The Padena algorithm supports FASTQ assembly (insofar as it needs only bases and makes no use of quality values) but it seems that PadenaUtil does not. We do have a parser for FASTQ.
Id #14114 | Release:
None
| Updated: Feb 13 at 7:43 PM by sjmercer | Created: Aug 17, 2011 at 8:46 PM by Rickbe
When calling QualitativeSequence.GetSubSequence(), the new QualitativeSequence object being returned does not retain the original information stored in the properties ID and metadata.
For exampl...
Id #13978 | Release:
None
| Updated: Feb 13 at 7:43 PM by reach2raziq | Created: Jul 22, 2011 at 10:55 PM by kch
verify that the results of a NUCmer alignment are correct. Do a multiple alignment on 4 sequences. You will receive 3 actual alignment objects containing an AlignedSequence object and a list of t...
Id #13633 | Release:
None
| Updated: Feb 13 at 7:43 PM by dourada | Created: Jun 2, 2011 at 1:48 AM by dourada
Self-contained archive containing solution and data to reproduce this bug can be downloaded at
http://bio.mquter.qut.edu.au/Downloads/GenBankParserBugReport.zip (5.5MB)
When parsing a “/note” qua...
Id #13552 | Release:
None
| Updated: Feb 13 at 7:43 PM by FadiF | Created: May 20, 2011 at 11:58 PM by lbuckingham
Greetings.
I have a couple of issues I would like to discuss ( I am not sure if these are bug or unfinished items - a roadmap of your progress in this regards will be useful). Sorry for the long d...
Id #13534 | Release:
None
| Updated: Feb 13 at 7:43 PM by FadiF | Created: May 18, 2011 at 5:58 PM by KPonCodeplex2011
Applied biosystems DNA sequence format file contains a dna sequence in addition to a set of metadata associated with that sequence identify the chromatogram information that was used to determine t...
Id #13506 | Release:
None
| Updated: Feb 13 at 7:43 PM by labchef | Created: May 15, 2011 at 7:07 PM by jkolpak
I have developed some code using MBF framework 1.0 (which uses MBF.dll) for sequence analysis. I just downloaded beta version of the 2.0 framework (which uses Bio.dll). To my amazement, my projec...
Id #13443 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: Apr 29, 2011 at 11:03 PM by KPonCodeplex2011
create commandline utility that will convert from one file format to another file format.
Id #13218 | Release:
None
| Updated: Feb 13 at 7:43 PM by beatriza | Created: Mar 22, 2011 at 1:36 PM by dourada
NOTE: Reported by dourada
I was able to get #1 working. There was a problem reading the app.config file for Color data. I'm still not entirely sure what the real problem was, there are article...
Id #12925 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: Jan 27, 2011 at 11:18 PM by zyskowski
Greetings,
I downloaded the 2.0 preview source code, compiled it, and have a few questions:
The contents of the directory SourceSamples\ReadGenerator are empty
Thanks so much for your help a...
Id #12924 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: Jan 27, 2011 at 11:16 PM by zyskowski
Hi MBF Team,
Both MBF 1.0 and Build 64483 fail to parse protein record w/ GI: 84618887. The error is: Invalid location string [<1].
Thanks.
Vince
Id #12339 | Release:
None
| Updated: Feb 13 at 7:43 PM by VivekX | Created: Oct 24, 2010 at 2:23 PM by vforget
Hi MBF Team,
I trust all is well. When parsing GenBank protein accession AAG48594.1 (http://www.ncbi.nlm.nih.gov/protein/12082743) the resulting object has the Genus property set to Human, but sh...
Id #12333 | Release:
None
| Updated: Feb 13 at 7:43 PM by manjs | Created: Oct 23, 2010 at 5:11 PM by vforget
Hi MBF Team,
Not sure if this is a bug, but when parsing a GenBank file I noticed that the parser identifies the species name as anything past the first space in in the ORGANISM field of the Genk...
