mbf Discussions Rss Feed

New Post: A utility like UCSC liftover

Rickbe — Fri, 07 Oct 2011 22:01:26 GMT

The LiftOver utility provided by UCSC converts genome annotations from one assembly to another. This requires a defined transform between the source and target assembly, or a route from source to target via intermediate assemblies – for the UCSC utility, these transforms are supplied in the form of chain files.

MBF does not provide equivalent functionality currently; while some of the groundwork to support annotations has been done, MBF as a whole does not yet contain a full-featured annotation model. This is one of the things we would like to see added to MBF by the community, and would appreciate any feedback on what the requirements would be, how it would be used by the community, and how to improve on the current LiftOver utility. We would be happy to provide assistance to any programmer interested in extending MBF in this way.

An alternative would simply be to port LiftOver to .NET – if done correctly, the resulting application could run on Windows, Linux and other platforms.

Rick Benge for the MBF team

New Post: A utility like UCSC liftover

mkhushi — Thu, 06 Oct 2011 11:42:59 GMT

Just wondering if MBF supply a liftover utility like the one provided by UCSC http://genome.ucsc.edu/cgi-bin/hgLiftOver

New Post: use of HPC pack 2008 to launch Microsoft Assembler like a cluster apliccation

Rickbe — Wed, 05 Oct 2011 21:18:48 GMT

Leonard and I have exchanged some emails and I wanted to recap for the community here.

The Sequence Assembler application is provided as a demonstration application only – it shows what can be done with MBF when the library is integrated with a GUI application, in this case one built using Windows Presentation Foundation and Silverlight. The Sequence Assembler application has not been tested for lab use, and would be non performant with any significant dataset.

None of our work has been designed to take advantge of a cluster at this point. In other words it will work in that environ but it is not architected specifically to take advantage of clustered hardware.

In our exchanges using his dataset he had used a Kmer value >32 as a parameter to padeNA and got the message ‘values of K over 32 are not supported’. Further details are available in the Padena paper, but kmer length is a parameter for the Padena assembly, not the length of the input sequences from the FASTA file.

Any dataset that contains many ‘N’ ambiguity characters, any characters other than ACGT, are not compatible with the current version of the Padena algorithm. There are two approaches to dealing with this:

1. Filter the reads, excluding those that contain N characters. Use the smaller remaining dataset in the assembly. This will work, but will lose a lot of data that could be valuable.

2. Split reads containing N characters, so the string AAAAAAAAAANGGGGGGGGGG would become two reads, AAAAAAAAAA and GGGGGGGGGG, etc. This will preserve more of the data and would be a better solution

The filtered reads can be assembled using PadenaUtil commandline utility, and should only take a minute or so to complete with the dataset he provided. I would recommend setting the parameter k to 32 initially, but for the best results you should try varying all the parameters; read the Padena paper to learn more.

I hope this information is helpful to other members of the community as well.

New Post: use of HPC pack 2008 to launch Microsoft Assembler like a cluster apliccation

Rickbe — Wed, 28 Sep 2011 18:05:42 GMT

Leonard, thanks for your post. Just to clarify you are trying to run the Sequence assembler GUI based sample app on a cluster. I guess the first thing to examine is your file location spelling. Presumably you have done that but just to make sure here.

If you want to flesh out more of what you are trying to accomplish here perhaps we can assist you more. I was just curious as to why for instance you wouldn't be using PadeNA assembler in this case.

As a side note - we are planning our V2 release shortly (although in this case that should not make a difference for this report)

If you care to share your location and MBF plans please either post here or you can reply to myself privately at a-rickbe@microsoft.com.

