BL!P: BLAST in Pivot

Closed Issue: Slow performance during DZI creation [205]

vforget — Thu, 16 May 2013 01:26:10 GMT

Creating DZI is slow due to constantly updating the UI i.e. the progress bar. Proposed fix: Update progress bar less often. Design strategy to update according to number of records i.e. more records less updating.

Updated Wiki: Home

vforget — Sun, 14 Apr 2013 02:16:02 GMT

!!ATTENTION!!

This website and code base is no longer maintained. Please visit our new home on GitHub at

https://github.com/vforget/blip

Project Description

BL!P [blip], or BLAST in Pivot, is a computer program that automates the NCBI BLAST alignment of coding DNA or protein sequences and processes the results for visualization in the Microsoft Live Labs program Pivot.

Download BL!P

Software requirements:

> Microsoft Windows XP or better.

> Microsoft .NET 4.0

> Microsoft Silverlight

> Microsoft Silverlight PivotViewer Control

Explore a sample data set

Watch a short video presentation

Question to ask, or bug to report?

Introduction

NCBI BLAST is a popular software program used to find regions of similarity between biological sequences, and can be used to infer functional and evolutionary relationships between sequences. A NCBI BLAST search using multiple query sequences (e.g. gene predictions from a genome sequencing project) typically generates a large dataset that must be explored for functional or evolutionary patterns on interest. Current approaches to exploring NCBI BLAST results include automated filtering of the dataset using a priori significance thresholds followed by manual inspection. While this approach is satisfactory, novel data exploration and visualization software exists that allows for patterns to be identified more easily and with less bias. One such program is Pivot, which can visualize the relationship between pieces of information allowing for the discovery of hidden patterns. Pivot structures its data into “collections”, which combines groups of similar items based on values of certain attributes (facet categories), and represents each item using an image. We have created a software application, BL!P, that automates the NCBI BLAST search of multiple biological sequences and converts the results into a Pivot collection. BL!P also provides an interface to construct custom image layouts for the collection of Pivot items.

BL!P was developed using C# and .NET 4.0, and uses the Microsoft Biology Foundation (MBF) bioinformatics toolkit to access NCBI resources such as NCBI BLAST and GenBank, as well as parsers to read/write biological sequence data.

BL!P automatically submits multiple FASTA formatted coding DNA or amino acid sequences to a NCBI BLAST protein database. Submissions are polled until complete, and the results are saved to disk for later use. Upon completion of the NCBI BLAST search, the GenBank records for each BLAST hit that meets user specified criteria is downloaded and saved to disk for later use. The results from BLAST and information in the GenBank records are parsed and converted to a Pivot collection. Using data from the Pivot collection, a custom image layout is constructed to represent each BLAST hit. The results are saved to disk and can be loaded into Pivot for exploration. BL!P is a member of the Microsoft Biology Initiative.

About the Author

Vince Forgetta, M.Sc.
Microsoft Intern: Summer 2010
Ph.D. Candidate, McGill University, Department of Human Genetics, Montreal, Quebec, Canada
vincenzo.forgetta@mail.mcgill.ca

Updated Wiki: Home

vforget — Sun, 14 Apr 2013 02:15:13 GMT

!!ATTENTION!!

This website and code base is no longer maintained. Please visit our new home on GitHub at

https://github.com/vforget/blip

Project Description

Download BL!P

Software requirements:

> Microsoft Windows XP or better.

> Microsoft .NET 4.0

> Microsoft Silverlight

> Microsoft Silverlight PivotViewer Control

Explore a sample data set

Watch a short video presentation

Question to ask, or bug to report?

Introduction

About the Author

Vince Forgetta, M.Sc.
Microsoft Intern: Summer 2010
Ph.D. Candidate, McGill University, Department of Human Genetics, Montreal, Quebec, Canada
vincenzo.forgetta@mail.mcgill.ca

Updated Wiki: Home

vforget — Sun, 14 Apr 2013 02:14:51 GMT

!!ATTENTION!!

This website and code base is no longer maintained. Please visit our new home on GitHub at

https://github.com/vforget/blip

Project Description

Download BL!P

Software requirements:

> Microsoft Windows XP or better.

