I believe that some Biostar members are EMBL employees - perhaps they can give some insights.

I have seen sample C# code for accessing certain EMBL web services, so it is not unknown to them. However, as Pierre mentioned, bioinformatics has a very strong open-source ethos and frankly, many of its practitioners despise Microsoft products. I count myself in that group :-)

Don't let that put you off. It's relatively easy to adapt to other languages once you have learned one and there are lots of opportunities for interesting programming work in bioinformatics. It will also help if you at least have an interest in biological research, if not a background. Other languages besides Perl are also popular and widely-used: Java, Python and Ruby is gaining some ground.

But if you're really keen on developing only C# projects - you should probably look elsewhere.

FWIW, our BioGPS application is partially built on .NET, as briefly described in our manuscript.

More generally, as a small group, we generally can remain pretty agnostic with respect to specific technologies. I tell the developers in my group to use whatever technologies will lead to the best product the most quickly, and that generally boils down to a combination of programmer experience/skill and available libraries. But as you get to bigger groups of developers with legacy applications, conforming to the group standards becomes more and more important.

I cannot say about EMBL, but in proteomics there are many applications that use .NET. But overall, .NET is a niche in bioinformatics and computational biology.

I've never heard about any tool using .net. A search returns 6 records in pubmed.

Most people use free/open-source languages and I'm afraid people/laboratories will avoid to use the products from Microsoft.

I guess SOAP and REST services for bioinformatics are primarily created with Perl and Java.

Outside of Microsoft Research, the only bioinformatics group I recall releasing .NET apps is Roland Dunbrack's (which is in the US): http://dunbrack.fccc.edu/Software.php (e.g. ArboDraw and the ProtBuD Windows client).

Edit Paulo Nuin's comment reminded me about MSQuant being a .NET app: http://msquant.alwaysdata.net.

For bioinformatics webservices, Java/Perl/Python/Ruby on Linux and OS X are the tools of choice. For desktop apps, people would tend to choose Java. In general, I think bioinformaticians would be very wary of a framework that is proprietary and tied to one particular OS. In theory, they could use Mono to make .NET apps cross-platform but in practice there's been very little uptake of it.

If you want to move into bioinformatics, then probably your best bet is to brush up on Java. Python and Ruby are increasingly popular alternatives to Perl.