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Application or Service to do some tasks in specific time slot

I've scenario to create an application(Windows service , Winforms app) which runs twice every day automatically on users PC. These Users are internal employees in the same network. So at morning and evening this application has to run. But it doesn't need to show any window or information saying its running. Its good to have a simple notification in system tray that its started execution.
My experience in with web application development. So I got a little stucked with these such application on deciding which is best.What my understandings are if its a standalone exe, we could ask all users to download the exe and install.
If its a windows service we may depend up on instalutil to install the service.
So I really needs an advice on this. The application is nothing, just requesting a TFS api and the resulting JSON has to store in Table. So the JSOn will be based on each user using their windows authentication.
Please suggest a good solution to achieve its the best,secure and easiest way even for non tech savvy users.

Instead of all user communicating to TFS server twice a day i guess better way is to install a service in one centralized machine which will run a window service twice a day and that machine will host that service using WCF so that other user will communicate with machine this will help you to distribute the load of tfs api. i used the same approach in my case where one machine talk to ALM and other talk to that machine to get the files.
Creating a window service is pretty simple and straight forward.
Follow the link to make one:
https://www.c-sharpcorner.com/UploadFile/naresh.avari/develop-and-install-a-windows-service-in-C-Sharp/
You can host the service in WCF using IIS, TCP, Webservice, Console application its upto you. Follow this link
https://www.codeproject.com/Articles/550796/A-Beginners-Tutorial-on-How-to-Host-a-WCF-Service
I guess i helped you :)

Cannot keep alive Web Application on IIS after Recycling or Restarting

I have an MVC application that send an e-mail periodically using Quartz.NET. Although the published application works properly on IIS, it cannot works after recycling application pool or restarting the application on IIS. Searching on the web I found several post suggesting to make some changes on config files or IIS, but none of them working properly. So, is there any method to solve the problem? I need a solution that can be applied on application side (or on IIS side if it is simple just making a config changes, etc.). I think this is a common problem when keeping an application on IIS, isn't it?
Note: I use Windows Server 2008 and IIS 7.5.

You do not mention in your question where your application is going to run so I guess it's going to be hosted in-house.
Following your comment I gather you do not have any problems installing and running a Windows Service on your server.
My suggestion - and something I've implemented in the past - is to use the ASP.NET MVC application only as a UI where you create, delete or suspend your jobs/triggers which will be persisted in a database so, whatever happens to your application, you won't lose your jobs/triggers and they will be executed as soon as the application goes back on-line.
The database will be shared with the other layer, the Windows Service, which will be responsible for running your scheduled jobs.
First step is to setup and use AdoJobStore to store Quartz.Net data. As you can see in the post there are a few providers you can use.
Second step is to create and configure your Windows Service. I would use TopShelf to host it. The implementation is very simple and straightforward; plus you can use the Quartz.Net integration provided here.
If you go through the documentation you won't find any problem integrating the solution.
Quartz.Net depends on some configuration you have to add in your app.config/web.config. In this answer there's a detail explanation about the configuration and AdoJobStore.
There are a few things to remember implementing this type of solution.
Your Web Application is going to set the property threadPool to ZeroSizeThreadPool in your config:
<add key="quartz.threadPool.type" value="Quartz.Simpl.ZeroSizeThreadPool, Quartz" />
or in your code:
properties["quartz.threadPool.type"] = "Quartz.Simpl.ZeroSizeThreadPool, Quartz";
and it's never going to start the Scheduler (your windows service is going to use that).

Run an application from the IIS application pool

I have a console application which basically sends emails once per day.
The Windows server administrator disallows this technique and doesn't want to allow extra software on the computer (launched by a scheduled task or a service).
I've been asked to evaluate the possibility of redeveloping a part of the application and integrate it into the IIS application pool but I don't think IIS can do this. Is it possible ? If so, how ?
The only approach I've looked at so far is to redevelop it as a web application and launch a web page everyday with a scheduled task, but I'd like to avoid that.

Let's analyze your options:
Use task scheduler in your server to launch console app
Use task schedule**r in your server to **web service hosted in IIS
Have an IIS application running 100% of time in an infinite loop that that checks time every minute and if it happens to be the correct time send the emails
Have a windows service.
Use task scheduler in a different server to invoke
Analyzing each one of them:
KO: Your administrator does not want console apps and process is not isolated.
KO: You have process isolated but still you are installing a console app.
OK: Not very good for performance but your fulfills your admin conditions.
KO: Your admin does not want windows services.
??: Probably your admin will not want to use an extra server
Proposed solution: As you can see only options 3 and 5 might pass the filter. Ask him
Correct solution I did similar things in the past and went for option 2. You have to convince your admin that solution 3 is a bad idea and probably 5 is already out of the question. When he had to choose the lesser of the evils option 2 is the best :-)
NOTE: You don't mention it but in case you have a SQL Server or similar you can store there an scheduled task too...