Id #11749 | Release:
None
| Updated: Feb 13 at 7:43 PM by vforget | Created: Aug 12, 2010 at 5:43 PM by vforget
The previous simulation operation results should get cleared in results pane upon loading new input sequence.
Repro steps :
a. Open read generator
b. Browse and load input sequence...
Id #11735 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: Aug 11, 2010 at 4:44 AM by ShankarH
Simulation operation always writes output sequences to FastA format though given output type is in different format.
Repro steps:
1. Open Read generator
2. Browse and load input seque...
Id #11734 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: Aug 11, 2010 at 4:41 AM by ShankarH
Hi,
After loading multiple sequences into sequence assembler it would be nice select/deselect multiple reads in the Sequence Tree View using the canonical Shift/Ctrl scheme i.e. Shift to select a...
Id #11518 | Release:
None
| Updated: Feb 13 at 7:43 PM by vforget | Created: Jul 14, 2010 at 9:53 PM by vforget
Hi,
I was able to load into the V1 assembler a dataset of 9660 reads (~470 bp each) dervied from the sequence of a plasmid (~120 Kb) (see issue http://mbf.codeplex.com/workitem/11459 for more det...
Id #11517 | Release:
None
| Updated: Feb 13 at 7:43 PM by vforget | Created: Jul 14, 2010 at 9:47 PM by vforget
Hi MBF Team,
I am testing the Sequence Assembler (M9 release) to see if it can assembly reads from a plasmid of ~120Kb (NCBI Accession: NC_014124). The procedure I used is:
1) Download the GenB...
Id #11459 | Release:
None
| Updated: Feb 13 at 7:43 PM by vforget | Created: Jul 8, 2010 at 4:31 PM by vforget
A help button or menu item would be useful, describing the purpose of the read generator and some of its limitations (only reads the first sequence from an input file, limited file format support)....
Id #11363 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: Jul 1, 2010 at 11:31 PM by sjmercer
The binary is ReadGenerator.exe
Once launched, the window name is ReadGenerator
If pinned to the Windows Start Menu, the name is 'Microsoft Biology Foundation Workbench'
Suggested behavior:
The b...
Id #11346 | Release:
None
| Updated: Feb 13 at 7:43 PM by VivekX | Created: Jul 1, 2010 at 7:55 PM by sjmercer
The overloaded method "SubmitRequest(IList<ISequence>, BlastParameters)" is not implemented in Azuer, EBI-WU & NCBI QBlast services.
Id #11331 | Release:
None
| Updated: Feb 13 at 7:43 PM by manjs | Created: Jun 30, 2010 at 10:24 AM by sorama
Uninstallation of Bio_Excel also removes MBF installed DLLs
Repro Steps,
Install MBF.msi
Install Bio_Excel.msi
Uninstall Bio_Excel.msi
Actual result :
Uninstalltion of Bio_Excel also removes ...
Id #11322 | Release:
None
| Updated: Fri at 7:04 AM by zyskowski | Created: Jun 30, 2010 at 6:59 AM by ShankarH
Hi MBF Team,
I was creating a test program to submit a sequence to BioHPC QBLAST:
using System;
using System.Collections.Generic;
using System.Threading;
using System.Web;
using MBF;
using MBF....
Id #11288 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: Jun 28, 2010 at 5:32 PM by vforget
Steps to build CHM file & Installers
[to generate MBF.msi & SequenceAssembler.msi]
1. Delete folder $TFS04\ mbf\Build if it exists.
2. Build MBI.sln in Debug & Relea...
Id #11286 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: Jun 28, 2010 at 3:59 PM by zyskowski
Hi MBF Team,
I am developing a batch BLASTp submitter which submits sequences to NCBI BLAST and saves the results as an XML file for later use. I've noticed two limitations which if fixed would r...
Id #11266 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: Jun 27, 2010 at 5:56 PM by vforget
We're really close to making the Excel Addin a good option for viewing and hand-editing sequence alignments. The problem is that we can't currently load all sequences in a single spreadsheet. If we...
