1, D-79104 Freiburg
fax:        <a href="tel:%2B49%20761%20203%206945" value="+497612036945" target="_blank">+49 761 203 6945
phone:      <a href="tel:%2B49%20761%20203%206989" value="+497612036989" target="_blank">+49 761 203 6989
homepage:   http://www.plant-biotech.net/
           http://www.cosmoss.org/
e-mail
:     [hidden email]

#################################################
My software never has bugs.
It just develops random features.
#################################################




------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: [Bioperl-l] scores in Bio::DB::BigBed

Fields, Christopher J
I generally follow these rules where I want a common set of possibly volatile features (e.g. specific transcriptome analysis) separate from my main 'stable' feature database (e.g. gene models):

1) BigBed - lightweight bundle of simple features where the ranges may overlap, but I'm not concerned about score.  I have found BED/BigBed scores of limited use in most cases to me unless I scale the data (since they must be 0-1000 integer values).  Document it very well if you do any scaling! YMMV

2) SAM/BAM - bundle of (possibly overlapping) features where summary stats are needed.  I've seen these used for BLAST/BLAT runs, etc.

3) BigWig - quantitative data of fixed or varying ranges covering entire genome, ranges can't overlap

4) BedGraph - quantitative sparse data, ranges can't overlap (these are converted over to BigWig for GBrowse, though)

5) Of course, one can also set up separate DB::SF::Store databases as well depending on your needs (I have used both the SQLite and MySQL adaptors for this).

I think this is almost begging for a 'best practices' chart/table somewhere, maybe a GBrowse 'cookbook' of common data representation cases.

chris

On Jul 4, 2011, at 8:22 AM, Lincoln Stein wrote:

> I had a look at the output of bigBedSummary, which is from Jim Kent's source
> tree (no Perl involved), and it appears that the statistics it provides are
> limited to coverage; so I don't think you can do anything with the scores if
> you're using BigBed indexing. Have a look at BedGraph=>BigWig and see if it
> meets your needs.
>
> Lincoln
>
> On Mon, Jul 4, 2011 at 9:04 AM, Lincoln Stein <[hidden email]>wrote:
>
>> Hi Dan,
>>
>> The documentation for BigBed is scanty; all I know about it is what is
>> provided by the bigbed library is in Jim Kent's bigbed.h include file. I had
>> thought that the scores in BED files would come through into the summary
>> statistics like those in BigWig, but now I'm looking at the example data
>> provided in Jim's source code, and see that the BigBed example source file
>> has scores of "0".
>>
>> I'll investigate whether there is an issue in the Perl layer, but it could
>> easily be a limitation in the library itself. Have you considered using a
>> BedGraph file and indexing it with bedGraphToBigWig? I know that the
>> Bio::DB::BigWig interface works perfectly to retrieve and summarize the
>> scores.
>>
>> Lincoln
>>
>>
>> On Sun, Jul 3, 2011 at 5:48 AM, Daniel Lang <
>> [hidden email]> wrote:
>>
>>> Hi,
>>>
>>> quick question about the BigBed adaptor: Is it correct that the bin and
>>> summary functions only return statistics about the number of features in
>>> the defined intervals?
>>> I was expecting them to deliver statistics about the score if the
>>> respective bb file has a defined score field.
>>> If this is true, does this also mean that I cannot plot the distribution
>>> of scores in BigBed files in gbrowse?
>>>
>>> This is the first time I'm using BigBed, maybe I'm doing something
>>> wrong...
>>>
>>> I had some trouble formatting the bed files correctly in order to see
>>> the score in the features returned by the Bio::DB::BigBed::features()
>>> routine. It seems the bigbed entries will only have a correctly assigned
>>> score field if you also provide a non-empty name field. Initially I
>>> thought that the order of columns is irrelevant if you use an .as file
>>> in the bedToBigBed call, but that doesn't seem to be the case.
>>>
>>> Best,
>>> Daniel
>>> --
>>>
>>> Dr. Daniel Lang
>>> University of Freiburg, Plant Biotechnology
>>> Schaenzlestr. 1, D-79104 Freiburg
>>> fax:        +49 761 203 6945
>>> phone:      +49 761 203 6989
>>> homepage:   http://www.plant-biotech.net/
>>>           http://www.cosmoss.org/
>>> e-mail <http://www.cosmoss.org/e-mail>:
>>> [hidden email]
>>>
>>> #################################################
>>> My software never has bugs.
>>> It just develops random features.
>>> #################################################
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> All of the data generated in your IT infrastructure is seriously valuable.
>>> Why? It contains a definitive record of application performance, security
>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>> sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-d2d-c2
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>>
>> --
>> Lincoln D. Stein
>> Director, Informatics and Biocomputing Platform
>> Ontario Institute for Cancer Research
>> 101 College St., Suite 800
>> Toronto, ON, Canada M5G0A3
>> 416 673-8514
>> Assistant: Renata Musa <[hidden email]>
>>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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Re: [Bioperl-l] scores in Bio::DB::BigBed