Thanks

New Post: use of HPC pack 2008 to launch Microsoft Assembler like a cluster apliccation

leonardoBio — Wed, 28 Sep 2011 17:06:18 GMT

hey everybody!!!! i'm using a cluster with microsoft technologys with 3 nodes, using windows server HPC 2008, with HPC pack 2008 , i need to run microsoft assembler, but its imposible, because i have the next error: Unable to open standard input file on node NODO1:Exception 'Failed to open standard input file 'D:\aplicaciones\Microsoft Biology Initiative\2.0\MBT\Sequence Assembler', Access is denied' reported creating the task. after i had this: Aborting: failed to launch 'Sequence Assembler.exe' on nodo1 Error (2) The system cannot find the file specified. i think i'm lauching the job to the right form. thanks for the help,

New Post: Attendance at Hackathon 2011

Rickbe — Wed, 10 Aug 2011 21:43:58 GMT

I was just curious if anyone in the community might be attending Hackathon 2011 - http://2011.biohackathon.org/home.

I would love to see an MBF entry but I haven't heard of anyone at this point and it starts in 11 days.

If you do plan to enter or attend would love to correspond about your experience and especially if it is using MBF.

Rick Benge

Community Program Manager – Microsoft Biology Foundation | Microsoft Research Connections | Office +1 425-538-4921

New Post: Another genome browser framework

sjmercer — Thu, 21 Jul 2011 20:20:33 GMT

Hello Wang,

Thanks for your interest in MBF, I'm sorry I missed you at the poster. I would be very interested in learning more about your project, and if there is any way in which MBF can assist you. As you know from the poster, we have a prototype genome browser built on top of MBF and which will be released in the coming months.

Please fell free to email me with more details, and we can discuss,

Many thanks,

Simon Mercer

New Post: Another genome browser framework

Rickbe — Tue, 19 Jul 2011 16:26:03 GMT

You attended the presentation done by Simon Mercer. His Microsoft email address is simon.mercer@microsoft.com. Feel free to include myself (Rick Benge) in the correspondence. I am the community program manager for MBF. My email address is a-rickbe@microsoft.com. There are several programs and additions that use MBF - you may have seen GenoZoom2 at his presentation. You can get additional information from this primary link http://research.microsoft.com/en-US/projects/bio/mbf.aspx but feel free to ask questions on our discussion area. Thanks for your interest.

Rick Benge

Community Program Manager for MBF

New Post: Another genome browser framework

kathleenxppp — Tue, 19 Jul 2011 16:00:18 GMT

I just listened the MBF introduction in vienna ISMB 2011 conference, and it's really beautiful. And I want to talk to you in face during poster session, but I did not find somebody in front of your poster...

Actually, we are now developing a genome browser framework for annotation visulization: http://www.abrowse.org/. Moreover, user can write on the genome instantly besides browsing. And built-in query system and BioMart are all supported for users to fetch bulk dataset.

Hope to learn from you. Thank you very much.

Wang Jun

Center for Bioinformatics

Peking University

P.R.China

New Post: Venn Diagram based on Genomic Intervals issue

kumar35885 — Mon, 18 Jul 2011 16:55:08 GMT

Thank you for the reply.

I am trying to do the following.

I have two ChipSeq results. These consist of interval data, chromosome, start, end, peak location and peak height.

I want to see the number of peaks that overlap in these two datasets and the number that is unique to each set.

Exp A has 2000 peaks and Exp B has 5000 peaks.

The Excel Addin for Venn Diagram is creating more than 9000 'regions' from these two data. This is incorrect for my purposes (because I only have 7000 total peaks).

I can send you some of my data as well as the analysis I have done so far.

Please tell me how to send the data.

Best,

Vivek

New Post: Venn Diagram based on Genomic Intervals issue

bobd00 — Mon, 18 Jul 2011 08:52:03 GMT

Hi Vivek,

It has been a while since I looked at the interval or VennDiagram code, so I am not sure exactly what you are trying to do and the steps you are using to do it.
It sounds like you want to join the two intervals A and B together to create the 'A and B' interval using the IntersectOutputType::OverlappingIntervals rather than the OverlappingPiecesOfIntervals modifier for the SequenceRangeGrouping in the CreateSequenceRangeGroupingForVennDiagram in VennToNodeXL.cs.

If you are writing C# and using the library to produce the Venn diagram, you might be able to clone a bit of the code into your source and set the IntersetOutputType for what you want to do. If you are doing it in excel, the plug-in and/or the library will have to be modified.

If you have a set of small sample files and the steps you are taking, we could arrange some discuss what you want to and how to do it.

