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Use Java Library in Javascript

I am planning a project where I will develop bots for Agar.io by using the NEAT algorithm, which is implemented in Java (this is called ANJI). I will use the open-source Agar.io server called Ogar, which is implemented in Javascript. The Javascript implementation should communicate with the Java library to evolve the bots while the game is running, but I have no previous experience of how to make Java and Javascript communicate. I have considered using Rhino, but it does not seem like it is possible to use in a browser. So, are there any way to let a Javascript implementation like Ogar use a Java library?

using the Rhino / Nashorm is not relevant in this case and as for performance focus its should be much hard to run nodeJS based application via Java JS engine.
the Agar.io server is a NodeJS server that expose a WebSocket API and the client solution need to communicate this way.
Using spring websocket client for example
have you seen Agar.io-bot ? its seems like the way they implement the BOT is javascript browser extension and communicate via the browser.

In common, Javascript and Java library communicate using Rest and Json, Java provide Rest API and Javascript send Json request to this API.
This is list of java library: for developing Java Rest API and working with JSON. I recommend using RESTEasy.

Rich web application (HTML5 +JS) with Java on the backend?

There are lots of great Javascript libraries out there these days for creating rich web applications and I would like to use one of them for the frontend of a website I'm working on as they seem to provide a way better interface than what you usually see with JSF, Facelets, PrimeFaces, etc...I read so many complaints about the presentation layer for Java EE and on the other hand things seem to be getting better and better when it comes to Javascript and HTML5.
I am wondering how to go about doing this? One JSP and Facelets you can have items in the presentation layer directly mapped to objects on the server. How would you deal with this when instead you use a Javacript library for your frontend?
I will use Java EE on the server but what is the best way of integrating this with a Javascript RIA library on the frontend?

If your question is only about mapping objects from the back-end to the JavaScript front-end, then I suggest using a JAX-RS implementation (RESTEasy, Restlet, Apache CXF, ...) in combination with Jackson (JSON provider).
This combination allows you to publish a REST API with your domain objects converted to JSON, so you can easily access these objects through JavaScript by using AJAX requests.
But of course this leaves a lot of communication handling open to the developer, if you want to have a more complete package, frameworks like Google Web Toolkit are probably a better solution.

A Google Web Toolkit frontend would be easiest to combine with a Java EE backend as it supports this out of the box with it's own communication system. Otherwise RESTful services are easy to communicate with from javascript and are easy to create in Java EE especially with the aid of an IDE like netbeans.

You can create a front end using JavaScript Libraries like JQuery, ExtJS, Dojo etc with HTML/ HTML5.
To communicate with a Java EE server, you can use an Ajax request with the response in xml/json format.

Clientsided data-cleaning and analysis with sturts2

right now I'm trying to implement a webapp that does data cleaning and analysis and I have already a prototype written in Java. For the analysis part I tend to use WEKA (http://www.cs.waikato.ac.nz/ml/weka/). Because of performance reasons I thought it might be a good idea to let the client do most of the work. I started to learn struts2 and I have no experience using JavaScript. My questions are:
Is struts2 the right choise for this task?
Should I write a Java Applet or can it also be done by Java Script?
I don't have enough experience nor have I found a good solution searching the internet. Can you perhaps post some tutorials or websites that might help me with my questions?

If you want to do it client-side then you need to distribute an app, or use an applet. JavaScript is not Java, and you can't use the browser's JavaScript to run Weka.
If you want to do it client-side, why are you trying to implement a web app?
Struts 2 is fine, but it depends on what you're actually doing. There are many JVM-based web frameworks: Spring MVC, Grails, Play, etc. If you want to move analysis onto the client it probably doesn't matter what framework you use, but it's impossible to say from the info you've provided.

UI technologies for Java EE applications

I need some guidance from the experts.
Till now I have worked on Java and Java EE stuff along with Unix scripting etc. But everything was on the backend side. So I never actually touched the UI code much other than occasional cosmetic changes.
But now I have got one project where we need to work on the frontend part as well.
As I learnt from my colleagues, we need to know CSS, Html, Javascript, XSLT/XPath etc to make a good user friendly UI.
So could you kindly guide as to where to start. I feel that there are lot of things put together.
I tried to read up these things separately e.g. CSS thru W3C , Javascript thru W3C and I understood them but when it comes putting all of these together I am faltering. Require your suggestions to overcome this