Daniel Lang
Hi all,

thanks a lot for your input on this!

I want to explore the repeat structure of our model genome derived by
lastz self-alignments (using %id as score).
Since this is a HUGE file and I initially wanted to have the ability to
access the information for individual repeat regions also in gbrowse, I
wanted to use BigBed. Having the data in hand, it seems not to be such a
good idea anyway since the resulting repeat graph is much more complex
that I expected. So summarizing using the score and/or coverage will do
just fine;-)

But as they are repeats they're overlapping. So if I see it correctly
BigWig/BedGraph aren't an option. Due to the size limitations, I have
not stored individual CIGAR strings that I could use to generate full-
blown SAM files. Or can I use BAM without sequence/qual data?

Or is there an existing tool that would allow me to collapse overlapping
ranges with average scores for use in BigWig?

Otherwise, I'll have to live with the coverage graphs for visualization
in gbrowse and use Bio::DB::BigBed::features to look at conservation
score at individual loci.

Chris, the proposed BP page would be extremely helpful :-D

Again, thanks a lot!

Best,
Daniel

Am 04.07.2011 18:10, schrieb Chris Fields:

> I generally follow these rules where I want a common set of possibly volatile features (e.g. specific transcriptome analysis) separate from my main 'stable' feature database (e.g. gene models):
>
> 1) BigBed - lightweight bundle of simple features where the ranges may overlap, but I'm not concerned about score.  I have found BED/BigBed scores of limited use in most cases to me unless I scale the data (since they must be 0-1000 integer values).  Document it very well if you do any scaling! YMMV
>
> 2) SAM/BAM - bundle of (possibly overlapping) features where summary stats are needed.  I've seen these used for BLAST/BLAT runs, etc.
>
> 3) BigWig - quantitative data of fixed or varying ranges covering entire genome, ranges can't overlap
>
> 4) BedGraph - quantitative sparse data, ranges can't overlap (these are converted over to BigWig for GBrowse, though)
>
> 5) Of course, one can also set up separate DB::SF::Store databases as well depending on your needs (I have used both the SQLite and MySQL adaptors for this).
>
> I think this is almost begging for a 'best practices' chart/table somewhere, maybe a GBrowse 'cookbook' of common data representation cases.
>
> chris
>
> On Jul 4, 2011, at 8:22 AM, Lincoln Stein wrote:
>
>> I had a look at the output of bigBedSummary, which is from Jim Kent's source
>> tree (no Perl involved), and it appears that the statistics it provides are
>> limited to coverage; so I don't think you can do anything with the scores if
>> you're using BigBed indexing. Have a look at BedGraph=>BigWig and see if it
>> meets your needs.
>>
>> Lincoln
>>
>> On Mon, Jul 4, 2011 at 9:04 AM, Lincoln Stein <[hidden email]>wrote:
>>
>>> Hi Dan,
>>>
>>> The documentation for BigBed is scanty; all I know about it is what is
>>> provided by the bigbed library is in Jim Kent's bigbed.h include file. I had
>>> thought that the scores in BED files would come through into the summary
>>> statistics like those in BigWig, but now I'm looking at the example data
>>> provided in Jim's source code, and see that the BigBed example source file
>>> has scores of "0".
>>>
>>> I'll investigate whether there is an issue in the Perl layer, but it could
>>> easily be a limitation in the library itself. Have you considered using a
>>> BedGraph file and indexing it with bedGraphToBigWig? I know that the
>>> Bio::DB::BigWig interface works perfectly to retrieve and summarize the
>>> scores.
>>>
>>> Lincoln
>>>
>>>
>>> On Sun, Jul 3, 2011 at 5:48 AM, Daniel Lang <
>>> [hidden email]> wrote:
>>>
>>>> Hi,
>>>>
>>>> quick question about the BigBed adaptor: Is it correct that the bin and
>>>> summary functions only return statistics about the number of features in
>>>> the defined intervals?
>>>> I was expecting them to deliver statistics about the score if the
>>>> respective bb file has a defined score field.
>>>> If this is true, does this also mean that I cannot plot the distribution
>>>> of scores in BigBed files in gbrowse?
>>>>
>>>> This is the first time I'm using BigBed, maybe I'm doing something
>>>> wrong...
>>>>
>>>> I had some trouble formatting the bed files correctly in order to see
>>>> the score in the features returned by the Bio::DB::BigBed::features()
>>>> routine. It seems the bigbed entries will only have a correctly assigned
>>>> score field if you also provide a non-empty name field. Initially I
>>>> thought that the order of columns is irrelevant if you use an .as file
>>>> in the bedToBigBed call, but that doesn't seem to be the case.
>>>>
>>>> Best,
>>>> Daniel
>>>> --
>>>>
>>>> Dr. Daniel Lang
>>>> University of Freiburg, Plant Biotechnology
>>>> Schaenzlestr. 1, D-79104 Freiburg
>>>> fax:        +49 761 203 6945
>>>> phone:      +49 761 203 6989
>>>> homepage:   http://www.plant-biotech.net/
>>>>           http://www.cosmoss.org/
>>>> e-mail <http://www.cosmoss.org/e-mail>:
>>>> [hidden email]
>>>>
>>>> #################################################
>>>> My software never has bugs.
>>>> It just develops random features.
>>>> #################################################
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> All of the data generated in your IT infrastructure is seriously valuable.
>>>> Why? It contains a definitive record of application performance, security
>>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>>> sense of it. IT sense. And common sense.
>>>> http://p.sf.net/sfu/splunk-d2d-c2
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>
>>>
>>>
>>> --
>>> Lincoln D. Stein
>>> Director, Informatics and Biocomputing Platform
>>> Ontario Institute for Cancer Research
>>> 101 College St., Suite 800
>>> Toronto, ON, Canada M5G0A3
>>> 416 673-8514
>>> Assistant: Renata Musa <[hidden email]>
>>>
>>
>>
>>
>> --
>> Lincoln D. Stein
>> Director, Informatics and Biocomputing Platform
>> Ontario Institute for Cancer Research
>> 101 College St., Suite 800
>> Toronto, ON, Canada M5G0A3
>> 416 673-8514
>> Assistant: Renata Musa <[hidden email]>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