> Microsoft .NET 4.0

> Microsoft Silverlight

> Microsoft Silverlight PivotViewer Control

Explore a sample data set

Watch a short video presentation

Question to ask, or bug to report?

Introduction

About the Author

Vince Forgetta, M.Sc.
Microsoft Intern: Summer 2010
Ph.D. Candidate, McGill University, Department of Human Genetics, Montreal, Quebec, Canada
vincenzo.forgetta@mail.mcgill.ca

Updated Wiki: Home

vforget — Sun, 14 Apr 2013 02:13:18 GMT

!!ATTENTION!!

This website and code base is no longer maintained. Please visit our new home on GitHub at

https://github.com/vforget/blip

Project Description

Download BL!P

Software requirements:

> Microsoft Windows XP or better.

> Microsoft .NET 4.0

> Microsoft Silverlight

> Microsoft Silverlight PivotViewer Control

Explore a sample data set

Watch a short video presentation

Question to ask, or bug to report?

Introduction

About the Author

Vince Forgetta, M.Sc.
Microsoft Intern: Summer 2010
Ph.D. Candidate, McGill University, Department of Human Genetics, Montreal, Quebec, Canada
vincenzo.forgetta@mail.mcgill.ca

Updated Wiki: Home

vforget — Sun, 14 Apr 2013 02:12:28 GMT

!!ATTENTION!!

This website and code base is no longer maintained. Please visit our new home on GitHub at

https://github.com/vforget/blip

Project Description

Download BL!P

Software requirements:

> Microsoft Windows XP or better.

> Microsoft .NET 4.0

> Microsoft Silverlight

> Microsoft Silverlight PivotViewer Control

Explore a sample data set

Watch a short video presentation

Question to ask, or bug to report?

Introduction

About the Author

Vince Forgetta, M.Sc.
Microsoft Intern: Summer 2010
Ph.D. Candidate, McGill University, Department of Human Genetics, Montreal, Quebec, Canada
vincenzo.forgetta@mail.mcgill.ca

New Post: Limitations of BL!P

leonardoBio — Mon, 01 Apr 2013 22:23:16 GMT

Hello all!

I want to know which is the maximal amount of sequences or genes supported by BLIP?
excuse me but i don´t understand so well the ~5000 genes threshold.

Regards,

Leo

Commented Issue: can't obtain the final pivot web browser view with alignement of DNA sequence [1478]

leonardoBio — Mon, 01 Apr 2013 17:58:18 GMT

Dear all

i'm triying to align a DNA sequence, the process ends correctly, but the browser doesn't show nothing.
i have already enable popup windows in the web browser originating from address 127.0.0.1 and i have too cleared the web browser cache and delete web browser cookies. but the results are the same. i have probed the same result in google chrome and IE.
I think BL!P give all the required files to obtain the correct view.

I attached a snapshot of the final browser result and another with the parameters that i have used for these process.

PD: i'm using BL!P v20

regards,

Leonardo
Comments: ** Comment from web user: leonardoBio **

Hello i have many Projects files, but i think 2 files are enough

this is the first file, all files generated by BL!P : https://dl.dropbox.com/u/56132327/BLIP_Glomus-ITS_1.zip
the second file, is larger: https://dl.dropbox.com/u/56132327/BLIP_EC_APECO1_plasmid.zip

regards,

Leo

Commented Issue: can't obtain the final pivot web browser view with alignement of DNA sequence [1478]

vforget — Fri, 22 Mar 2013 22:36:05 GMT

How big is the blip project that you are testing? If not too big, zip it and send it to me by whatever way you want.

If too big, can you create a smaller one with fewer query sequences and sent it to me.

Thanks

Commented Issue: can't obtain the final pivot web browser view with alignement of DNA sequence [1478]

leonardoBio — Fri, 22 Mar 2013 21:48:49 GMT

pd: I know BLIP has his own server

Commented Issue: can't obtain the final pivot web browser view with alignement of DNA sequence [1478]

leonardoBio — Fri, 22 Mar 2013 21:47:47 GMT

Now i have executed run BLIP, with and without IIS, and the results are the same

another suggestion?

