XWAS toolset, quality contol for X-chromosome - genetic-algorithm

I am new in the genetic studies, I will analyze some data specific of the X-chromosome and I will use the Xwas toolset.
I would like to know if there is somone who uses XWAS toolset? I need help to begin.
Thanks

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Code smells reporting/tracking tool

I was wondering if you know any tools that help keep track of "code smells". So that team members could report some finding in the code and then possibly vote on the most problematic ones (in terms of future project development).
Any experiences?
Have you looked at find bugs or check style? Both of these are pretty good for this.
I would also recommend pmd. These let you analyse common problems such as not setting method parameters final.
Lastly, I'd recommend using Sonar as this will highlight any code errors in order of priority. Such as code that is knowingly going to through a NPE, it will highlight this to you and can be integrated with Jenkins.
All these together can really help you move towards the "Clean Code" mantra.

Someone to explain the mechanics for DSL language creation "in plain english"

Basically the problem is that I'm starting doing somme development of Visual Studio 2010 extensions and language definitions are rather complex, so anyone giving a small intro and pointing some good docs would be great
Thanks in advance,
EDIT My basic problem is that I want to define a simple language to create some models on Visual Studio 2k10 and generate some source code using such models. The problem is where can I find some nice books, or do I have to dig into MSDN to unveil the mask... :)
Again, thanks
Have you tried starting with the documentation here? If you found this difficult to start with, how could we make it easier to follow?

What are the different Work Items in Team Foundation Server used for?

Please read this entire question before you try to mark this as "too controversial". I am actually setting up my Project Management/Bug Tracking environment with Team Foundation Server for the first time(I have used JIRA,Mantis and some other PM software before). I am fairly knew to using team foundation to anything else besides source control.
I am really trying to use the Work Items for what they were intended to be used for. Having said that, I want to make sure that when I am adding new work items, I am classifying them correctly.
When I choose to add a work Item, If have the following options to select from:
1)Bug
2)Issue
3)Shared Step
4)Task
5)Test Case
6)User Story
Obviously I am aware of what classifies a bug, this is not what is confusing me. What I would really like to know is, what classifies an issue? What technically classifies a Task? What is a user story? etc.
I know there may be some opinion in this, but I am really trying to organize the project, and separate all of these correctly.
This question talks about some of the stuff you've mentioned here
You can find the MSF Agile 5.0 process template guidance here. When you create a team project you should receive an option, after it's complete to read the process guidance. This is what that will take you too if you choose MSF Agile 5.0. Also take a look at the VS Scrum Process Template. It's very simple and as true to Scrum as any tool or process guidance. It was shipped out-of-band, but will be included in the next version of TFS (if not SP1).

Ruby and Enterprise Architect

I'm trying to build a class diagram in Sparx Enterprise Architect for future usage in Ruby project.
How should I set up base code datatypes (Settings -> Code Datatypes...)?
It should be something like: Datatype = Common Type (additional notes, if any). Does anyone know what pairs should be input?
I'd also highly appreciate advice on how to import the whole ruby/rails library into Sparx.
Update 1: added links to resources. It's also stated here, that they don't support reverse engineering of ruby code. So, can anyone suggest a different tool for my case?
Many thanks!
Update 2: there is actually one that I've found, but it's quite out of date. Any other ideas?

.Net XML comment into API Documentation

Is there an easy way to produce MSDN-style documentation from the Visual Studio XML output?
I'm not patient enough to set up a good xslt for it because I know I'm not the first person to cross this bridge.
Also, I tried setting up sandcastle recently, but it really made my eyes cross. Either I was missing something important in the process or it is just way too involved.
I know somebody out there has a really nice dead-simple solution.
I'm reiterating here because I think my formatting made that paragraph non-inviting to read:
I gave sandcastle a try but had a really hard time getting it set up.
What I really have in mind is something much simpler.
That is, unless I just don't understand the sandcastle process. It seemed like an awful lot of extra baggage to me just to produce something nice for the testers to work with.
You're looking for Sandcastle
Project Page: Sandcastle Releases
Blog: Sandcastle Blog
NDoc Code Documentation Generator for .NET used to be the tool of choice, but support has all but stopped.
Have a look at Sandcastle, which does exactly that. It's also one of the more simpler solutions out there, and it's more or less the tool of choice, so in the long run, maybe we could help you to set up Sandcastle if you specify what issues you encountered during setup?
You should also use the Sandcastle Help File Builder. It provides you with a ndoc like GUI for generating help files so you don't have to do anything from a command prompt.
Welcome to the Sandcastle Help File Builder Project
I've just set up Sandcastle again. Try installing it (the May 2008 release) and search for SandcastleGui.exe or something similar (it's in the examples folder or so).
Click Add Assembly and add your Assembly or Assemblies, add any .xml Documentation files (the ones generated by the compiler if you enabled that option) and then Build.
It will take some time, but the result will be worth the effort. It will actually look up stuff from MSDN, so your resulting documentation will also have the Class Inheritance all the way down to System.Object with links to MSDN and stuff.
Sandcastle seems a bit complicated at first, especially when you want to use it in an automated build, but I am absolutely sure it will be worth the effort.
Also have a look at Sandcastle Help File Builder, this is a somewhat more advanced GUI for it.
Follow this simple 5 step article and you are pretty much done. As a bonus you can use H2Viewer to view Html Help 2.x files.
I use NDoc3

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