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...]

WPF + Prism + Biology!

I spend a lot of time in WPF – both in teaching it around the world, and also in assigning in development of applications for various companies.  I also work a bit in the Bioinformatics space – doing applications and research in genomics.  This post is the start of a series which will combine these efforts and attempt to give others some helpful ideas on doing bioinformatics with .NET – and creating visualizations with WPF! .NET and Biology? To start out, let me introduce a somewhat unknown … [Read more...]

rCAT 2.0 is online, 3.0 is coming

The main project I’ve been working on the past few months has been a rRNA sequencing application.  It’s a joint project involving Microsoft Research and the University of Texas in Austin.  The goal being to produce lightning fast visualizations (nucleotide, 2D and 3D) with very large (100,000 sequence) data sets on WPF.  It’s been a big learning experience for me in many ways because the traditional mechanisms for dealing with things in WPF just flat out fail when we load big … [Read more...]

rCAT 1.0 beta is online

A project I've been working on for the last two months is finally online in beta form - check out http://rcat.codeplex.com/ It's essentially a biological alignment viewer for RNA sequences.  Here's a couple of screen shots: Alignment Viewer 2D Structure Viewer 2D Circle relationship Viewer You can download the source code from the above link to play with it - it's a MVVM implementation and has quite a bit of interesting optimizations in it for performance purposes, including a read-only … [Read more...]