--

Dr. Daniel Lang
University of Freiburg, Plant Biotechnology
Schaenzlestr. 1, D-79104 Freiburg
fax:        +49 761 203 6945
phone:      +49 761 203 6989
homepage:   http://www.plant-biotech.net/
            http://www.cosmoss.org/
e-mail:     [hidden email]

#################################################
My software never has bugs.
It just develops random features.
#################################################




------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: [Bioperl-l] scores in Bio::DB::BigBed

Timothy Parnell
Hi Daniel,

Since you have a need to collapse your data into useable genomic bins, I
may have a tool that might help you. Have a look at this program
http://code.google.com/p/biotoolbox/wiki/Pod_get_datasets
(Disclosure: I am the author) This is normally used for data analysis, but
you can also use it collapse data into single value bins.

You can collect scores from a BigBed file over genomic intervals and the
scores will be combined in your favorite manner (mean, median, min, max,
etc). For example, to take the median score value from all bed features in
500 bp windows across the genome, the command would look like this

get_datasets.pl --new --db chromosomes.gff3 --feature genome --win 500
--method median --dataf my_data_file.bb --out output.txt

where chromsomes.gff3 is just a simple GFF3 file containing the
chromosomes or contigs, and my_data_file.bb is your BigBed file. The other
options simply tell the program to make a new genomic interval data file
across the genome.

Once you have your data file, you can then convert it to a wig or bigWig
file using data2wig.pl, found in the same biotoolbox collection.