I guess you are mostly interested in web applications development. In any case, it's good to know CSS (mainly CSS3) and HTML (preferably HTML 5) as well as a javascript library such as jQuery. Regarding the web frameworks to start with. Here are some choices. You may look around to see their pros and cons. So, here they are some of these:
JSF 2.0 is a brilliant framework following the Model View Controller pattern, that can be combined with an off the shelf javascript component library for JSF such as richfaces, primefaces, icefaces to give you a Rich Internet Application experience.
Groovy on Grails is also an excellent framework enabling you to write also in Groovy, starting usually from the domain layer and creating automatically a scaffold to work with - Similarly, Ruby on Rails offers the possibility to work with Ruby.
Spring MVC is also a great and popular framework to work with.
Django Python is a popular framework for writing in python, "Play!" framework to work with scala and many more.
So, choose the flavor you prefer and try delving into its details. Hope I have helped you.

If you are using Java EE, there's already a good UI framework available in that stack called JSF.
A good text to get started with it is JSF 2.0 tutorial with Eclipse and Glassfish

GWT or DOJO or something else?

I come from the Microsoft world (and I come in peace). I want to rapidly prototype a web app and if it works out, take it live - and I don't want to use ASP.Net.
I am not sure which web application toolkit to use though. Should I use GWT, DOJO...other recommendations? I am open to any server-side language but am looking at RoR, Php or even Java (J2EE to be precise). I am not much of a Javascript/CSS guy so a toolkit that might make it relatively easy on me on those fronts would be preferable.
Also, I am a mac user at home. What IDEs go along with the framework you would recommend?
Any recommendations guys?

If you're open to doing Java, GWT is the way to go. It allows you to have a relatively uniform codebase across client-server, and to only use one language on both.
There are some limitations to doing very off-the-beaten-path AJAXy things (which GWT makes difficult, but not impossible), but it doesn't sound like that's your use case anyway.
GWT will allow you to scale up by using more of its features as your app gets more complex - and your prototype won't be throwaway code.

If you want to write the front and back end in JAVA, and want to do complex ajax type thing, then GWT is a great way to go.
The easiest way to think about it is that building a GWT app is kind of like building a JAVA swing application that hooks into a server. Just like a swing app that uses a server you can make it fat or thin. When you're done it all compiles down into HTML and javascript, and has very good modern browser support (ie6+ ff, opera, safari).
It does abstract all the javascript and HTML away, but if you want it to look good you'll still need to understand CSS.
I think anyone who says that that it ruins MVC or that it's a muddying of client vs server doesn't understand GWT. GWT is a CLIENT side framework. And it is only used on the CLIENT. GWT does provide an RPC mechanism to hook it into JAVA (and other) back ends, but that's just a communication protocol, it doesn't mean that your server code magically becomes your client code. Sure you can write a whole bunch of business rules into your UI if you really wanted to, but you can do this with any framework, so it would be silly to say that GWT is somehow different in that respect.

GWT is a good choice, while if you choose more powerful JavaScript framework based on GWT (e.g. SmartGWT), the compiled stuff is too heavyweight.
Choose direct JavaScript if you need a compact project.

I am a fan of GWT, however I am very familiar with Java. I found it to be intuitive, and surprisingly easy to get good results quickly. If you are to use GWT, then you'll definitely want to use the free, and immensely powerful Eclipse IDE.
One disadvantage of GWT is that it requires Javascript to be supported by the browser, there is no "graceful degradation".

We have evaluate a large list of frameworks and have decide us for Echo2.
You need only to code in Java. Javascript you need only if you want write your own components.
There are no startup performance problems with large projects like GWT.
You can use the full range of Java in your client code because it run on the server. In GWT you can use only very small set of Java classes.
The IDE for Java is Eclipse. This is independent of the used framework.

I'm a fan of jQuery, the chainability of actions, traversals, and commands is really powerful. A good friend of mine is crazy about Mootools, he works at a Java shop FWIW. He mentioned a cool feature of Mootools is that you can specify the functionality you want the framework to include and it will generate the entire library on a single line in a file that you can include on your page to minimize the weight of the framework (pretty cool feature). Really it just depends on what you are most comfortable with. jQuery has great tutorials, is super fast, and can be used along with other javascript frameworks.

Not related to GWT, but have you considered other backends that GWT could work nicely with?
Grails is one backend that ties quite nicely with GWT.

Personally, I would avoid server-side frameworks that try to embed or hide the client-side framework. I'm sure that GWT is great for getting something going quickly, and is probably fine for certain kinds of applications, but you'll probably run into lots of problems "on the edges" for more complex applications. Decoupling the client framework from the server-side framework avoids those problems.