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  • How can I apply a PSSM efficiently?

    - by flies
    I am fitting for position specific scoring matrices (PSSM aka Position Specific Weight Matrices). The fit I'm using is like simulated annealing, where I the perturb the PSSM, compare the prediction to experiment and accept the change if it improves agreement. This means I apply the PSSM millions of times per fit; performance is critical. In my particular problem, I'm applying a PSSM for an object of length L (~8 bp) at every position of a DNA sequence of length M (~30 bp) (so there are M-L+1 valid positions). I need an efficient algorithm to apply a PSSM. Can anyone help improve performance? My best idea is to convert the DNA into some kind of a matrix so that applying the PSSM is matrix multiplication. There are efficient linear algebra libraries out there (e.g. BLAS), but I'm not sure how best to turn an M-length DNA sequence into a matrix M x 4 matrix and then apply the PSSM at each position. The solution needs to work for higher order/dinucleotide terms in the PSSM - presumably this means representing the sequence-matrix for mono-nucleotides and separately for dinucleotides. My current solution iterates over each position m, then over each letter in word from m to m+L-1, adding the corresponding term in the matrix. I'm storing the matrix as a multi-dimensional STL vector, and profiling has revealed that a lot of the computation time is just accessing the elements of the PSSM (with similar performance bottlenecks accessing the DNA sequence). If someone has an idea besides matrix multiplication, I'm all ears.

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  • Embedding Lua functions as member variables in Java

    - by Zarion
    Although the program I'm working on is in Java, answering this from a C perspective is also fine, considering that most of this is either language-agnostic, or happens on the Lua side of things. In the outline I have for the architecture of a game I'm programming, individual types of game objects within a particular class (eg: creatures, items, spells, etc.) are loaded from a data file. Most of their properties are simple data types, but I'd like a few of these members to actually contain simple scripts that define, for example, what an item does when it's used. The scripts will be extremely simple, since all fundamental game actions will be exposed through an API from Java. The Lua is simply responsible for stringing a couple of these basic functions together, and setting arguments. The question is largely about the best way to store a reference to a specific Lua function as a member of a Java class. I understand that if I store the Lua code as a string and call lua_dostring, Lua will compile the code fresh every time it's called. So the function needs to be defined somehow, and a reference to this specific function wrapped in a Java function object. One possibility that I've considered is, during the data loading process, when the loader encounters a script definition in a data file, it extracts this string, decorates the function name using the associated object's unique ID, calls lua_dostring on the string containing a full function definition, and then wraps the generated function name in a Java function object. A function declared in script run with lua_dostring should still be added to the global function table, correct? I'm just wondering if there's a better way of going about this. I admit that my knowledge of Lua at this point is rather superficial and theoretical, so it's possible that I'm overlooking something obvious.

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  • car parking management software development

    - by George2
    Hello everyone, I am planning to develop a car parking management software (for a car parking company). I am currently in the planning phase. I am wondering whether there are any existing/popular car parking management software/platform/companies -- so that maybe I can make some reference from them or buy them directly? :-) Appreciate if the referred materials are based on Windows technolgoies, but not a must. thanks in avdance, George

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  • chef-solo example

    - by intern
    We are learning chef-solo and need a good example for better understanding.. Have searched a lot on net but the ideas are very confusing. can anyone suggest some examples.. and also how to run them.. We have installed chef-0.8.16 gem but couldnt figure out how to work with it.. We are using windows platform..Its urgent..

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  • Controlled execution of computationally expensive tasks

    - by Sergio
    Say you have an application where a user is typing some text and as she types you'd want to perform some expensive computations in the background (related to the text that is being typed). Although you would like to do lots of things, your main priority is that the system responsiveness stay at acceptable levels so the user doesn't notice such a heavy load. Is there a way (ideally platform/language independent) to control what algorithms should be executed in the background based on the system load and responsiveness?

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  • Beginner to PHP web services

    - by Manjula
    What is the best way to implement web services in PHP? I have heard about libraries like NuSOAP and WSO2 web service platform, But don't know what is the best ( or a good and easy to learn) for using web service in PHP?

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  • UI Code Level Patterns?

    - by DTS
    Is there a book or some other online resource that covers common code-level UI patterns (not widgets/components per se) and idioms. I'm looking for a resource that goes into some depth on MVC, event models, delegates, etc. Something in a similar vein to the POSA series would be excellent. I'm looking for something that is as platform-agnostic as possible, but I'm not sure if that even IS possible.

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  • What is Sharepoint? What are its main advantages for programmer?

