The latest version of Biovista Vizit introduces two much requested features:
- A new High Throughput Layout, and
- A new Copy/Paste mechanism to transfer named Entities in and out of Vizit.
Here’s a quick rundown of the new features:
High Throughput Layout
Biovista Vizit is frequently used for systematic exploration of a biomedical domain. For example, one can explore all the Genes or Pathways associated with a Disease in the scientific literature with just one click of the “Explore” button in Vizit’s context menu, creating “rich” graphs with several entities and links.
To help Vizit users navigate large, highly interconnected graphs, we have implemented a new High Throughput Layout engine for all Vizit “Explore” and “Connect” actions. The High Throughput Layout arranges nodes (aka, the biomedical entities) in higher order layers depending on how strong the relationship is with the expanding entity. The inner layer contain the most highly connected nodes to the starting entity, the next layer contains nodes with weaker association with the starting entity and so on. That way, Vizit remains snappy even with hundreds of nodes in the whiteboard.
Here’s an example of the older vs the new layout:
|
Before High Throughput Layout |
After High Throughput Layout |
A new Copy/Paste mechanism
An often requested feature from Vizit users has been the ability to bulk insert (and/or export) entities to and from the Vizit whiteboard. A researcher may have a list of Genes from a high-throughput experiment that she/he would like to analyze using Vizit. It is now possible to just copy a list of biomedical terms and paste it onto the Vizit whiteboard. In a similar manner one can select several Vizit nodes and then paste them to an Excel file for further analysis or presentation.
Take the following example table containing a mix of biomedical entities. Try copying the contents of the table and then pasting them into Biovista Vizit (https://www.biovista.com/vizit/)
Example Data
| Entity Name | Entity Type |
|---|---|
| Breast Cancer | Disease |
| BRCA1 | Gene |
| BRCA2 | Gene |
| DNA repair | Pathway |
The format of the text to be copy/pasted is expected to be row based and tab delimited where the tab separates the entity name from the entity type.
Note that with the High Throughput Layout in place you can easily paste hundred of entities for further analysis. Therefore, by mere copying all the entities from a Biovista Vizit graph you can have your data available to other programs.
Hope you will enjoy the new Biovista Vizit features.
Copy/Paste works in Firefox/Chrome/IE 11/Edge browsers and is invoked with the standard Ctrl+C/Ctrl+V (Cmd+C/Cmd+V for Mac) keyboard actions. Depending on your OS and browser alternatives ways to copy paste may work as well.