-bobd-

New Post: Venn Diagram based on Genomic Intervals issue

kumar35885 — Sun, 17 Jul 2011 03:10:54 GMT

Hello Everyone,

I have results from two ChipSeq experiments.

Experiment A has 1900 peaks and Experiment B has 4000 peaks.

When I create Venn Diagram using the interval data, the total number of resulting regions numbers almost 10000. This is much higher than the sum of the two groups.

This occurs because certain interval from the two Experiments are being split.

So if interval 1 is 10-100 and interval 2 is 50-150, this results in 3 separate genomic regions (0-50 (A only), 50-100 (A and B), and 100-150 (B only)).

Is there a way to control this behavior. For instance, I do not want these intervals to be split into three, but treated as one. So even if there is only one base pair overlap, it should be called A and B.

Otherwise, 5900 peaks end up in 10,000 genomic regions which is hard to explain to biologists.

Any help is appreciated on this matter.

Vivek

New Post: NUCmer parameters "--maxmatch" and "--nooptimize"

sjmercer — Fri, 24 Jun 2011 16:47:33 GMT

Sending for Bob, who is on vacation:

Hi Robert,

You should be able to use the -maxmatch flag to nucmerutil.exe. (I think the short form is -x) You can look at the code in nucmerutil if you want to see how it is used to get the library to do what you want. I found the use of a default parameter and setting it to true can be a bit confusing, so be careful there.

I don’t know the situation on –noopt off the top of my head, and I am on vacation right now, but I’ll see what I can dig up when I get back if it has not been addressed before then.

-bobd-

New Post: NUCmer parameters "--maxmatch" and "--nooptimize"

rboissy — Thu, 23 Jun 2011 18:58:14 GMT

Hi,

The NUCmer aligner in MBF uses different names for some of the MUMmer/NUCmer parameters. Why didn't you use the same parameter names in MBF as in NUCmer/MUMmer?

In addition, some of these parameters don't seem to be exposed as public properties at all, or at least not yet.

For example, at the link below there's an excellent set of instructions from the MUMmer developers for using NUCmer to align short DNA sequence reads to a genome:

How to use MUMmer to align short reads to the human genome: http://www.cbcb.umd.edu/research/mummer_reads.shtml

Unfortunately, you can't set the following two parameters in MBF's NUCmer, which as the instructions in the link mentioned above indicate, are important for aligning short DNA sequence reads to a genome:

--maxmatch
Necessary; otherwise legitimate hits may be missed
--nooptimize
This encourages nucmer to extend the alignment all the way to the end of the read; without this, nucmer may fail to include ends where a substitution occurs close to an end

Looking at the MBF source code, it seems straightforward to hard code the "--maxmatch" parameter, i.e., in your own custom version of "Bio.dll". In the "NUCmer.cs" source code file you just need to change:

isUniqueInReference = true

isUniqueInReference = false

at two points in the source code (see below)

***********************************************************************

NUCmer.cs (excerpts from the original, in build 78593)

ln 211-215:

/// <param name="isUniqueInReference">flag to indicate that the matches should be unique in reference.</param>
/// <returns>Returns clusters.</returns>
public IList<Cluster> GetClusters(
ISequence querySequence,
bool isUniqueInReference = true)

ln 277-281:

/// <param name="isUniqueInReference">Whether MUMs are unique in query or not.</param>
/// <returns>List of enumerable of delta alignments.</returns>
public IEnumerable<DeltaAlignment> GetDeltaAlignments(
ISequence querySequence,
bool isUniqueInReference = true)

***********************************************************************

However, I'm not exactly sure how to set the "--nooptimize" flag in the source code (I don't mind compiling my own derivative of Bio.dll with the "--maxmatch" and "--nooptimize" flags set).

At the following NUCmer.cs lines:

715
781
790
803
898
915

There is a statement (where the tooltip message is shown as a trailing comment)

methodName |= ModifiedSmithWaterman.OptimalFlag; // Maximise the alignment score

My guess is that to set the "--nooptimize" flag, at one or more of these lines the value used should be as follows:

methodName |= ModifiedSmithWaterman.SeqendFlag; // Align till end of shortest sequence

But I'm not sure which lines I should change.