    - by netmajor
    Hey, For some time I’ve seen employers demanding Sharepoint knowledge from programmers, but I have a problem understanding what it is :/ But today I was at IT training, and the main guy said something like: “Sharepoint is platform for commit code for programmer, control of version etc...” Is that true? It sounds like SVN. Can someone explain me what advantages it has for a C# programmer? Thanks ;)

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  • Emulating Dynamic Dispatch in C++ based on Template Parameters

    - by Jon Purdy
    This is heavily simplified for the sake of the question. Say I have a hierarchy: struct Base { virtual int precision() const = 0; }; template<int Precision> struct Derived : public Base { typedef Traits<Precision>::Type Type; Derived(Type data) : value(data) {} virtual int precision() const { return Precision; } Type value; }; I want a function like: Base* function(const Base& a, const Base& b); Where the specific type of the result of the function is the same type as whichever of first and second has the greater Precision; something like the following pseudocode: template<class T> T* operation(const T& a, const T& b) { return new T(a.value + b.value); } Base* function(const Base& a, const Base& b) { if (a.precision() > b.precision()) return operation((A&)a, A(b.value)); else if (a.precision() < b.precision()) return operation(B(a.value), (B&)b); else return operation((A&)a, (A&)b); } Where A and B are the specific types of a and b, respectively. I want f to operate independently of how many instantiations of Derived there are. I'd like to avoid a massive table of typeid() comparisons, though RTTI is fine in answers. Any ideas?

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  • running .net application over a network

    - by Marlon
    Hello, I need some advice please. I need to enable a .Net application to run over a network share, the problem is that this will be on clients network shares and so the path will not be identical. I've had a quick look at ClickOnce and the publish options in VS2008 but it wants a specific network share location - and I'm assuming this location gets stored somewhere when it does its thing. At the moment the job is being done with a old VB6 application and so gets around all these security issues, but that application is poorly written and almost impossible to maintain so it really needs to go. Is it possible for the domain controller to be set up to allow this specific .Net application to execute? Any other options would be welcomed as I want to get this little application is very business critical. I aught to say that the client networks are schools, and thus are often quite locked down as are the client machines, so manually adding exceptions to each client machine is a big no no. Marlon --Edit-- Apologies, I forgot to mention we're restricted to .net 2.0 for the moment, we are planning to upgrade this to 4.0 but that won't be immediate.

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  • What's a Java alternative to Google App Engine for developing iPhone Push Notification services?

    - by bpapa
    I'm a Java programmer who is working on an iPhone application. I'd like it to use Push Notification services. I originally thought I could use Google App Engine to provide the payloads to Apple, but I see now that it won't be possible because App Engine doesn't support the low-level socket programming that is needed to communicate with Apple. Are there any alternatives to Google App Engine that let me use Java? In brief, I'm wondering if there is a free hosting platform that supports Java and Socket Programming

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  • Access Parallels Windows localhost from Mac

    - by Ranch
    I use Windows (7) OS as a development platform, running on a Mac / Parallels Desktop 5. I would like to access the Windows localhost - from the Mac side for testing purposes. I've found many solutions of accessing the other way around (access Mac's localhost from Windows) - but found no solution for this access direction (if any). Any idea ? Is it possible ?

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  • ASP.NET 4.0 hosting

    - by Paul
    We have built an application on the ASP.NET 4.0 platform. We need to go live in the next two weeks and I want to find a host that will offer the RTM of .NET 4.0. Any ideas of any hosts that have plans to offer the newest version shortly after Monday's launch? I see a bunch with RC1 hosting, but I can't find any hard dates for offering the RTM.

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  • PHP - "Fat Free Framework" Find Methods and Showing Results in Template

    - by user1672808
    Just started trying the "Fat Free Framework" I'm building a site using a MySQL DB with 265 fields, and 5000+ rows in the DB; I can load() a specific record easily, no problems. When using find(), afind(), and even "select()", template will show blank lines or lines with "filler" text, with the correct number of rows for the query results, but no text/data from the DB itself; Same problem whether using objects or simply arrays from result (afind() and find()). I've copied/pasted the code verbatim from examples and from documentation, with only the DB specific items changed. Still, no luck. CODE IN PHP FILE (function from CLASS): static function home() { $featured=new Axon('boats'); $F3::set('boatlist',$featured->afind('D_CustomerID=173')); F3::set('content',TEMPLATE_DIR .'/home.html'); echo Template::serve(TEMPLATE_DIR .'/layout.html'); } TEMPLATE home.html: <div class="span8"> <h3> Featured Boats </h3> <F3:repeat group="{{@boatlist}}" value="{{@boat}}"> <div style="margin-left: 2em" class="thumbnails"> <p> <a href="boat/{{@boat['D_BoatNum']}}">{{trim(@boat['D_Description'])}}</a> by {{@boat['D_CustomerID']}} </p> <p> {{@boat['D_Price']}} </p> </div> </F3:repeat> </div> The number of rows this produces coincides with the correct number of rows in the DB. However, the actual data from each field does not show. Any ideas?

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  • What is the most efficient way to clone a JavaScript object?

    - by jschrab
    What is the most efficient way to clone a JavaScript object? I've seen: obj = eval(uneval(o)); but that's not cross platform (FF only). I've done (in Mootools 1.2) things like this: obj = JSON.decode(JSON.encode(o)); but question the efficiency. I've also seen recursive copying function, etc. I'm pretty surprised that out-of-the-box JavaScript doesn't have a method for doing this.

