Developer / Tutorials / Scifeon App

Scifeon App Tutorial

Last updated on 2-Oct-2020 by Jakob Jakobsen Boysen
Jakob Jakobsen Boysen

Platform Lead
boysen@scifeon.com
, Frej Nøhr Larsen
Frej Nøhr Larsen

Bioinformatician
larsen@scifeon.com

Introduction

Welcome to the Scifeon App Tutorial!

In this tutorial you can follow along as a custom app is being developed. Each section of the app will be carefully explained, but it is also possible to either download the sample set and try to build the app by yourself, or simply download the entire app straight away.

The app is meant as an example of how to implement your own software in Scifeon in order to customize your data handling experience.

The app is capable of reading a custom data layout from a Microsoft Excel file, load it into Scifeon, and then display the data in a graph.

Making a Scifeon Instance

If you haven't got a running instance of Scifeon yet, head over to the SDK installation guide.

Follow the installation guide to get started with Scifeon. Once you have verified that the Scifeon CLI is working (by typing scifeon-cli -V in your commando prompt) you can create a Scifeon instance by following the next couple of steps.

If you haven't already, make a new folder (either by right-clicking in the explorer or typing mkdir <directory-name> in the commando prompt) where you wish to save your Scifeon instance. We suggest the user directory C:\Users\User.

Navigate to the new folder (typing cd <directory-name> in the commando prompt). This is where we will place the new Scifeon instance. Creating a Scifeon instance is done by typing scifeon-cli new in the commando prompt and filling out the requested forms as shown below:

In the above example our new folder is called "sandbox" and our scifeon instance is called "demo_instance".

You now have a Scifeon instance! To run the application, enter the instance folder with cd <instance-name> and type scifeon-cli debug. After a short while a new window should then be opened in Chrome, displaying the log-in screen of Scifeon. If not, open the browser yourself and go to http://localhost:5000/.

You can log in using the username admin and the password 12345678.

Setting up Visual Studo Code

When you are ready to start coding, go back to the commando prompt and navigate to the folder you created earlier. Your current path should look something like: C:\Users\FrejNøhrLarsen\sandbox\demo_instance> but with your username and the folder names you used earlier.

Open this folder in your favorite editor, we suggest Visual Studio Code. It should look something like this:

To make a new app, open the src folder (by clicking the arrow called srcin the top-left corner) and make a new folder (by right-clicking the same place and selecting "New Folder"). We named the folder "demo_app", but you are free to name it however you like.

This folder is where we will place all code related to the new app.

To start customizing your Scifeon instance, make a new file and get ready to code! Once you have an instance up and running, you can start creating apps. We suggest making a new folder in the src folder for each new app you are developing.

This is also where you can place the unzipped demo folder if you wish to install it.

Files

You can get the finished app by clicking here.

You can get the Excel file containing the demo data by clicking here. Note that you need Microsoft Excel or similar software to view the data, but not if you simply want to upload it to Scifeon.