User Interface

Introduction

This section describes the main components of the OmicsBox application interface.

The interface is organized into the following elements:

1. Menu Bar: The main application menu contains three sections:
   • File: Provides options to open, save, and close OmicsBox files. It also allows you to manage your license and open the application preferences.
   • View: Allows access to utility tabs such as the File Manager, Application Messages, or the Java Memory Monitor.
   • Help: Offers access to support resources. From here, you can review your subscription details, send an email to th Support Team, access your BioBam Account, open the OmicsBox User Manual, and more.
2. Main Analysis Icons: These icons provide access to the main OmicsBox Modules. Clicking on a module icon displays the bioinformatics analyses available within that module.
   • General Tools: Includes actions such as creating Venn diagrams, performing Fastq quality control and preprocessing, and opening the Genome Browser, etc.
   • Genome Analysis Module: Supports genome characterization and analysis, from raw reads to gene structures. Tools include eukaryotic and prokaryotic gene finding, repeat masking, DNA-Seq de novo assembly, and more.
   • Genetic Variation Module: Provides tools to identify and analyze genetic variation. Includes variant calling and filtering, variant annotation, genome-wide association studies (GWAS), and more.
   • Transcriptomics Module: Processes RNA-Seq data from raw reads to functional analysis. Functions include RNA-Seq de novo assembly, alignments, count table creation, differential expression analysis, single-cell RNA-Seq analysis, and long-reads analysis, and more.
   • Functional Analysis Module: Offers tools for functional characterization of sequences such as BLAST, InterProScan, GO Mapping, and Annotation, EggNOG, and more. Pathway annotation with Reactome and KEGG is also supported.
   • Metagenomics Module: Enables execution of analyses in a semi-automated way using predefined workflows.
   • Workflows: Enables execution of analyses in a semi-automated way using predefined workflows. It is also possible to create custom workflows de novo by combining individual analysis steps.
3. Application Tabs:
   • Progress: Displays running, queued, and finished jobs. Jobs can be stopped, and logs can be opened in a separate viewer. Each finished job shows its runtime. Individual jobs can be removed with the cross button, or all finished jobs can be cleared using the triangle button in the top-left corner.
   • Local Files: Allows navigation through local directories to view, open, and organize OmicsBox files. A context menu is available by right-clicking on files (Figure 2). The Merge option can combine multiple files of the same type (not available for all data types).
   • Cloud Files: Provides access to files stored in the cloud.
   • Application Messages: Shows progress updates and general messages from the application.
   • Job Messages: Displays additional logs for analysis steps. Logs can be accessed via the "Show Job Progress" icon next to the corresponding progress bar.
4. Data Tabs: Results generated by OmicsBox tools are displayed in two viewers:
   • Main Viewer: Displays the main results table of an analysis. It includes saving options (top-right corner) and a Side Panel (right side) with sections for Actions, Charts, and Export.
   • Side Viewer: A smaller viewer in the bottom-right corner. It displays secondary results from the Main Viewer, such as charts or summary reports.

Main Results Viewer

Results from bioinformatic analyses are displayed in the Main Viewer as a spreadsheet-style table (Figure 3). Columns can contain strings, numbers, or tags, this last one representing the status of each row depending on the object type.

Columns can be filtered by clicking on the filter icon to the left of the column name. They can be sorted by clicking on the column header. A right-click on any column header opens a checkbox menu to show or hide specific columns.

Table Context Menu

Rows in the results table can be marked individually or in groups. Right-clicking on a marked row opens the context menu (Figure 4). * To select multiple rows, hold Ctrl (Windows/Linux) or ⌘ Command (Mac) while clicking. * To select all unfiltered rows, use Ctrl+A (Windows/Linux) or ⌘+A (Mac).

The context menu actions apply to the marked row(s). Actions at the top are specific to the type of result; their detailed explanation can be found in the corresponding manual section. Actions at the bottom are common to all OmicsBox result objects:

• Extract Selection to new Tab: Creates a new project including the marked rows. Available for most, but not all, OmicsBox objects.
• Copy Row: Copies the marked rows to the clipboard in tabular format.
• Copy Cell: Copies the content of a specific table value to the clipboard.
• Create ID List of Column: [Column Name]: Generated an ID list of a specific column and opens it in a new tab in the Main Viewer. ID-Lists can be used in some OmicsBox tools like Fisher's Exact Test or Heatmaps.
• Create ID Value-List of [Column Name] and [Column Name]: Opens an ID-List with two specific columns on a new tab.
• Create Distribution Chart of Column: [Column Name]: Generates a distribution chart of a certain column.
• Create Category Chart of Column: [Column Name] and: [Column Name]: Creates a category chart of two columns.

Filter Rows

The OmicsBox table allows filtering rows (Figure 5) based on search criteria defined for each column. A small filter icon at the left in each column header opens a context menu with filter options.

• Filters can be applied in various columns and are joined via an AND condition.
• Filter options depend on the column type. For example:
  • Numeric columns support conditions such as "Greater Than" or "Smaller Than".
  • String columns support conditions such as "Starts With" or "Contains".
• When a filter is applied on a column the filter icon turns red. Double-clicking the icon will remove the filter.
• A status message in the top-right corner shows how many sequences match the applied filters.
• The button next to the status message (crossed-out document icon) removes all filters at once.

Note: Algorithms are always executed on all rows of the table, not only on the filtered rows. To execute further analysis only on a subset, extract the desired rows to a new tab.

Configure Columns

This feature allows hiding columns in the results table.
Right-click on any column header to open a menu and select the columns you want to hide (Figure 6).

Auto-Save

OmicsBox supports automatic and continuous saving of results after a defined time interval (Figure 7).

Export

Data stored in OmicsBox objects can be exported to external formats (e.g., FASTA, text, etc.) via the Export section of the Side Panel. Some export options are specific to the object type, whereas the general Export Table option is available for all objects.

The Export Table function exports all currently visible columns in the Main Viewer into a tab-separated values (TSV) file. Alternatively, you can manually select columns and customize their display names (Figure 8).

The Export Table will export all currently visible columns of the Main Viewer into a tab-separated values (TSV) file. It is also possible to enable column selection to choose specific columns and customize their display names.

• The left area of the wizard lists all available columns.
• The right area lists the columns selected for export.
• Click a column name and use the > and < icons to add or remove columns.
• Click a column name and use the up and down arrows to change column order.
• Click a column name and use the Rename Column Header option to edit column names before export.

File Types

All OmicsBox results can be saved as .box files, which can be reopened within OmicsBox. File icons differ depending on the type of object (Figure 9).