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  • What kinds of problems are most likely to occur? (question rewritten)

    - by ChrisC
    If I wrote 1) a C# SQL db app (a simple program consisting of a gui over some forms with logic for interfacing with the sql db) 2) for home use, that doesn't do any network communication 3) that uses a simple, reliable, and appropriate sql db 4) whose gui is properly separated from the logic 5) that has complete and dependable input data validation 6) that has been completely tested so that 100% of logic bugs were eliminated ... and then if the program was installed and run by random users on their random Windows computers Q1) What types of technical (non-procedural) problems and support situations are most likely to occur, and how likely are they? Q2) Are there more/other things I could do in the first place to prevent those problems and also minimize the amount of user support required? I know some answers will apply to my specific platforms (C#, SQL, Windows, etc) and some won't. Please be as specific as is possible. Mitch Wheat gave me some very valuable advice below, but I'm now offering the bounty because I am hoping to get a better picture of the kinds of things that I'm most reasonably likely to encounter. Thanks.

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  • Modeling a Generic Relationship (expressed in C#) in a Database

    - by StevenH
    This is most likely one for all you sexy DBAs out there: How would I effieciently model a relational database whereby I have a field in an "Event" table which defines a "SportType"? This "SportsType" field can hold a link to different sports tables E.g. "FootballEvent", "RubgyEvent", "CricketEvent" and "F1 Event". Each of these Sports tables have different fields specific to that sport. My goal is to be able to genericly add sports types in the future as required, yet hold sport specific event data (fields) as part of my Event Entity. Is it possible to use an ORM such as NHibernate / Entity framework / DataObjects.NET which would reflect such a relationship? I have thrown together a quick C# example to express my intent at a higher level: public class Event<T> where T : new() { public T Fields { get; set; } public Event() { EventType = new T(); } } public class FootballEvent { public Team CompetitorA { get; set; } public Team CompetitorB { get; set; } } public class TennisEvent { public Player CompetitorA { get; set; } public Player CompetitorB { get; set; } } public class F1RacingEvent { public List<Player> Drivers { get; set; } public List<Team> Teams { get; set; } } public class Team { public IEnumerable<Player> Squad { get; set; } } public class Player { public string Name { get; set; } public DateTime DOB { get; set;} }

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  • Get instance of type inheriting from base class, implementing interface, using StructureMap

    - by Ben
    Continuing on my quest for a good plugin implementation I have been testing the StructureMap assembly scanning features. All plugins will inherit from abstract class PluginBase. This will provide access to common application services such as logging. Depending on it's function, each plugin may then implement additional interfaces, for example, IStartUpTask. I am initializing my plugins like so: Scan(x => { x.AssembliesFromPath(HttpContext.Current.Server.MapPath("~/Plugins"), assembly => assembly.GetName().Name.Contains("Extension")); x.AddAllTypesOf<PluginBase>(); }); The difficulty I am then having is how to work against the interface (not the PluginBase) in code. It's easy enough to work with PluginBase: var plugins = ObjectFactory.GetAllInstances<PluginBase>(); foreach (var plugin in plugins) { } But specific functionality (e.g. IStartUpTask.RunTask) is tied to the interface, not the base class. I appreciate this may not be specific to structuremap (perhaps more a question of reflection). Thanks, Ben

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  • Adaptive user interface/environment algorithm

    - by WowtaH
    Hi all, I'm working on an information system (in C#) that (while my users use it) gathers statistical data on what pieces of information (tables & records) each user is requesting the most, and what parts of the interface he/she uses most. I'm using this statistical data to make the application adaptive to the user's needs, both in the way the interface presents itself (eg: tab/pane-ordering) as in the way of using the frequently viewed information to (eg:) show higher in search results/suggestion-lists. What i'm looking for is an algorithm/formula to determine the current 'hotness'/relevance of these objects for a specific user. A simple 'hitcounter' for each object won't be sufficient because the user might view some information quite frequently for a period of time, and then moving on to the next, making the old information less relevant. So i think my algorithm also needs some sort of sliding/historical principle to account for the changing popularity of the objects in the application over time. So, the question is: Does anybody have some sort of algorithm that accounts for that 'popularity over time' ? Preferably with some explanation on the parameters :) Thanks! PS I've looked at other posts like http://stackoverflow.com/questions/32397/popularity-algorithm but i could't quite port it to my specific case. Any help is appreciated.

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  • Customizing Router Firmware

    - by beakersoft
    Hi, i've got a netgear DG834 router, and i want to have a go at hacking the firmware on it to try and add a Wake on Lan option. Netgear let you download the source and the tools to build an image, but i'm not sure where to start. I've never programmed on a unix platform before, and never done any firmware hacking, just wondering if anyone knows any good resources i can look through Ta

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