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Prerequisites for our training course (self guided or at one of our venues)
  • Install .NET Bio
  • Install the Sho scripting environment
  • Download source code from here
  • Install Visual Studio 2010: which is available from a variety of avenues:
    1. Purchase the retail version that meets your requirements
    2. Free to students and educators through the Microsoft DreamSpark program
    3. Through the MSDN Academic Alliance (if your academic department is a member)
    4. Visual Studio Express is free but product registration is required. The course will utilize features in the professional and ultimate editions of Visual Studio, so if you use the Express version there will be features you will not see in your product.

Self guided course
If our course locations aren't convenient for you or if you prefer to go through the training materials on your own you can download the training files yourself. There is a zipped folder here that you can download. You will need to unzip the folder and each training module will then be in it's own folder.

As part of our community support of .NET Bio we do hold courses to foster more participation and to engage with our users. If you would like us to host a course at your university or institution Click Here and someone will contact you to discuss the logistics.
  • Please note that you may get a warning about allowing a control. Please allow the control - so we can start your mail application with the proper email address and subject for you.

.NET Bio course locations and registration

We will be having a .NET Bio training course March 22nd and 23rd at Cornell University in Ithaca, NY. You can register for the course at this site.

There are currently no scheduled courses for .NET Bio training. As new courses are coordinated and scheduled we will post that information here.

Here is the zipped folder of the demo files from our December 2011 workshop in Redmond. If you have any questions or issues with the files please post in the discussion forum and we can address for everyone. Thanks to all of you who attended the course. Mark and I are anxious to see your new contributions to the project.

Here are the samples from our UCSD workshop that our trainer mentioned he would make available.

Course material

Module 1: Introduction to .NET Bio and Command Line Tools
This module provides an overview of .NET Bio, its intended scenarios, and included command-line tools. It shows you how to obtain .NET Bio, what is required to use it, and, most importantly, how to get started with .NET Bio by using scripting environments such as Python and PowerShell. It also introduces several free tools for batch file analysis that were built with .NET Bio, as well as a few add-ins for popular numeric and scientific analysis programs that you can use even if you do not have much programming knowledge.

Module 2: Programming with Visual Studio 2010 and C#
This is a comprehensive introduction to the Microsoft Visual Studio programming environment and Microsoft .NET. Learn how to create a project, what is .NET, how to get started with C#, and runtime debugging. The hands-on lab helps you get experience building applications in Visual Studio 2010. It walks you through the steps that are required to create a console application, interfaces and types that implement those interfaces in C#, a library to hold common (shared) code, and a simple Windows Presentation Foundation (WPF) application by using the shared library.

Module 3: Building Applications with .NET Bio
To really take advantage of the power that is offered by .NET Bio, you can write programs in .NET that build on top of the core features .NET Bio provides. This module provides an overview of the types that are included in .NET Bio, and introduces you to the core features of the programming platform—including how to represent sequences, load and save data, and analyze and run algorithms on sequences. The hands-on lab helps you gain experience working with sequences, parsers, formatters, and the transcription algorithm that is supplied in .NET Bio. It walks you through the steps that are required to build a simple Windows Forms application that can load a set of sequences from a file, transcribe them, and then write those sequences to the same or a different file.

Module 4: Working with Sequences
This module examines the Sequence data type in NET Bio. Learn how to load sequences into memory and save them, the different sequence types that are available, how to use sequence metadata, and how data virtualization support enables support for large data sets. The hands-on lab familiarizes you with managing sequences and sequence items by using .NET Bio interfaces, properties, and methods to create a WPF application to visualize the data.

Module 5: Parsers and Formatters
This module explores .NET Bio’s built-in sequence parsers, formatters, alphabets, and encoders. It also introduces the method of expanding .NET Bio with custom alphabets, parsers, and formatters. The hands-on lab walks you through the steps that are required to build a simple custom parser and formatter for a fabricated biology data format, and then plug it into .NET Bio and the sequence viewer/editor that were created in Module 3.

Module 6: Algorithms
This module examines the algorithms that are defined in .NET Bio for sequence alignment, multi-sequence alignment, sequence fragment assembly, transcription, translation, and pattern matching against sequences, and explains how to create custom algorithms. The hands-on lab walks you through the required steps to build an application that runs algorithms against sequences that are loaded with .NET Bio and perform sequence alignment, assembly, and transformations.

Module 7: Web Services
This module introduces Microsoft .NET web services, the web service architecture in .NET Bio, the built-in web service support in .NET Bio for BLAST, and ClustalW; how to call these services asynchronously; and presents a detailed example of how to build custom service wrappers. The hands-on lab walks you through the steps of building an application that executes the BLAST algorithm by using web services against sequences loaded with .NET Bio. You will get some experience loading and identifying web service handlers for BLAST, passing sequences and sequence fragments to BLAST, changing the BLAST parameters, and displaying the results from a BLAST run.

Module 8: Sho
Sho is a data analysis tool that utilizes IronPython and enables high performance matrix manipulation and graphing. In this lab we use Sho along with .NET Bio to do some quick analysis of sequences without resorting to writing a full program. Here you will see how to load and manipulate biological sequences within the Sho environment, graphing your results in a variety of forms to visually show the details.

Last edited Jul 25, 2013 at 7:18 PM by Rickbe, version 45


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