Hope that helps you
Tim


On 7/6/11 1:54 AM, "Daniel Lang" <[hidden email]>
wrote:

>Hi all,
>
>thanks a lot for your input on this!
>
>I want to explore the repeat structure of our model genome derived by
>lastz self-alignments (using %id as score).
>Since this is a HUGE file and I initially wanted to have the ability to
>access the information for individual repeat regions also in gbrowse, I
>wanted to use BigBed. Having the data in hand, it seems not to be such a
>good idea anyway since the resulting repeat graph is much more complex
>that I expected. So summarizing using the score and/or coverage will do
>just fine;-)
>
>But as they are repeats they're overlapping. So if I see it correctly
>BigWig/BedGraph aren't an option. Due to the size limitations, I have
>not stored individual CIGAR strings that I could use to generate full-
>blown SAM files. Or can I use BAM without sequence/qual data?
>
>Or is there an existing tool that would allow me to collapse overlapping
>ranges with average scores for use in BigWig?
>
>Otherwise, I'll have to live with the coverage graphs for visualization
>in gbrowse and use Bio::DB::BigBed::features to look at conservation
>score at individual loci.
>
>Chris, the proposed BP page would be extremely helpful :-D
>
>Again, thanks a lot!
>
>Best,
>Daniel
>
>Am 04.07.2011 18:10, schrieb Chris Fields:
>> I generally follow these rules where I want a common set of possibly
>>volatile features (e.g. specific transcriptome analysis) separate from
>>my main 'stable' feature database (e.g. gene models):
>>
>> 1) BigBed - lightweight bundle of simple features where the ranges may
>>overlap, but I'm not concerned about score.  I have found BED/BigBed
>>scores of limited use in most cases to me unless I scale the data (since
>>they must be 0-1000 integer values).  Document it very well if you do
>>any scaling! YMMV
>>
>> 2) SAM/BAM - bundle of (possibly overlapping) features where summary
>>stats are needed.  I've seen these used for BLAST/BLAT runs, etc.
>>
>> 3) BigWig - quantitative data of fixed or varying ranges covering
>>entire genome, ranges can't overlap
>>
>> 4) BedGraph - quantitative sparse data, ranges can't overlap (these are
>>converted over to BigWig for GBrowse, though)
>>
>> 5) Of course, one can also set up separate DB::SF::Store databases as
>>well depending on your needs (I have used both the SQLite and MySQL
>>adaptors for this).
>>
>> I think this is almost begging for a 'best practices' chart/table
>>somewhere, maybe a GBrowse 'cookbook' of common data representation
>>cases.
>>
>> chris
>>
>> On Jul 4, 2011, at 8:22 AM, Lincoln Stein wrote:
>>
>>> I had a look at the output of bigBedSummary, which is from Jim Kent's
>>>source
>>> tree (no Perl involved), and it appears that the statistics it
>>>provides are
>>> limited to coverage; so I don't think you can do anything with the
>>>scores if
>>> you're using BigBed indexing. Have a look at BedGraph=>BigWig and see
>>>if it
>>> meets your needs.
>>>
>>> Lincoln
>>>
>>> On Mon, Jul 4, 2011 at 9:04 AM, Lincoln Stein
>>><[hidden email]>wrote:
>>>
>>>> Hi Dan,
>>>>
>>>> The documentation for BigBed is scanty; all I know about it is what is
>>>> provided by the bigbed library is in Jim Kent's bigbed.h include
>>>>file. I had
>>>> thought that the scores in BED files would come through into the
>>>>summary
>>>> statistics like those in BigWig, but now I'm looking at the example
>>>>data
>>>> provided in Jim's source code, and see that the BigBed example source
>>>>file
>>>> has scores of "0".
>>>>
>>>> I'll investigate whether there is an issue in the Perl layer, but it
>>>>could
>>>> easily be a limitation in the library itself. Have you considered
>>>>using a
>>>> BedGraph file and indexing it with bedGraphToBigWig? I know that the
>>>> Bio::DB::BigWig interface works perfectly to retrieve and summarize
>>>>the
