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What are the prerequisites I need on my machine to build code in this project?
I found a bug - how do I report it?
  • Go to the issue tracker tab on the menu.
  • Choose create new item
  • Choose a descriptive title
  • Select the component you found the problem in by choosing from the pulldown menu on the right
  • List all the steps to reproduce the problem and include files if necessary
  • Describe the impact to you - like blocks all my development or minor usability issue

How do I get a copy of Microsoft Visual Studio?
Visual Studio is an Integrated Development Environment (IDE), which presents a programmer with all the tools they need to write a program. Although Visual Studio is not free or open source, many potential users are eligible to obtain a copy free of charge or for a very small fee: Visual Studio Professional Edition is required to run the .NET Bio unit tests - other than this, any version of Visual Studio may be used with .NET Bio.

I would prefer not to use Microsoft Visual Studio as my IDE. What alternatives are available?
  • You can use Xamarin Studio. It plays well with Visual studio solution files, and is built more for C#/F#.
  • You may also want to check the Visual Studio site for things like VsVIM- Vim Emulation layer which integrates the familiar key binding experience of Vim directly into Visual Studio's editor.
  • The MONO Project provides a plug-in for the Eclipse IDE, enabling .NET development on a number of platforms. Please visit the MONO pages for specifics.
  • Other Eclipse plug-ins are available, for instance Emonic (http://emonic.sourceforge.net/)

I am using the BioExcel add-in with Microsoft Excel 2010 and want to use the Chart option under the .NET Bio tab to chart my DNA sequence distribution table. What steps do I need to do?
  • Load the gene sequence you want to chart
  • Under the Excel File menu choose the Options submenu
  • Select Customize ribbon
  • From the right side list of displayed choices enable/check the developer tab
  • The Developer tab will now display in Excel, choose macro security and follow the directions for enabling macros in the BioExcel user guide including adjusting the security settings
  • After the macro security settings are set, choose the Macros option under the Developer tab, give your new macro a name and choose create
  • Right click on VBAproject and choose import file
  • Import DisplayDNASequenceDistribution.bas - this could be located under c:\program files (x86)\.NET Bio\1.01\Tools\.NET Bio Extension for Excel\
  • Double click Module 11
  • Do a Save As, Excel macro enabled workbook - .xlsm
  • Close VB for applcations and return to Excel
  • The Chart display macro is now enabled and functionable in your revised sheet

I am a new developer to the project and I want to build the project
  • First download the source code you want to start with (under the Source Code tab)
  • Start Visual studio, then select File->Open -> Project/Solution
  • Select “Bio.sln” in the open project dialog box.
  • Mouse or tab to the solution Explorer Window, right click on the solution and then choose build solution

What is a contribution license agreement and where do I get it?
  • A contrbution license agreement defines how and what you can contribute to this open source project
  • A project coordinator (listed under the people tab) will ask the Outercurve Foundation to provide a contribution license agreement for you to sign
    1. You will need to supply your Codeplex ID and email address associated with it so a contributation license agreement can be sent to you

How do I contribute my code to .NET Bio?
  • There is a Code contribution guide under the documentation tab please read this for specifics.
  • First you must become a contributor of the project by signing a contribution license agreement
  • Next you must configure Visual Studio to access this project:
    1. When you select the source code tab on this site, on the right side it will display this conrol box:
source control.png
  1. Click on Visual Studio Team Explorer under the source control section
  2. Use the information displayed for server name, path, protocol as needed for your TFS project
  • Write your new code following the project coding guidelines described under the documentation tab
  • Include end user documentation for the feature, and document the source code for maintainability
  • Write Unit Tests to test that your feature works as expected
  • Apply and Review a contributor patch
  • Prepare a Visual Studio shelveset for code review
  • Request a code review from project coordinators
  • Upon acceptance submit your patch for inclusion in the project

What are the terms of contribution?

License - .NET Bio is licensed under the Apache 2.0 license and code submitted to the project must be submitted under that license and must be the original work of the author.

Copyright - Copyright attribution should be included in any contribution, but existing copyright attribution should not be modified in any way.
  • Contributions should include a header file referencing that it is licensed under the Apache 2.0 for code management purposes.
  • Existing header files with attribution can be modified to include additional attribution where appropriate.
  • Copyright attribution will in no way affect the terms of the license under which the code is distributed.
Code Standards - Adherence to the coding guidelines, as outlined on the Codeplex documentation section, should be maintained. This document will be available to all users and potential contributors to the project. The purpose of this is to ensure consistency in readability as well as quality throughout the code, making it easier for others to read and comprehend as well as maintaining a high quality bar.


What alignment algorithms are part of the .Net Bio library and therefore availble in the Biology Extension for Excel add-in?
  • Smith-Waterman
  • Needleman-Wunsch
  • Pairwise-Overlap
  • MUMmer
  • NUCmer

I have a suggestion for a new feature or some new ideas for the project. How do I make a suggestion?

Is .NET Bio compatible with Mono?
.NET Bio has been successfully used under Mono for many tasks, though the entire library has not been thoroughly tested.

Why do I get the error message from PadenaUtil when doing an assembly “character not supported”?
  • Gene sequence reads containing 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 using the FilterReadsUtil utility, excluding those with ambiguous characters. This will work, but will lose a lot of data that could be valuable.
    2. Write a script or program to split reads containing ambiguity characters (like N), so for example the string AAAAAAAAAANGGGGGGGGGG would become two ‘subreads’, AAAAAAAAAA and GGGGGGGGGG. Note that any ‘subread’ generated in this manner will need to be longer than the kmer size used in a subsequent sequence assembly step, or the subread will be ignored. This approach makes more of the data usable in assembly, at the cost of breaking up some of the reads.
    3. Ambiguous characters are typically found at the beginning and ends of reads, usually associated with poor base qualities. If this is the case in your data (and you are using a data format that records quality information such as FASTQ), you can trim the start and ends of your reads using one of several applications. A .NET Bio application for this purpose will be available shortly.

What's the recommended K-mer length when using Padenutil?
  • K-mers can be any value from 2 to 32 in PadenaUtil
  • If a short K-mer is used, then any error in the data will be represented in fewer K-mers, so shorter values are better for noisy data
  • If a longer K-mer length is used, there is a higher chance of K-mers being unique, so less ambiguity in assemblies
  • Since each dataset is different, the best approach is to evaluate the quality of an assembly using different K-mer lengths, to see what works best. If a run is likely to take a long time, do this on a subset of the data.
  • Failing that, choose k=32. Assembly will be slower with longer K-mers, but for the reason given above it is likely to produce more reliable contigs

The import menu doesn't appear when I use the Excel Add-in for .NET Bio
This is an Excel bug which occasionally happens when you open an existing spreadsheet. Follow these steps once and it should not happen again:
  • Open Excel by double-clicking on your spreadsheet
  • Click on the .NET Bio tab to display the .NET Bio ribbon
  • Select File -> Options -> Customize ribbon
  • Find the .NET Bio entry in the list of Main Tabs on the right, and click to expand it
  • Select the Sequence Data entry
  • Use the arrow buttons to the right of the list to move it down one place
  • Close the dialog

The Import options should reappear on the ribbon, but to the right of the Aligners. If you would like to move it back to the left, reopen the dialog and select Sequence data, then move it one place back up the list.

Last edited Sep 24, 2013 at 6:03 PM by Rickbe, version 43

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