This section describes briefly the main parts of the OmicsBox applications.
Main User Interface
The general components of the OmicsBox main user interface are:
Menu Bar: The main application menu contains 3 items:
File: This menu groups all functions for opening, saving and closing OmicsBox files as well as to load or export data in many different formats.
View: This menu allows to open different utility taps like the file manager, the application messages or the Java memory monitor.
Help: The help menu provides access to various support features. You can review your subscription details, the CloudBlast history and the App-Manager. The App-Manager allows to install and update additional tools for OmicsBox.
Main Analysis Icons: These will execute the whole analysis.
start: Quick start to load an OmicsBox Project or recent projects or fasta sequences or annotation file.
workflows: Allows to run workflows to execute analysis in a semi-automatic way.
genome browser: Allows to visualize genomic structures from different files types in a side-scrolling way.
functional analysis module: Contains functions for functional characterization of sequences: Blast, InterProScan, GO Mapping, Functional Annotation, Coding Potential and Enrichment Analysis. In addition, charts can be generated to offer the researcher an overview of the results obtained in each step to facilitate the decision for parameter choice in latter annotation steps.
genome analysis module: Allows to characterize and analyze newly sequenced genomes, from raw reads to gene structures. It contains actions for Eukaryotic and Prokaryotic Gene Finding, Repeat Masking and DNA-Seq de novo Assembly.
transcriptomics module: Allows to process RNA-seq data from raw reads down to their functional analysis. It incorporates functions for RNA-Seq de novo Assembly, RNA-Seq Alignments, Create Count Tables and perform Differential Expression Analyses.
metagenomics module: Allows to combine and integrate all necessary steps for a complete metagenome analysis: Taxonomic Classification, Metagenomic Assembly and Gene Prediction, Functional Annotation and Comparative Analysis.
general tools: Includes different general actions: draw Venn Diagrams, obtain Tag Statistics charts and tools to perform quality control and pre-processing of Fastq files.
Progress tab: Shows running, queued and finished jobs. Allows to stop jobs and open a separate log-viewer. Each finished job shows the time it took to execute. A finished job can be removed using the cross button. All finished jobs can be removed by clicking on the small triangle in the top left corner.
Application Messages tab: Displays information on the progress of the analysis.
File Manager: The File Manager allows to view, open and organize different OmicsBox related files.
Java Memory Monitor: Provides information about the memory consumption of the application.
Log tabs: Most of the analysis steps provide additional logging. These logs can be viewed via the Progress tab.
Data Tabs: Each object type can be opened and saved in a separate tab. In general, table viewer tabs like e.g. the OmicsBox sequence table will be opened by default in the upper-wide area while result tabs will be opened in the lower-right area (e.g. charts, graphs, etc.).
The OmicsBox File Manager allows to view, organise and open different OmicsBox related files.
The "Merge'' option allows combining various file into one. The merge function may not be available for all data types and can only be used to object of the same type.
Figure 2: OmicsBox Main User Interface
Figure 3: File Manager menu
The table allows opening different types of objects (.box/.b2g files) in a spreadsheet style. Additionally to the columns representing the dataset, it contains a TAG column which represents the different status of each line according to the object type.
The table allows to hide or show single columns via a checkbox menu by right-clicking on the column header. In case, multiple objects are viewed (e.g. OmicsBox plus Rfam results), column headers are colored differently. In this example (Figure 4) tags show if a functionally enriched GO term is over or under-represented.
Figure 4: Table
Table Context Menu
The context menu allows to create ID lists of a selected column, extract subsets of entries as well as to copy part of the content into the clipboard. The values of a given column can also be visualized as a category or distribution plot in various formats (bar-chart, pie-chart, etc.).
Show Sequence: Allows seeing the sequence information.
Show Blast Result: Revise the Blast results in detail:, hits, species, identifiers, etc.
Show InterProScan Result: Revise the InterProScan results in detail: databases, GOs, etc.
Show Mapping Result: Revise the retrieved candidate GO terms in detail: Accessions, Evidence Codes, Databases.