>>>> scores.
>>>>
>>>> Lincoln
>>>>
>>>>
>>>> On Sun, Jul 3, 2011 at 5:48 AM, Daniel Lang <
>>>> [hidden email]> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> quick question about the BigBed adaptor: Is it correct that the bin
>>>>>and
>>>>> summary functions only return statistics about the number of
>>>>>features in
>>>>> the defined intervals?
>>>>> I was expecting them to deliver statistics about the score if the
>>>>> respective bb file has a defined score field.
>>>>> If this is true, does this also mean that I cannot plot the
>>>>>distribution
>>>>> of scores in BigBed files in gbrowse?
>>>>>
>>>>> This is the first time I'm using BigBed, maybe I'm doing something
>>>>> wrong...
>>>>>
>>>>> I had some trouble formatting the bed files correctly in order to see
>>>>> the score in the features returned by the Bio::DB::BigBed::features()
>>>>> routine. It seems the bigbed entries will only have a correctly
>>>>>assigned
>>>>> score field if you also provide a non-empty name field. Initially I
>>>>> thought that the order of columns is irrelevant if you use an .as
>>>>>file
>>>>> in the bedToBigBed call, but that doesn't seem to be the case.
>>>>>
>>>>> Best,
>>>>> Daniel
>>>>> --
>>>>>
>>>>> Dr. Daniel Lang
>>>>> University of Freiburg, Plant Biotechnology
>>>>> Schaenzlestr. 1, D-79104 Freiburg
>>>>> fax:        +49 761 203 6945
>>>>> phone:      +49 761 203 6989
>>>>> homepage:   http://www.plant-biotech.net/
>>>>>           http://www.cosmoss.org/
>>>>> e-mail <http://www.cosmoss.org/e-mail>:
>>>>> [hidden email]
>>>>>
>>>>> #################################################
>>>>> My software never has bugs.
>>>>> It just develops random features.
>>>>> #################################################
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>----------------------------------------------------------------------
>>>>>--------
>>>>> All of the data generated in your IT infrastructure is seriously
>>>>>valuable.
>>>>> Why? It contains a definitive record of application performance,
>>>>>security
>>>>> threats, fraudulent activity, and more. Splunk takes this data and
>>>>>makes
>>>>> sense of it. IT sense. And common sense.
>>>>> http://p.sf.net/sfu/splunk-d2d-c2
>>>>> _______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Lincoln D. Stein
>>>> Director, Informatics and Biocomputing Platform
>>>> Ontario Institute for Cancer Research
>>>> 101 College St., Suite 800
>>>> Toronto, ON, Canada M5G0A3
>>>> 416 673-8514
>>>> Assistant: Renata Musa <[hidden email]>
>>>>
>>>
>>>
>>>
>>> --
>>> Lincoln D. Stein
>>> Director, Informatics and Biocomputing Platform
>>> Ontario Institute for Cancer Research
>>> 101 College St., Suite 800
>>> Toronto, ON, Canada M5G0A3
>>> 416 673-8514
>>> Assistant: Renata Musa <[hidden email]>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>--
>
>Dr. Daniel Lang
>University of Freiburg, Plant Biotechnology
>Schaenzlestr. 1, D-79104 Freiburg
>fax:        +49 761 203 6945
>phone:      +49 761 203 6989
>homepage:   http://www.plant-biotech.net/
>            http://www.cosmoss.org/
>e-mail:     [hidden email]
>
>#################################################
>My software never has bugs.
>It just develops random features.
>#################################################
>
>
>
>
>--------------------------------------------------------------------------
>----
>All of the data generated in your IT infrastructure is seriously valuable.
>Why? It contains a definitive record of application performance, security
>threats, fraudulent activity, and more. Splunk takes this data and makes
>sense of it. IT sense. And common sense.
>http://p.sf.net/sfu/splunk-d2d-c2
>_______________________________________________
>Gmod-gbrowse mailing list
>[hidden email]
>https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
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|