I had similar questions when I was moving from Apache servers (where it's dead easy to send a nightly email) to Windows (where you have options).
Clients have sometimes pushed me towards SQL Mail. It's not terrible. If your web app has a SQL backend, and it's okay to schedule things there, it's capable of sending emails when properly configured.

I don't think this is possible. With an IIS application you'd need something to trigger loading the application (call the web page). This itself would require a scheduled task.
You need to pound some sense into your administrator. Sorry.

IIS vs Windows Service?

I have a C# application that needs to always be running. I originally planned on making this a windows service but I now have a requirement to make the application host a web admin console.
I haven't played with IIS in quite a few years so my question is this:
What would you recommend I use?
I've thought about making a windows service and embedding a web server such as Cassini but so far I'm not very happy with the open source web servers I've looked at.
Can IIS handle this? Do people use it for this type of scenario, and if so how?

This sounds like a job for two separate projects.
One is the original Windows Service. Windows Services are well suited for what you're doing.
The second is the Web Project that will be used to administer the Windows Service. This is the part that runs in IIS.

It depends on what you mean by always running. An ASP.NET web application deployed in IIS could very well be unloaded by the web server if there aren't any requests for certain amount of time killing all background threads. So if you want an ever running background thread it would be better suited to use a Windows Service. As far as the web admin is concerned, well, here you don't have much choice: ASP.NET in IIS. In order to do something useful those two applications should be able to find a common language to talk. So you could use a database to store the results into which could be used by both applications.

IIS will run your app on first request, not on server boot. So you will still need to run a service to ensure your app is always running.
You can use IIS as a webserver for your web admin part, and link your ASP.net app with your service by means of a configuration database (easy) or webservices (a little more tricky).

Windows and Web services are two very different creatures. A web service will expose external methods that you can implement against an application, while a windows service is an entity within itself. If you're planning on using this service on a timed interval to perform an operation, a Windows service would be the right way to go. If you use a web service, you will need to invoke the method you wish to run from a secondary application.
If you need to queue commands against your windows service, you could always create a database that was accessible by both your website and your windows service. This way you could send commands and query data between the two. Placing a web service in to serve as an intermidary between the two may be overkill.

Windows Application in future to be controlled over browser

I am writing a Windows application using C#. I am planning on later to allow it to be controlled over the intranet using browser also. So in future we should be able to control it both using the local interface or over the intranet from the browser.
Is there any pre-defined architecture which will allow me to do this? What are the methods of achieving this? I am new to C#/.Net.
EDIT:
The windows application needs to access the communication ports extensively, and needs to be pretty stable and would probably run for some days together.
Thanks...

I can't tell you if a specific package exists that would ease the development. But, if I were to attempt it, after Googling and not finding something already available and meeting my needs, I would likely make my application a WCF host. Create service entry points to accept control messages remotely. You would also need some well-know location where to register your application so the remote system could find it. You should be sure to provide the user with a way of disabling the application remote control feature.
Your host interface will need to run on its own thread to remain performant. Since you are new to C#, and presumably windows forms application development, you will need to read up on how to properly talk to the GUI controls from a non-GUI thread.
Alternatively, you may want to implement your application as two distinct units, one with a GUI that does all the user interaction. It would form service requests to send to the host portion (with no GUI). Your app could then operate locally or be controlled remotely.

One solution I have used in a similar situation has three parts :-
1) Win32 (local) Service
Manages the COM ports and does whatever is necessary with the attached hardware
2) WinForms/Console Application
Runs on the local machine and communicates with the local service via named pipes or TCP.
3) Web Server + Web App
Runs on local or remote machine & communicates with local service.
The local user can shut the WinForms application down and log-off without affecting the service or remote users.

The newest version of Silverlight (the version that ships with Visual Studio 2010) allows what Microsoft terms the "Out Of Browser Experience" (OOB for short).
This allows the user to set up the Silverlight application as a desktop application as well as running through a browser.
Rudi Grobbler has just blogged about how he went about setting this up on his PC.