This document contains developer documentation for BioImage Suite Web.

Why JavaScript ?

A quick history

We use JavaScript as our primary programming language. JavaScript was originally designed to work in webpages — a quick Google search will tell you much more than can be written here — and many “serious” programmers considered/consider it an inappropriate language for anything but the most trivial piece of software. This last point is contested by the fact that some of the post popular and complex software available, Gmail, Facebook, and Twitter to name a few, is written in JavaScript.

JavaScript has the unique advantage that it is the only programming language that is built-in to all major web browsers; hence, anything written in JavaScript has the advantage that it can be made available to any user with Internet access and a browser. This is a massive advantage compared to any other programming language out there. Furthermore, over the past ten years, JavaScript has acquired the type of functionality (e.g. Typed Arrays) that make it suitable for use in scientific or medical applications. The recent standardization of the latest version of JavaScript — ECMA Script 6 (ES6) — has added many new features to the language and made it even more suitable for large-scale software development.

Node.js

A key step in the history of JavaScript was the Node.js project which made the JavaScript interpreter, specifically the Chrome JavaScript engine, available as a stand alone tool. This enabled an explosion of server-side JavaScript programming and the creation of a serious JavaScript based set of development tools, e.g. grunt, gulp, mocha, electron, some of which we will discuss later. In the context of web-programming, Node enabled programmers to use the same programming language (JavaScript) both for back-end/server programming, a task often done in Java or PHP, and front-end/browser programming, a task that was always done in JavaScript. This led to the concept of “Isomorphic JavaScript”, which is a mode of programming where the server and client/browser code overlap significantly and share common functionality. Hence, if one transmits complex data from the server to the client, the same code that parses this in the browser can also be used in the server.

Node.js extends standard JavaScript with functionality for manipulating the local file system, executing external processes, and adding C/C++ (among other) extensions. This type of functionality is off-limits to a browser, which for security purposes can not access your local files other than through explicit user interaction — more on this later. This makes it possible to write JavaScript code that automatically reads multiple files and performs complex operations on them. Web applications traditionally used database servers for this purpose, but more recently, web “file systems” such as Dropbox begun to play a similar role.

Desktop JavaScript Applications

A final key step in the creation of this project was the development of tools for desktop JavaScript applications. The older one of these is nw.js, formerly known as Node-Webkit, and a more recent tool in this space is Electron. Both are essentially combinations of the Node.js command line and a packaged version of Chrome, which enables the creation of full multi-platform, desktop applications that can integrate with the operating system and local file system much like any other desktop application written in languages such as C++/Objective C/Python etc. We will use Electron in this text but much of the comments on Electron also apply to nw.js.

“Multi-context” JavaScript

Right now, we can write JavaScript in three different contexts:

While each of these contexts has their own specific needs, we can write core libraries that can be shared by applications that function in these four different contexts. This allows significant code reuse.

This page is part of BioImage Suite Web. We gratefully acknowledge support from the NIH Brain Initiative under grant R24 MH114805 (Papademetris X. and Scheinost D. PIs, Dept. of Radiology and Biomedical Imaging, Yale School of Medicine.)