Re: [Bioperl-l] scores in Bio::DB::BigBed

Daniel Lang
Hi Timothy,

thanks a lot for sharing this great tool! It worked as you said:-)

Best,
Daniel

Am 06.07.2011 22:45, schrieb Timothy Parnell:

> Hi Daniel,
>
> Since you have a need to collapse your data into useable genomic bins, I
> may have a tool that might help you. Have a look at this program
> http://code.google.com/p/biotoolbox/wiki/Pod_get_datasets
> (Disclosure: I am the author) This is normally used for data analysis, but
> you can also use it collapse data into single value bins.
>
> You can collect scores from a BigBed file over genomic intervals and the
> scores will be combined in your favorite manner (mean, median, min, max,
> etc). For example, to take the median score value from all bed features in
> 500 bp windows across the genome, the command would look like this
>
> get_datasets.pl --new --db chromosomes.gff3 --feature genome --win 500
> --method median --dataf my_data_file.bb --out output.txt
>
> where chromsomes.gff3 is just a simple GFF3 file containing the
> chromosomes or contigs, and my_data_file.bb is your BigBed file. The other
> options simply tell the program to make a new genomic interval data file
> across the genome.
>
> Once you have your data file, you can then convert it to a wig or bigWig
> file using data2wig.pl, found in the same biotoolbox collection.
>
> Hope that helps you
> Tim
>
>
> On 7/6/11 1:54 AM, "Daniel Lang" <[hidden email]>
> wrote:
>
>> Hi all,
>>
>> thanks a lot for your input on this!
>>
>> I want to explore the repeat structure of our model genome derived by
>> lastz self-alignments (using %id as score).
>> Since this is a HUGE file and I initially wanted to have the ability to
>> access the information for individual repeat regions also in gbrowse, I
>> wanted to use BigBed. Having the data in hand, it seems not to be such a
>> good idea anyway since the resulting repeat graph is much more complex
>> that I expected. So summarizing using the score and/or coverage will do
>> just fine;-)
>>
>> But as they are repeats they're overlapping. So if I see it correctly
>> BigWig/BedGraph aren't an option. Due to the size limitations, I have
>> not stored individual CIGAR strings that I could use to generate full-
>> blown SAM files. Or can I use BAM without sequence/qual data?
>>
>> Or is there an existing tool that would allow me to collapse overlapping
>> ranges with average scores for use in BigWig?
>>
>> Otherwise, I'll have to live with the coverage graphs for visualization
>> in gbrowse and use Bio::DB::BigBed::features to look at conservation
>> score at individual loci.
>>
>> Chris, the proposed BP page would be extremely helpful :-D
>>
>> Again, thanks a lot!
>>
>> Best,
>> Daniel
>>
>> Am 04.07.2011 18:10, schrieb Chris Fields:
>>> I generally follow these rules where I want a common set of possibly
>>> volatile features (e.g. specific transcriptome analysis) separate from
>>> my main 'stable' feature database (e.g. gene models):
>>>
>>> 1) BigBed - lightweight bundle of simple features where the ranges may
>>> overlap, but I'm not concerned about score.  I have found BED/BigBed
>>> scores of limited use in most cases to me unless I scale the data (since
>>> they must be 0-1000 integer values).  Document it very well if you do
>>> any scaling! YMMV
>>>
>>> 2) SAM/BAM - bundle of (possibly overlapping) features where summary
>>> stats are needed.  I've seen these used for BLAST/BLAT runs, etc.
>>>
>>> 3) BigWig - quantitative data of fixed or varying ranges covering
>>> entire genome, ranges can't overlap
>>>
>>> 4) BedGraph - quantitative sparse data, ranges can't overlap (these are
>>> converted over to BigWig for GBrowse, though)
>>>
>>> 5) Of course, one can also set up separate DB::SF::Store databases as
>>> well depending on your needs (I have used both the SQLite and MySQL
>>> adaptors for this).
>>>
>>> I think this is almost begging for a 'best practices' chart/table
>>> somewhere, maybe a GBrowse 'cookbook' of common data representation
>>> cases.
>>>
>>> chris
>>>
>>> On Jul 4, 2011, at 8:22 AM, Lincoln Stein wrote:
>>>
>>>> I had a look at the output of bigBedSummary, which is from Jim Kent's
>>>> source
>>>> tree (no Perl involved), and it appears that the statistics it
>>>> provides are
>>>> limited to coverage; so I don't think you can do anything with the
>>>> scores if
>>>> you're using BigBed indexing. Have a look at BedGraph=>BigWig and see
>>>> if it
>>>> meets your needs.
>>>>
>>>> Lincoln
>>>>
>>>> On Mon, Jul 4, 2011 at 9:04 AM, Lincoln Stein
>>>> <[hidden email]>wrote:
>>>>
>>>>> Hi Dan,
>>>>>
>>>>> The documentation for BigBed is scanty; all I know about it is what is
>>>>> provided by the bigbed library is in Jim Kent's bigbed.h include