So, if a developer needs to set the "--nooptimize" flag in the source code and compile their own derivative of Bio.dll with the "--maxmatch" and "--nooptimize" flags set for NUCmer, could you please describe exactly how that should be accomplished?

Thanks in advance for your help!

Robert

New Post: Setting Similarity Matrix in MBF

FadiF — Tue, 24 May 2011 21:55:32 GMT

Hi kponcodeplex2011

One of our Developers gave me the below infromation:

We have 11 well defined Similarity Matrices in Bio.dll. These matrices are constructed from the resource files (.txt). You can find the .txt files under ….Bio\Source\Framework\Bio\SimilarityMatrices\Resources\SimilarityMatrices. We have generic class SimilarityMatrix which does the construction based our  StandardSimilarityMatrix enum.

Example:

sm = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);

This will get you Blosum50 matrix.

We also support custom matrix by passing your file. Currently, we support ('\t', ' ', ',') delimited matrix files.

SimilarityMatrix sm = new SimilarityMatrix(blosumFilePath);

Please let me know if you need any more clarification.

Fadi Fakhouri on behalf of the MBF Team

New Post: Setting Similarity Matrix in MBF

kponcodeplex2011 — Mon, 23 May 2011 23:32:07 GMT

Greetings,

I am using Bio library (MBF 2.0) for sequence alignment, and I have a general Question. While we can select various options for an aligner, such as Gap Open Cost, etc, including similarity matrix, I cannot tell exactly where the matrix data comes from. For example, if I choose Blosum50 as my similarity matrix, where is this matrix actually constructed that the algorithm will look for by default. Is each and every algorithm creates a matrix based on the options specified on the fly?

If you can show me exactly where in Bio.dll this is constructed or selected, I would greatly appreciate it. I know you set similarity matrix that an aligner will use, but where is this matrix?

Thank you, KPOnCodeplex2011

New Post: Where and how do you set match and mismatch score before doing alignment

FadiF — Thu, 05 May 2011 15:17:09 GMT

Hi Chris, and thanks for your post.

One of our developers have suggested the following, hope it helps:

Match and Mismatch scores are properties of similarity matrices and not aligners. It is used only with DiagonalSimilarityMatrix. Other similarity matrices have their own standard and well defined scores(which are called as BLOSUM50 etc…)

So if one has to use custom scores, he can always go ahead and use a DSM which has a constructor which takes Match and Mismatch scores and assign this SM to any aligner.

public DiagonalSimilarityMatrix(int matchValue, int mismatchValue)

Please let us know if this resolves your question.

Thanks

The MBF Team

New Post: Where and how do you set match and mismatch score before doing alignment

kponcodeplex2011 — Wed, 04 May 2011 23:41:24 GMT

I know we can set GapOpenCost or GapExtensionCost etc. to aligner, for example:

Bio.Algorithms.MUMmer.MUMmerAligner myMummer = new Bio.Algorithms.MUMmer.MUMmerAligner ();
SimilarityMatrix mySimMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
myMummer .GapOpenCost = -1;
myMummer.SimilarityMatrix = mySimMatrix;

//now perform the alignment

Where and how do you actually set MatchScore and MisMatchScore before doing alignment? A code snippet would be quite useful. Thank you
Chris

New Post: MBF installer - wrong .dll reference

Rickbe — Mon, 02 May 2011 23:56:36 GMT

The V2 beta 1 MBF installer will install .CSproj files to your machine, however the references are set to the wrong .dll's. If you open the project from the beta you will be missing references.

We are tracking this under TFS item 28559 - you can manually correct the binaries or remove the .csproj file as noted in the work item.

I am posting because I thought this visibility would help prevent any initial frustrations in getting this working.

Rick Benge

Comunity Program Manager MBF

New Post: Building MBF v2.0 Preview

bitdisaster — Sat, 30 Apr 2011 21:30:00 GMT

You can unblock the zip file before extracting and then all extracted files become unblocked as well. Also extracting with WinRar should produce unblocked files since WinRar doesn't care about this attribute on the archive.