Introducing BioWF – Workflow Bioinformatics Designer

One of the projects that was really interesting was Trident - https://tridentworkflow.codeplex.com/.  It provided a graphical designer based on Windows Workflow 3.0 to create scientific analysis applications.  The .NET Bio team created some activities to introduce bioinformatics into that platform and it was a sample application that was shown off in some of the training sessions.  Unfortunately, WF 3.0 was deprecated when .NET 4.0 shipped (and replaced by a completely different version of … [Read more...]

Using .NET Bio with Windows Store apps

We recently published .NET Bio 1.1 (see bio.codeplex.com) and included a version for Mono in the source tree which allows you to use C# and .NET Bio but run the applications on Linux or Mac machines when Windows just isn't available.  You can even use Xamarin Studio to build the apps which is quite cool.  [Check out the Bio.Mono solution in the source code on codeplex for that project!] Lately, I've spent a lot of time in Windows Store land building Windows Store apps - so I thought I'd try to … [Read more...]

.NET Bio 1.1 alpha available now

One of the open source projects I'm actively involved in is a bioinformatics library for .NET called, appropriately enough, .NET Bio. You can check it out at bio.codeplex.com. We have just put out the alpha version of the next release for community testing - this has several significant changes in it: A new (more standard) implementation of the Smith-Waterman alignment algorithm. A new (more standard) implementation of the Needleman-Wunsch alignment algorithm. Several improvements to the … [Read more...]

.NET Bio is now available via NuGet!

For those of you who have always wanted to write a cool bioinformatics analysis program using .NET I have some great news!  It’s now even easier to add support for the open-source .NET Bio project (http://bio.codeplex.com). If you aren’t familiar with NuGet, it’s a package repository which allows you to add dependencies to a Visual Studio project directly from an online source (vs. just what you have on your machine) and keep them up to date as they change.  Check out … [Read more...]

Sequence Dot Plots part II

In the last post, we built a simple WPF application to display a dot plot – this is a graphical representation to compare two streams of data against each other to determine similarity.  It is often used in bioinformatics to compare genomic sequences and determine if they are related in some fashion.   Comparing the same sequence against itself (obviously has a high degree of similarity) generated a lot of false positives in our application - Here you can see the white diagonal … [Read more...]

Dot-plotting with .NET Bio

One of the most common analysis done with genetic sequences is a dot-plot.  This is where we plot two sequences against each other – in the X and Y direction to get a sense of the similarity between them.  The dot-plot provides a simple, visual tool which can quickly identify consensus between the sequences.  While it was originally developed for the genetic field, the actual concept can be applied to any style of data – allowing professors to detect plagiarism for example. .NET Bio doesn’t … [Read more...]

MVVM Helpers 2.0 is live

… and available on codeplex in beta form:  http://mvvmhelpers.codeplex.com There are several new features in this release that I've been tinkering with for a while.  First, I now use MEF to link things together.  I waited until .NET 4.0 was released to push this out because MEF is part of the framework now.  If you don't want to take a dependency on it (in 3.5) then please stay with 1.06 which is also available.  Managing Services with the Service Locator pattern + MEF … [Read more...]

MVVM Helpers for .NET 4.0

I have updated MVVM Helpers against the RTM of Visual Studio 2010.  I will be updating the codeplex site (http://mvvmhelpers.codeplex.com) shortly, but in the meantime, here’s the project template for Visual Studio 2010.  Copy the .zip into your templates directory, mine is located at: C:UsersMarkDocumentsVisual Studio 2010TemplatesProjectTemplatesVisual C# Here’s the file. … [Read more...]

ATAPI.NET and ITAPI3 source code availability!

I cannot count how many times people have requested the source code to the ATAPI.NET or ITAPI3 projects.  My response has always been that I was unable to release it due to ownership issues (it was developed under contract for a client).  I am pleased to announce this morning that I have worked through those issues and have been granted permission to release the project in it’s entirety as source code on CodePlex! Here’s their new homes:  http://atapi.codeplex.com/ and … [Read more...]