The NGB user interface is implemented as the main menu on the left side and a set of panels that can be resized, moved, docked anywhere within the browser window, maximized or hidden.
Main menu contains the following items:
- INFO - to view the current NGB version and links to the NGB GitHub project and to the documentation page:
- OPEN FILE - to open and view separate file from the NGB server or from external URL:
- VIEWS - to see the complete list of available panels and select the panels to be shown or hidden
- SHARE LINK - to share a link to the current view of the opened files with other NGB users:
- SETTINGS - to open the main settings pop-up:
You can use the VIEWS menu to see the complete list of available panels and select the panels to be shown or hidden. The VIEWS menu is located on the main toolbar of the application:
By default, only following panels are shown: Browser, Datasets, Genes and Variants.
The Browser panel is one of the main panel where user can open, view and configure file track and also view datasets' summary details.
Let's take a look at panels below.
You can rearrange the layout of the NGB as follows:
- To resize a panel - click and drag the panel's edge
- To move and dock a panel - click and hold the panel's title tab and start dragging the panel. As you are dragging the panel, the application will visualize places where the panel can be docked. Hover the panel over the desired place and release the mouse button to dock the panel. Panels could be also arranged as adjacent tabs: to do so, dock the hovered panel's tab next to the other panel's tab.
- To maximize a panel (full screen size) - click the [ ] button on the panel's header. To restore the panel to the previous size, click the the [ ] button again.
- To close a panel - click the X button on the panel's header tab.
- To show again a panel that was closed - select it from the VIEWS menu.
This panel is used to show the list of variants loaded from the project's VCF files in a tabular view. If no VCF files were loaded, the table will be empty.
To navigate to a variant, click the variant's row in the table. This variant will be opened in the "Browser" panel, at the corressponding VCF track.
By default in the panel, only the following columns are shown: Type, Chromosome, Gene, Position.
You can rearrange the list of variants as follows:
- To sort the variants by a property - click on the header of the corresponding column. To invert the sorting order, click on the header again:
- To display or hide extra columns - select/unselect them from the panel options menu. The menu is located on the bar above the table (hamburger icon):
- To restore the original table view - click the corresponding item in the panel options menu (hamburger icon). This will hide all addition columns, show default columns and restore their order, cancel all configured sortings and filters:
For more details, options and capabilities see here.
This panel displays a list of genes/transcripts/exons and other features of the current dataset (from corresponding GFF/GTF and GenBank files) in a tabular view.
By default in the panel, only the following columns are shown:
- Chr - chromosome/sequence name
- Name - feature name
- Id - feature ID
- Type - feature type
- Start - start position of the feature on the chromosome/sequence
- End - end position of the feature on the chromosome/sequence
- Strand - feature strand
- Info - button to open the certain feature full info
You can rearrange the list of features as follows:
- To sort the genes table by a property - click the header of the corresponding column. To invert the sorting order, click the header again:
- To sort the genes table by several properties - click the header of the column by which you wish to sort firstly, then holding Shift key click the column header by which to sort secondly, etc.
All columns, by which the sorting was performed, will be numerated:
- To display or hide extra columns - select/unselect them from the panel options menu. The menu is located on the bar above the table (hamburger icon):
There are two types of additional columns in this list:- mandatory feature fields from origin gene files (Feature, Frame, Gene, Score, Source) are shown as is
- optional feature attributes from the "Attributes" column of the origin gene files are shown in format
<Attribute_name> (attr)
Example:
- Another way to hide an extra column - use the corresponding item in the menu appeared by click the arrow icon near the column name, e.g.:
- To filter displayed features - use one or more parameters to filter features in the Genes panel. The approach is fully the same as described for the Variants panel:
- To restore the original table view - click the corresponding item in the panel options menu (hamburger icon). This will hide all addition columns, show default columns and restore their order, cancel all configured sortings and filters:
For more details, options and capabilities see here.
You can bookmark a specific location in the browser.
This action saves the state of the browser and opened tracks as well - so, it is called "saving the session".
It can be performed as follows:
- Click the Location icon located in the main menu on the left page side.
Note: the Location icon is being displayed only when any position/chromosome/reference is opened. - The pop-up will appear where session name (mandatory) and description (optionally) should be specified:
- Once all desired data is specified - click the Save button to confirm:
Note: session bookmarks are stored globally. Panel will show all saved Sessions - from all NGB users.
The Sessions panel has the following columns:
- Name - session name
- Description - session description
- Reference - reference name that was opened when the session was saved
- Chr - chromosome name that was opened when the session was saved
- Start position - start position at the reference
- End position - end position at the reference
- Owner - user name who saved the session
To sort the sessions according to a specific property - click the header of the corresponding column, e.g.:
To filter displayed sessions - use one or more parameters to filter sessions in the Sessions panel. The approach is similar to described for the Variants panel:
To navigate to a location bookmarked in the certain session - click the corresponding row of the table:
To delete a session bookmark - click the Trash icon of the corresponding row.
Note: Additionally, if any model was opened in the Molecular viewer at the saving session moment - full state of the opened model will be stored in such session. The following options will be saved:
- model, selected structure and chain
- view of the model - display mode and color scheme
- the set angle
- the set zoom level
So, if user will open such session - the Molecular viewer panel will be opened with the full same model image as it was saved.
The Molecular Viewer panel shows the 3D structure of a protein.
This panel is hidden by default. Select Molecular Viewer from the VIEWS menu to show the panel.
To view a protein's 3D structure, navigate to a specific location in a browser and click a gene or a transcript on the gene's track.
This will load the 3D structure of the protein from the RCSB database. To enable this, external databases are used:
- A call to
Ensemblis performed to retrieve a list of transcripts of a gene and the link to uniprot entry for each transcript - A list of corresponding PDB IDs with the current chain in a PDB is retrieved from the uniprot entry
- Finally, a PDB file is retrieved from RCSB and visualized.
If several PDB files are available for a gene/protein, they will be shown as a dropdown list on the top of the panel:
If a PDB file contains multiple protein chains, they will be listed in a dropdown list above the viewer.
By default, the chain that contains a protein corresponding to the gene will be selected.
The selected chain or multiple changes are opaque, non-selected chains are semi-transparent:
You can:
- rotate the protein's 3D structure
- zoom in/out on the protein's 3D structure
- change the color scheme - click the
icon:
- change the display mode - click the
icon:
Via this panel users can perform BLAST search nucleotide/amino acid sequences over BLAST databases and view the corresponding results.
BLAST databases should be previously uploaded into NGB (this could be as downloaded NCBI databases or custom ones).
The BLAST panel contains two sub-tabs:
- Search (opened by default) - to display and specify search settings, and also start a new search
- History - to display the history of searches
Once the BLAST search setup is finished - click the Search button to start:
Since the BLAST search can take a long time, the results are not displayed immediately - and for each search - a new "search task" is being created.
The list of such tasks is displayed at the History sub-tab.
This sub-tab is being opened automatically after the search starts:
Just-started search task is shown on the top of the tasks list.
User can click such hyperlink (or just a row) to open the corresponding search results. Search results will be opened in the same tab (History):
User can click any row in the Sequence table and the form with details about all matches (alignments) of the search query to the certain sequence will be opened.
This form is being opened in the same tab (History), e.g.:
For more details, options and capabilities see here.
Heatmap is a data visualization technique that shows magnitude of a phenomenon as color in two dimensions.
NGB supports heatmaps displaying.
In NGB, heatmaps can be shown in the Heatmap panel, as separate track or even at the Summary dataset view in the Browser panel.
Besides their main function to visualize data, heatmaps can also be used to navigate over NGB objects, e.g.:
For more details see here.
Lineage is a one-directional graph where each node represent a strain (genome) and each edge between nodes represent an impact used to create a progeny from a parent strain.
NGB supports visualization of a lineage for a family of strains or reference genomes.
Any lineage node (strain) can be associated with a NGB reference ID - in this case, node's name is displayed as a hyperlink.
User can click such link to navigate to the corresponding reference track (at the same time, the lineage panel remains opened), e.g.:
For more details see here.
Metabolic pathways are series of chemical reactions that start with a substrate and finish with an end product.
These pathways are being displayed as certain kind of infographics, often called "maps".
NGB supports visualisation maps that can be as public ones received from different sources like BioCyc database and as well as internal, produced by pathway modelling software:
For more details see here.
Via the Target Identification panel users can collect identification information about targets of interest (genes), store this information and use it for their own research purposes.
Target identification panel includes sub-tabs:
- Targets (opened by default) - sub-panel where user can manage targets
- Identifications - sub-panel where user can view and manage target identification reports
To launch a new identifying process, find the target in the Targets table and click the button to launch identification process, e.g.:
In the appeared pop-up, specify:
- genes of interest - list of genes of interest. Corresponds to species for which gene (target) the identification will be performed
- translational genes - list of genes in species to which the gene comparison shall be performed during the identification
Once the identifying process is finished, the Identifications sub-tab will be automatically opened with the identification results (report):
For more details about identification process and report see here.
To take a screenshot of a browser, click the Camera icon located in the right side of the "Browser" panel. The Camera icon is transparent by default and becomes opaque when you hover over it:
The screenshot will be saved to the Downloads folder of your Web browser.