Laverne is your virtual research assistant, librarian and data cruncher- without any human drama. She allows you to browse unbiased, bioinformatics data related to your gene, pathway or disease of interest. This bioinformatics tool helps you gain an understanding of biological neighborhoods in your research space. Laverne also helps you find products useful for research related to your gene, pathway or disease of interest.
How to Get Started
1. Go to Laverne: www.novusbio.com/explorer
2. Start by clicking into box shown:
3. Select from the drop down menu the Gene, Pathway or Disease that you would like to search. For example, if you want to explore a specific Disease, select “Disease” from the drop down box.
4. Start to type in the name of the disease you would like to search such as “Hypoxia” and select it from the drop down box:
5. You will be taken to the Start Exploring option. Click on the circle and select where you would like to explore. Laverne will then go to work searching for relationships for that term and display the matches as follows: :
6. Browse the list of matches and select the most appropriate one by clicking on it.
7. Once you click on the term that you wish to explore, it will appear in the middle of the Laverne tool.
8. You can now explore relationships between your term of interest and related Genes, Pathways, Diseases, Cell Lines or PTMs (post-translational modifications). Click on the relationship that you would like to display and Laverne will show the top 10 relationships. For example, if you click on Genes, Laverne will display the top 10 Genes related to Hypoxia:
9. From this web view, you can continue exploring relationships with Genes, Pathways, PTMs and Diseases.
10. By clicking on the + button you can view other related Genes, Pathways, Disease, Cell Line and PTM based on that term of interest, as well as view the number of Products Available (if you are exploring a Gene). For example, Pathways, and start to type in “C CELL CARCINOMA” it will track it in the drop down menu and you can select it from there:
11. By clicking on the “C CELL CARCINOMA”, you will see it added to the work area and “Explore” or “Connect” options will let you detailed webpage of all of these products, where you can filter by product type, species reactivity, useful applications, and many more.
12. To explore another Gene, Pathway or Disease, return to the main Laverne page and enter another search term.
13. You can always reset your search, by using the 'ARROW' buttons in the top left hand corner of Laverne:
The Brains That Drive Laverne
Laverne displays relationships between Genes, Pathways, PTMs and Diseases based on the co-citation of terms in scientific publications. The bioinformatics data used to power this tool is supplied by Biovista Inc. Biovista's Biolab Experiment Assistant (BEA), a literature mining platform, allows users to search relationships between concepts of interest such as genes, diseases, compounds and cell types to obtain an overview of the knowledge that is captured in scientific literature (Medline) and patent databases (USPTO).
Laverne's 'web' connects these data relationships between Genes, Pathways, PTMs and Diseases using a line. Each connector line displays a small publication icon on it:
By clicking on this publication icon, a window will open that displays the Literature related to these two terms. For example, when clicking on the publication icon that connects the HIF-1 Gene to Hypoxia, the following is displayed:
By clicking on a title, Laverne will take you to PubMed and display the abstract of that article.