Id #11235 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: Jun 24, 2010 at 5:29 PM by jcarlson
Need to have one more activity which reads list of sequence and returns all sequence string.
Id #11158 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: Jun 21, 2010 at 7:16 PM by ShankarH
Consider adding a sample Excel file with the Macros pre-set to work for end users to start with. Current methodology to enable macros is very complex and not likely to be found by the end user bio...
Id #11099 | Release:
None
| Updated: Feb 13 at 7:43 PM by VivekX | Created: Jun 17, 2010 at 5:26 AM by zyskowski
When attempting to install the M9 Sequence Assembler, I received the attached error indicating I had to remove the previous version to install it. Need to ensure we are reving the version of each ...
Id #10909 | Release:
None
| Updated: Fri at 7:04 AM by VivekX | Created: May 21, 2010 at 5:16 AM by zyskowski
The following methods need to be implemented in VirtualSequenceList,VirtualQualitativeSequenceList and VirtualAlignedSequenceList. Currently all of them throw new NotSupportedException(Properties.R...
Id #10896 | Release:
None
| Updated: Feb 13 at 7:43 PM by zyskowski | Created: May 18, 2010 at 9:08 AM by ShankarH
This the Bayes package from the MSR eScience group, with significant interest from both MSR and the community. This is a "precise" version of Bayes Network in comparison to the Infer.NET inexact v...
Id #10742 | Release:
None
| Updated: Feb 13 at 7:44 PM by zyskowski | Created: Apr 30, 2010 at 6:38 PM by zyskowski
Input via Mark Smith:
6) Now that MEF is in the framework, it would be nice to connect some of this all up with MEF - instead of having a static list of algorithms, parsers, formatters, etc. that...
Id #10739 | Release:
None
| Updated: Feb 13 at 7:44 PM by DKX | Created: Apr 30, 2010 at 6:01 PM by zyskowski
As reported by many of our partners, we find that many files in this domain to not strictly adhere to the letter of file format specefications. We currently stop and fail on parsing any file which...
Id #10738 | Release:
None
| Updated: Feb 13 at 7:44 PM by zyskowski | Created: Apr 30, 2010 at 5:59 PM by zyskowski
As reported by Kishore Doshi and Mark Smith:
4) There doesn't appear to be any way to add to the existing alphabets - i.e. if I have a proprietary format I use in my lab where I add some addition...
Id #10737 | Release:
None
| Updated: Feb 13 at 7:44 PM by zyskowski | Created: Apr 30, 2010 at 5:52 PM by zyskowski
I would like to start or participate in the connector for R the statistical programming language.
Id #10604 | Release:
None
| Updated: Feb 13 at 7:44 PM by escobarebio | Created: Apr 7, 2010 at 11:07 PM by escobarebio
This (stand-alone projects attached) adds a few simple things to the Bio.Phylogenetics namespace:
one simple data structure – DistanceMatrix
3 classes of algorithms:
ISubstitutionModel for compu...
Id #10378 | Release:
None
| Updated: Feb 13 at 7:44 PM by zyskowski | Created: Mar 8, 2010 at 5:51 AM by rbyers
Repro Steps
Place the Addins folder (PAMSAM.dll and PaDeNA.dll) where the installation binaries for Excel Addin is plaed.
Install excel addin.
Actual
PamSam and PaDeNA Aligner was not enabled under...
Id #10256 | Release:
None
| Updated: Feb 13 at 7:44 PM by zyskowski | Created: Feb 16, 2010 at 5:46 AM by BhaskarS
ExcelWorkbench should have the db_xref components that come through to have business logic associated with the tags in the entry to turn the reference into a live link that will open a web browser ...
Id #10203 | Release:
None
| Updated: Feb 13 at 7:44 PM by zyskowski | Created: Feb 16, 2010 at 5:32 AM by BhaskarS