>>>>> file. I had
>>>>> thought that the scores in BED files would come through into the
>>>>> summary
>>>>> statistics like those in BigWig, but now I'm looking at the example
>>>>> data
>>>>> provided in Jim's source code, and see that the BigBed example source
>>>>> file
>>>>> has scores of "0".
>>>>>
>>>>> I'll investigate whether there is an issue in the Perl layer, but it
>>>>> could
>>>>> easily be a limitation in the library itself. Have you considered
>>>>> using a
>>>>> BedGraph file and indexing it with bedGraphToBigWig? I know that the
>>>>> Bio::DB::BigWig interface works perfectly to retrieve and summarize
>>>>> the
>>>>> scores.
>>>>>
>>>>> Lincoln
>>>>>
>>>>>
>>>>> On Sun, Jul 3, 2011 at 5:48 AM, Daniel Lang <
>>>>> [hidden email]> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> quick question about the BigBed adaptor: Is it correct that the bin
>>>>>> and
>>>>>> summary functions only return statistics about the number of
>>>>>> features in
>>>>>> the defined intervals?
>>>>>> I was expecting them to deliver statistics about the score if the
>>>>>> respective bb file has a defined score field.
>>>>>> If this is true, does this also mean that I cannot plot the
>>>>>> distribution
>>>>>> of scores in BigBed files in gbrowse?
>>>>>>
>>>>>> This is the first time I'm using BigBed, maybe I'm doing something
>>>>>> wrong...
>>>>>>
>>>>>> I had some trouble formatting the bed files correctly in order to see
>>>>>> the score in the features returned by the Bio::DB::BigBed::features()
>>>>>> routine. It seems the bigbed entries will only have a correctly
>>>>>> assigned
>>>>>> score field if you also provide a non-empty name field. Initially I
>>>>>> thought that the order of columns is irrelevant if you use an .as
>>>>>> file
>>>>>> in the bedToBigBed call, but that doesn't seem to be the case.
>>>>>>
>>>>>> Best,
>>>>>> Daniel
>>>>>> --
>>>>>>
>>>>>> Dr. Daniel Lang
>>>>>> University of Freiburg, Plant Biotechnology
>>>>>> Schaenzlestr. 1, D-79104 Freiburg
>>>>>> fax:        +49 761 203 6945
>>>>>> phone:      +49 761 203 6989
>>>>>> homepage:   http://www.plant-biotech.net/
>>>>>>           http://www.cosmoss.org/
>>>>>> e-mail <http://www.cosmoss.org/e-mail>:
>>>>>> [hidden email]
>>>>>>
>>>>>> #################################################
>>>>>> My software never has bugs.
>>>>>> It just develops random features.
>>>>>> #################################################
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ----------------------------------------------------------------------
>>>>>> --------
>>>>>> All of the data generated in your IT infrastructure is seriously
>>>>>> valuable.
>>>>>> Why? It contains a definitive record of application performance,
>>>>>> security
>>>>>> threats, fraudulent activity, and more. Splunk takes this data and
>>>>>> makes
>>>>>> sense of it. IT sense. And common sense.
>>>>>> http://p.sf.net/sfu/splunk-d2d-c2
>>>>>> _______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Lincoln D. Stein
>>>>> Director, Informatics and Biocomputing Platform
>>>>> Ontario Institute for Cancer Research
>>>>> 101 College St., Suite 800
>>>>> Toronto, ON, Canada M5G0A3
>>>>> 416 673-8514
>>>>> Assistant: Renata Musa <[hidden email]>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Lincoln D. Stein
>>>> Director, Informatics and Biocomputing Platform
>>>> Ontario Institute for Cancer Research
>>>> 101 College St., Suite 800
>>>> Toronto, ON, Canada M5G0A3
>>>> 416 673-8514
>>>> Assistant: Renata Musa <[hidden email]>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> [hidden email]
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> --
>>
>> Dr. Daniel Lang
>> University of Freiburg, Plant Biotechnology
>> Schaenzlestr. 1, D-79104 Freiburg
>> fax:        +49 761 203 6945
>> phone:      +49 761 203 6989
>> homepage:   http://www.plant-biotech.net/
>>            http://www.cosmoss.org/
>> e-mail:     [hidden email]
>>
>> #################################################
>> My software never has bugs.
>> It just develops random features.
>> #################################################
>>
>>
>>
>>
>> --------------------------------------------------------------------------
>> ----
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--

Dr. Daniel Lang
University of Freiburg, Plant Biotechnology
Schaenzlestr. 1, D-79104 Freiburg
fax:        +49 761 203 6945
phone:      +49 761 203 6989
homepage:   http://www.plant-biotech.net/
            http://www.cosmoss.org/
e-mail:     [hidden email]

#################################################
My software never has bugs.
It just develops random features.
#################################################




------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse