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  • What do you think is the best language for Bioinformatics?

    - by Ben Fossen
    I have done a couple research jobs in Bio-informatics and I have used Matlab for them. Matlab had a lot of powerful tools and was easy to use. I did thinks with genome sequencing and predicting metabolic pathways. I am wondering what other people think is best? or there might not be one specific language but a few that lend themselves best to Bio-informatics work that is math heavy and deals with a large amount of data.

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  • Rack middleware deadlock

    - by Joel
    I include this simple Rack Middleware in a Rails application: class Hello def initialize(app) @app = app end def call(env) [200, {"Content-Type" => "text/html"}, "Hello"] end end Plug it in inside environment.rb: ... Dir.glob("#{RAILS_ROOT}/lib/rack_middleware/*.rb").each do |file| require file end Rails::Initializer.run do |config| config.middleware.use Hello ... I'm using Rails 2.3.5, Webrick 1.3.1, ruby 1.8.7 When the application is started in production mode, everything works as expected - every request is intercepted by the Hello middleware, and "Hello" is returned. However, when run in development mode, the very first request works returning "Hello", but the next request hangs. Interrupting webrick while it is in the hung state yields this: ^C[2010-03-24 14:31:39] INFO going to shutdown ... deadlock 0xb6efbbc0: sleep:- - /usr/lib/ruby/gems/1.8/gems/actionpack-2.3.5/lib/action_controller/reloader.rb:31 deadlock 0xb7d1b1b0: sleep:J(0xb6efbbc0) (main) - /usr/lib/ruby/1.8/webrick/server.rb:113 Exiting /usr/lib/ruby/1.8/webrick/server.rb:113:in `join': Thread(0xb7d1b1b0): deadlock (fatal) from /usr/lib/ruby/1.8/webrick/server.rb:113:in `start' from /usr/lib/ruby/1.8/webrick/server.rb:113:in `each' from /usr/lib/ruby/1.8/webrick/server.rb:113:in `start' from /usr/lib/ruby/1.8/webrick/server.rb:23:in `start' from /usr/lib/ruby/1.8/webrick/server.rb:82:in `start' from /usr/lib/ruby/gems/1.8/gems/rack-1.0.1/lib/rack/handler/webrick.rb:14:in `run' from /usr/lib/ruby/gems/1.8/gems/rails-2.3.5/lib/commands/server.rb:111 from /usr/local/lib/site_ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require' from /usr/local/lib/site_ruby/1.8/rubygems/custom_require.rb:31:in `require' from script/server:3 Something to do with the class reloader in development mode. There is also mention of deadlock in the exception. Any ideas what might be causing this? Any recommendations as to the best approach to debug this?

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  • ASMX Web Service online works when all of the code is in one file without code-behind

    - by Ben McCormack
    I have an ASMX Web Service that has its code entirely in a code-behind file, so that the entire contents of the .asmx file is: <%@ WebService Language="C#" CodeBehind="~/App_Code/AddressValidation.cs" Class="AddressValidation" %> On my test machine (Windows XP with IIS 5), I set up a virtual directory just for this ASP.NET 2.0 solution and everything works great. All my code is separated nicely and it just works. However, when we deployed this solution to our Windows Server 2003 development environment, we noticed that the code only compiled when all of the code was dropped directly into the .asmx file, meaning that the solution didn't work with code-behind. We can't figure out why this is happening. One thing that's different about our setup in our development environment is that instead of creating a separate virual directory just for this solution, we dropped it into an existing directory that runs a classic ASP application. So here we have a folder with an ASP.NET 2.0 application within a directory that contains a classic ASP application. Granted, everything in the ASP.NET 2.0 application works if all of the code is within the .asmx file and not in code-behind, but we'd really like to know why it's not recognizing the code-behind files and compiling it correctly.

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  • software for sorting algorithms animation

    - by Dinesh
    I am planning on working on an interactive application that graphically animates the various sorting algorithms in action. Most of the examples of this kind on the web seems to be using java applets. I was wondering what other software/tools would be well suited to develop an application like this. It may or may not be web-based. Any help would be greatly appreciated. Thanks Dinesh

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  • Usage of Maven (and open source in general) in high governance and risk-averse large organizations (

    - by bart
    Does anyone have any good stories of these kinds of organizations being open to using open source (such as tools like Maven etc). Many staff I've encountered have little or no exposure to open source/systems and open source is treated with great suspicion. Some reasons given for this are lack of support and robustness, which is ironic given the number of end-of-life unsupported vendor products that are in production. Bonus points for any success stories where you've seen open source go into orgs like this and have a real benefit!

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  • PEAR/PHPUnit installation on shared hosting

    - by Sergei Morozov
    I’ve installed a local (per-account) PEAR instance on shared web-hosting. After that I’ve installed PHPUnit. It doesn’t work in command-line mode because PHPUnit classes are not under default include_path that is ".:/usr/local/lib/php". The same, I think, would happen with local phing and other command-line tools installed via PEAR. Is there a way to specify per-account include_path value that will contain my local PEAR path "~/pear/php"?

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  • How can I create a finger scrollable Textbox in WM 6.5?

    - by Papajohn
    Hi everybody. I just noticed something weird in WM 6.5 emulators. Unlike 6.1 where finger panning kind of worked, the only way to scroll a Textbox appears to be through scrollbars. This behaviour is in contrast to what they have done for comboboxes: they are now gesture-friendly without the programmer's intervention. I.e. the user can select a choice from a standard drop down menu by panning and scrolling. Previously, you had to use the embedded scrollbar. The combobox's case implies that MS took some measures to provide standard gesture support for classic finger gestures, yet I cannot see something similar for textboxes. This makes me ask the following: Is there anything that can be done to make textboxes finger scrollabe easily? Note that I refer to managed .NET CF development. It is my understanding that in native development I could use the new Gestures API to achieve the scrolling effect. Yet, I am not sure if there is an easier and more straightforward method that I have missed.

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  • How to run SQL that contains bind variables in the ODT Query Window?

    - by dnorthut
    How do you run SQL that contains one or more bind variables in the Oracle Developer Tools for Visual Studio Query Window? For example, the following works fine in SQL*Plus: variable x NUMBER; BEGIN :x := 0; END; / SELECT 1 FROM DUAL WHERE :x <> 1; When executed in the ODT Query Window, the following exception is raised in the Query output pane: ERROR ORA-01008: not all variables bound

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  • How to develop good debugging skills? [closed]

    - by Sasha
    Possible Duplicate: Debugging techniques How can I improve my debugging skills? I am thinking in the context of C++ under UNIX, C#, and in general. Please suggest how I can improve in these areas in terms of: Approaches to take, where to start, and how to proceed. Tools to use, and how use them effectively. Recommended material (books, articles) to read and lectures to watch.

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  • lexers vs parsers

    - by Naveen
    Are lexers and parsers really that different in theory ? It seems fashionable to hate regular expressions: coding horror, another blog post. However, popular lexing based tools: pygments, geshi, or prettify, all use regular expressions. They seem to lex anything... When is lexing enough, when do you need EBNF ? Has anyone used the tokens produced by these lexers with bison or antlr parser generators?

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  • interactive window to execute dos commands in visual studio

    - by Anirudh Goel
    Hi, I know using External Tools options i can run a batch script or a cmd prompt. But here is what i need to do I want to be able to call a dos prompt inside visual studio, which must be interactive. That way i won't be outside visual studio and can run all my dos commands in it. Is it possible? Or can i extend the command window and capture the commands which are typed and process them using my custom code? Thanks

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  • interactive window to execute dos commands in visual studio

    - by Anirudh Goel
    Hi, I know using External Tools options i can run a batch script or a cmd prompt. But here is what i need to do I want to be able to call a dos prompt inside visual studio, which must be interactive. That way i won't be outside visual studio and can run all my dos commands in it. Is it possible? Or can i extend the command window and capture the commands which are typed and process them using my custom code? Thanks

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  • Is my fragment usage correct, seems to be slow on adnroid

    - by Robertoq
    My app structure is that i have a menu with 5 menu-point om the left side, and the content on the right side. MainActivity.xml <RelativeLayout xmlns:android="http://schemas.android.com/apk/res/android" xmlns:tools="http://schemas.android.com/tools" android:layout_width="match_parent" android:layout_height="match_parent" > <fragment android:id="@+id/fragmentMenu" android:name="com.example.FragmentMenu" android:layout_width="@dimen/MenuWidth" android:layout_height="match_parent" /> <LinearLayout android:id="@+id/content" android:layout_width="match_parent" android:layout_height="match_parent" android_layout_toRightOf="@+id/fragmentMenu" android:orientation="vertical"/> </RelativeLayout> MainActivity.java public class FragmentActivityMain extends FragmentActivity { @Override protected void onCreate(final Bundle arg0) { super.onCreate(arg0); setContentView(R.layout.fragment_activity_main); FragmentManager fm = getSupportFragmentManager(); FragmentMenu fragmentMenu = (FragmentMenu) fm.findFragmentById(R.id.fragmentMenu); fragmentMenu.init(); } } And certainly I have a FragmenMenu class, public class FragmentMenu extends ListFragment { @Override public View onCreateView(final LayoutInflater inflater, final ViewGroup container, final Bundle savedInstanceState) { View view = inflater.inflate(R.layout.fragment_menu, container, false); return view; } public init() { FragmentManager fm = getFragmentManager(); FragmentTransaction ft = fm.beginTransaction(); FragmentNowListView lw = new FragmentCarListView(); ft.add(R.id.content, lw); ft.commit(); } } The FragmentCarList is a simple list, now with static test data, only five items in a List My Problem: Slow. I tested the app on my phone (Galaxy S3) and I see white screen when app starting, around 0,5 second and this is the log: 10-29 11:43:44.093: D/dalvikvm(29710): GC_CONCURRENT freed 267K, 5% free 13903K/14535K, paused 10ms+2ms 10-29 11:43:44.133: D/dalvikvm(29710): GC_FOR_ALLOC freed 215K, 6% free 13896K/14663K, paused 12ms 10-29 11:43:44.233: D/dalvikvm(29710): GC_FOR_ALLOC freed 262K, 6% free 13901K/14663K, paused 12ms 10-29 11:43:44.258: D/dalvikvm(29710): GC_FOR_ALLOC freed 212K, 6% free 13897K/14663K, paused 13ms 10-29 11:43:44.278: D/dalvikvm(29710): GC_FOR_ALLOC freed 208K, 6% free 13897K/14663K, paused 12ms 10-29 11:43:44.328: D/dalvikvm(29710): GC_FOR_ALLOC freed 131K, 4% free 14098K/14663K, paused 12ms 10-29 11:43:44.398: D/dalvikvm(29710): GC_CONCURRENT freed 20K, 3% free 14559K/14919K, paused 1ms+4ms And when I tested on Xperia Ray, the whit screen appear longer time. How can I optimize my fragments? Thx

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  • Targeting Android with Scala 2.8 Trunk builds

    - by Kevin Wright
    The definitive reference for using Scala on android seems to be here: http://www.scala-lang.org/node/160 Unfortunately, all the references on using scala with android are based around Scala 2.7 and refer to a custom build android-library.jar, with a couple of cryptic references suggesting that this custom build isn't needed for later versions of android (I'm using 2.1 / API v7) So... What are the steps needed to use Scala 2.8 in an android project? Preferably using eclipse and the Android tools that Google supplies for that IDE.

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  • Is there a user provisioning API, and/or account migration/transition tool for Gmail on Google Apps?

    - by Olaseni
    I've decided to move all the mail accounts in my domain to Google Apps: Is there a subtle migration tool that can make the transition painless, since I want all the mail history and folders to be intact. I'm also looking to duplicate the user provisioning API with Google Apps Users alternative. Are my goals realistic? Are there any tools out there that already make this task simpler?

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  • MSBuild file for deployment process

    - by Lee Englestone
    I could do with some pointers, code examples or references that may help me do the following in an msbuild file to help speed up the deployment process.. This scenario involves getting a developers 'local' version onto a 'development' server.. Increment a developers local Web Applications Assembly version number Publish a developers local Web Application files somewhere .rar the publsihed files or folder into the format v[IncrementedAssemblyNumber].rar Copy the .rar to somewhere Backup (.rar) the existing live website folder (located elsewhere) in the format Pre_v[IncrementedAssemblyNumber].rar Move the backed up .rar to a /Backup folder. Overwrite the development web files with the published local web files Should be simple for all those MSBUILD Gurus out there. Like I said, answers or 'Good and applicable' links would be much appreciated. Also i'm thinking of getting one of the MSbuild books. From what I can tell there are 2, possibly 3 contenders. I am not using TFS. Can anyone recommend a book for beginning MSBUILD? Ideally from people that have read more than one book on the subject. Cheers, -- Lee

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  • Flash like animation editing and container format for OpenGL environment?

    - by tbarbe
    Are there ANY tools that lets an animator / designer create scripted animations that can export to an OpenGL compatible format -- that are similar to the timeline editing in Flash or After Effects? Does OpenGL ES have some kind of animation playback or container format? ( is there something similar to .swf for OpenGL? ) Im looking for something that lets a designer / animator do his work with a timeline and in a traditional animation environment... meanwhile still having integration with OpenGL.

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  • SVN supports historical merges so how is Mercurial better?

    - by radman
    Hi, I'm a long time SVN user and have been hearing a lot of brou ha ha with regard to mercurial and decentralised version control systems in general. The main touted feature that I am aware of is that merging in Mercurial is much easier because it records information for each merge so each successive merge is aware of the previous ones. Now as stated in the red book, in the section to do with merging, SVN already supports this with mergeinfo. Now I have not actually used this feature (although I wanted to, our repo version wasn't recent enough) but is this SVN feature particularly different to what Mercurial offers? For anyone who is not aware the suggested work flow for historical merging in svn is this: branch from the development trunk to do your own thing. Regularly merge changes from trunk into your branch to stay up to date. Merge back when your done with the mergeinfo to smooth the process. Without historical data merging this is a nightmare because the comparison is strictly on the differences in the files and does not take into account the steps taken on the way. So each change in the development trunk puts you further into possible conflict when you merge back. Now what I would like to know is: Does merging using Mercurial provide a significant advantage when compared with mergeinfo in SVN or is this just a lot of hot air about nothing? Has anyone used the mergeinfo feature in SVN and how good is it actually in practice?

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