Commented Issue: can't obtain the final pivot web browser view with alignement of DNA sequence [1478]

leonardoBio — Thu, 21 Mar 2013 21:12:18 GMT

the attached image, my apologies.

Commented Issue: can't obtain the final pivot web browser view with alignement of DNA sequence [1478]

leonardoBio — Thu, 21 Mar 2013 21:11:07 GMT

I have tried your suggestion, but i have the same results, so i have instaled and configured IIS7 correctly again, because i was thinking that IIS maybe was the responsable. but let me tell you, my IIS is running correctly. i don´t know if this issue is due to the version of .NET Bio that i'm actually using, because BLIP uses MBF.

PD: My localhost works correctly with localhost and 127.0.0.1 (see the attached image)

Leo

Commented Issue: can't obtain the final pivot web browser view with alignement of DNA sequence [1478]

vforget — Thu, 21 Mar 2013 00:29:28 GMT

I can reproduce the results you get by doing this:

1. When accessing a public bl!p demo I made at:

http://www.genomequebec.mcgill.ca/compgen/public/blip/blip_demo/blip.html

and changing the url to:

http://genomequebec.mcgill.ca/compgen/public/blip/blip_demo/blip.html

2. For a locallay running bl!p this works:

http://127.0.0.1:8085/blip.html?t=634994079412890180

but this does not:

http://localhost:8085/blip.html?t=634994079412890180

Maybe it is something with you web server configuration?

Maybe try to replace 127.0.0.1 with localhost?

Vince

Commented Issue: can't obtain the final pivot web browser view with alignement of DNA sequence [1478]

vforget — Thu, 21 Mar 2013 00:19:52 GMT

Hi Leonardo,

Does loading other PivotViewer demos work, like the ones found here:

http://xamlgeek.net/2011/01/27/pivotviewer-demos/

If not we can discuss this at length via personal email. I will post the solution here when we find one.

Vince

Commented Issue: can't obtain the final pivot web browser view of a Sample Data Dataset #1 [1480]

leonardoBio — Wed, 20 Mar 2013 22:54:35 GMT

Dear all

I have downloaded the sample data and I have used the genes.fasta protein sequence file, to align using blastp, using the BL!P v20. but i have the same error that the last reported issue (see the snapshot attached). the browser doesn´t show nothing, also show me the next message, when the fourth stage of the process has finalized:

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Error parsing GenBank records: 38347984,157412141,226807724,157412142,226807725,157412143,226807726,157412144,38347989,157412145,38347991,157412146,157412147,21233812,157412148,32765050,161867949,18466630,38348012,38348116,157412231,226807750,157412151,38348014,157412152,38348015,157412153,157412154,157412155,38348018,38348019,157412157,410652785,157412158,410652786,157412159,157412160,157412232,38348024,157412161,410652789,157412162,410652790,38348026,38348027,157412164,38348029,410652794,38348030,157412167,38348032,157412168,38348033,157412169,190410361,157412170,157412233,38348035,157412171,38348036,38348037,157412173,38348038,157412174,157412175,38348049,410652806,157412177,226807778,157412178,38348052,157412179,157412180,38348119,157412234,38348055,157412181,157412182,38348056,157412183,38348057,157412184,157412185,226807786,157412186,157412187,10957290,157412188,38348066,157412189,157412190,157412235,38348068,157412191,226807817,157412192,157412193,38348073,38348074,157412195,38348075,157412196,157412197,157412198,38348082,157412199,226807820,157412200,32765050,161867949,157412201,38348085,157412202,38348086,157412203,157412226,157412116,157412206,38348108,38348106,157412208,226807841,157412209,157412210,38348109,157412237,157412211,38348101,157412212,38348100,157412213,38348099,157412214,157412215,157412216,38348096,410652616,157412015,38347832,157412016,38347833,157412017,38347834,157412218,410652620,157412019,38347836,157412020,38347837,157412021,38347838,157412022,157412023,38347840,157412024,38347841,38347842,38347843,157412027,38347844,157412028,157412219,38347845,157412029,157412030,38347847,157412031,38347848,157412032,38347849,157412033,407470123,157412034,410691088,38347850,38347851,157412036,157412037,157412038,157412220,157412238,38347854,157412039,157412040,410652645,226807593,157412041,38347857,157412042,157412043,38347859,157412044,38347860,410652653,38347861,38347862,157412047,38347863,157412221,226807602,157412049,157412050,38347867,157412051,157412052,38347869,157412053,38347870,157412054,38347871,157412055,157412056,410652665,38347873,226807610,38347874,38348091,157412222,157412059,38347875,38347876,157412060,38347877,38347878,157412062,38347879,226807616,157412064,38347881,157412065,410652676,157412066,157412067,157412068,190410439,157412223,157412069,38347889,157412070,38347890,157412071,156933959,38347891,157412073,156933963,38347893,157412075,157412076,157412077,157412078,157412224,157412079,407468635,157412080,157412081,38347901,157412082,157412083,410691144,15800695,157412085,156933975,157412086,157412087,237728598,157412088,38348088,157412225,237728599,38347914,226807651,157412090,226807655,157412091,190410267,157412092,157412093,292671042,157412094,157412095,15983525,17530574,157412098,157412116,157412226,422381238,157412099,10955228,134047089,134047129,410502919,134047141,157412105,157412108,157412109,157412110,157412227,38347954,157412112,38347956,38347957,157412115,157412226,157412116,157412117,218697190,38347959,38347960,218697189,157412120,157412228,157412121,38347963,156936337,38347964,260600073,386706751,157412124,38347966,38347967,38347968,38639712,38347970,423106640,38347972,157412229,423106639,38347973,38347974,156936349,152973498,38347976,152973496,38347977,260600057,38639703,38347979,156936354,218697170,38347980,226807721,157412139,410652761,157412140,157412230,293404550,.

This is likely due to an unsupported field in the GenBank record. Contact the MBF development team at http://mbf.codeplex.com, and include one of the GI numbers in the bug report.

You can copy this message to the clipboard using Ctrl-C.

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Aceptar
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regards
Comments: ** Comment from web user: leonardoBio **

ok, thanks for the answer

Commented Issue: can't obtain the final pivot web browser view with alignement of DNA sequence [1478]

leonardoBio — Wed, 20 Mar 2013 22:47:13 GMT

hi vince,

i'm running over windows 7, in the initial step I look something like the next attached snapshot, this is just for a few seconds, after, i get the a blank page just like the last image (BLIP_3_parameters.jpg), and no, i can't see the silverlight load wheel.

yes i have installed all the requeriments including silverlight and PivotViewer (i have downloaded of this page: http://www.microsoft.com/en-us/download/details.aspx?id=17747), and lastely i'm the administrator of my windows user account. and never request me "Allow access" dialog, because i'm the admistrator so everything is allowed for me.

waiting for your answer,

Leo

New Post: How to execute BL!P in a local web server

leonardoBio — Wed, 20 Mar 2013 20:14:00 GMT

thanks for you answer i will contact to your personal email. i'm very interested in make great things with pivot and obviously with BLIP

Leonardo

Commented Issue: can't obtain the final pivot web browser view of a Sample Data Dataset #1 [1480]

vforget — Wed, 20 Mar 2013 13:45:12 GMT

The issue with the blank web page is being address in your other request.

For the GenBank error, this is because BL!P cannot parse data due to upsupported fields within the GenBank records. Regrettably, this is "normal" for this version of BL!P. Future version will address this issue. The program should still work, with the exception that these records will not appear in the results.

Commented Issue: can't obtain the final pivot web browser view with alignement of DNA sequence [1478]

vforget — Wed, 20 Mar 2013 13:42:22 GMT

Hi,

Sorry you are having trouble.

What version of windows are you running?

Did you see a rotating blue wheel in the web browser prior to the blank page?

Have you installed all the requirements for making this work in a web browser?

> Microsoft Silverlight
> Microsoft Silverlight PivotViewer Control

If running BL!P as a non-admin user, did you get prompted for access for lauching the local webserver ("Allow access" dialog). If so, did you allow access?

Vince