Show GO Description: Review information about annotated GOs.
Copy Sequence Names to Clipboard: Copies the sequence name to the clipboard.
Change Annotation and Description: Allows to manually change/add annotations.
Annotate Sequence: This function allows changing annotation parameters for the selected sequence and re-running automatic annotation.
Make Graph of GO-Mapping-Results with Annotations Score: Displays a DAG with all GO terms related to one sequence. Shows all the GOs from the mapping step as well as final annotations (highlighted).
Extract Selection to new Tab: Create a new project from the marked sequences (Shift or Ctrl).
Copy Selection to Clipboard (tabular format): Copies the marked sequence to the clipboard in tabular format for further processing in a spreadsheet editor.
Copy Content of Column: SeqName to Clipboard: The content of a specific column will be copied to the clipboard.
Create ID List of Column: Sequence: Allows creating an ID list of a specific column which can then be used for Fisher's Exact Test or Selection of sequences (see Figure 6).
Create ID Value-List of SeqName and Length: Allows creating a list with two specific columns e.g. SeqName and Length.
Create Category Chart of Column: Length: Create a category chart of a certain column e.g. sequence length.
Create Distribution Chart of Column: InterProScan IDs: Create a distribution chart of a certain column.
Figure 5: Sequence Context Menu
Create ID lists:
To generate an ID list the desired sequences have to be marked and then right click on "Create ID list from selected Entries (SeqName column)''.
A new tab is opened containing the ID list of the marked sequence names. This list can now be saved for further use (e.g. enrichment analysis, selections, etc.). It is also possible to generate sequence ID lists from Graphs (see Quantitative Analysis).
To mark all the sequences on the table do: Ctrl + A (Windows/ Linux) and Apple + A (Mac).
Figure 6: Create ID List from Sequence Name
The ID lists can be used in:
Fisher Exact Test
Load Annotations from BioMart (online)
The Gene Set Enrichment Analysis (GSEA) needs a ranked list and this can also be generated by OmicsBox with the Create ID Value List.
Here is an example of the Open File dialog of the Fisher's Exact Test Wizard shows the available ID lists if the selected file type in the checkbox (bottom left) is set to B2G ID list.
Figure 7: Select ID list from Fisher Exact Test Wizard
Filter out Sequences
The OmicsBox table allows filtering out rows, depending on different search criteria for each column. Each column header shows a small icon which opens a context menu when left-clicked.
Filters can be applied in various columns and are joined via an AND condition.
Different data-types allow different filter settings (e.g. numbers allow greater than).
When a filter is applied on a column the filter icon turns red - double-clicking the icon will remove the filter.
On the top-right corner, there is a small status message showing how many sequences pass your filter.
The button next to it (crossed out a document) removes all current filters.
All the algorithms, blast, mapping, annotation, etc., work on the selected sequences and not only on the filtered ones. This means if one has a filter but there are some sequences selected on your project and one runs e.g. remove blast results, it will work on all selected sequences and not only on the ones you see on the table.
Figure 8: Filter Criteria
This feature allows hiding the columns of the sequence table.
By right clicking on a column and a menu will be displayed and one can select those columns to hide from the table.
In combination with Export Table from File > Export, this can be used to customize the output.
Figure 9: Hide Columns
From version Blast2GO 3.1 upwards the .b2g file type replaces the previous .dat file. The .dat files will still be supported for opening and export. All OmicsBox project and results (enrichment results, charts, graphs, etc.) will be saved with the new file type .b2g/.box. This files can be viewed and opened directly within the FileManager tab. All other file types can be open form the FileManager via the systems default application.
.box/.b2g: File type for all OmicsBox objects (project, results, id lists, etc.). Some OmicsBox objects can be opened with different viewers like for example the OmicsBox Table or the Generic Table.
.dat: Legacy format for previous OmicsBox projects. This format had been replaced in 2015 by the more flexible and performance .b2g/.box format. The .dat format is still maintained for compatibility with older datasets and application versions as well as the OmicsBox plugins.