Manual

Software architecture

The image below depictes the correlation of software package, data library and workspace. CarbArrayART has two different locations for data storage: Workspace and Library. Workspace, which is to be created by a user, is used to store experiment related data. Library is automatically generated when a user start CarbArrayART. Any amendment must be done via CarbArrayART software application and the data saving process.

CarbArrayART download

CarbArrayART has been tested in Windows 7 (64bit), Windows 10, Mac OS X Lion (10.7.5), Mac OS X Yosemite (10.10.5) and Mac OS Big Sur (11.1).

Java SE Runtime Environment 8
Java SE Runtime Environment 8 (JRE 1.8) is required on your computer. You can download the JRE from here.
Please select the product for your operation system (Windows or Mac OS) and run the installation.

Installation and Starting CarbArrayART

Go to the location on your file system where you’ve extracted the zip file.

Windows

Double click the CarbArrayART icon to start the software.

Mac

Double click the CarbArrayART execute icon under Mac OS to start the software.

Select workspace

To open the software for the first time, users are required to create a workspace folder in which the microarray data will be saved.

By clicking Browse and Make New Folder buttons, users can create a new workspace.

Key terminologies

**Images and terms used in CarbArrayART**
	*Workspace.* A folder that contains projects and related information for a given laboratory.
	*Project.* A user-defined folder within the workspace where data files of a single or a group of analytes (carbohydrate-binding samples) are saved. Users are also able to store and manage project metadata here.
	*Analyte (carbohydrate-binding sample).* Glycan-binding sample and its metadata.
	*Glycan Array Data (scan data).* GPR or Excel files generated from scanners such as GenePix and Proscan, respectively.
	*Array (slide).* Slide which may contain a single array or multiple subarrays.
	*Subarray (block or pad).* A block of printed glyco-probes (spots) often with replicates at specified concentrations (or doses).
	*Glycan glyco-probe (glyco-probe).* Monosaccharides, oligosaccharides, polysaccharides or other glycoconjugates printed with or without tag moieties.

**Other terms**
Sample	A glycan binding sample refers to a protein
Experiment design	A tool to record an experiment protocol

Mininum information required for glycan microarray data presentation

The table below lists the data entry tools and the minimum information required for presentation of tables and charts.

**Preparation for visualising the glycan microarray scan data in tables and charts**
Data entry tools in CarbArrayART	Minimum information to have in hand
Glycan glyco-probe	Glycan library (the list of glyco-probes) included in the array Glycan sequence information would be required in order to use the sequence-based filtering and sorting functions in Tabulation View. GlycoCT{condensed}, 2D TEXT, CFG-IUPAC, Glyco Workbench Sequence (GWS) and WURCS formats can be used for entering glycan sequences.
Subarray layout	Layout of printed spots associated with glyco-probe IDs and concentrations (or doses) and the number of replicates in each Subarray (block or pad). Examples illustrated are of 16x16 spots/subarray of 64 glyco-probes at 2 doses (2 and 5 fmol) printed in duplicate or 12x18 spots/subarray of 36 probes printed at a single dose or concentration and 6 replicates.
Array layout	Examples illustrated are of the layout of array(s) on a microarray slide: single array/slide or 2x8 subarrays/slide or 4x4 subarray/slide)
Project	User-defined name for the project
Analyte	Name of the carbohydrate-binding sample
Glycan array data	Quantified array data in the form of a gpr file (GenePix scanner) or an Excel file (Proscan)

Front page

This is a screenshot of a top page of the software. This page contains four major sections.

A. Main menu and shortcut icons

Users are able to access the main functions for CarbArrayART from the main menu bar. The name of shortcut icons are:

	Create a new Project
	Create a new Analyte
	Create a new Archive
	Upload a new scan data
	Merge glycan microarray results for further comparison
	Create a new Experiment Design for an analyte

B. Project explorer area The saved data are listed in this area. Users can search and filter Project, Analyte and Scan data by entering the key word in the text box.

C. Data view area The selected data in [B] Project explorer tree are displayed in this area.

D. Data edit area This area is displayed in Project view and Experiment Design view to support the data entry systems.

Before closing software

Once a user modifies the data, an asterisk will be added on the tab in Data View Area.

Users can save the latest data by selecting Save from the main menu (File -> Save) or by pressing ‘Ctrl + S’.

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