The content in Bionemo (except the Help Pages) can be browsed by using the lists contained at the menu on the top/right corner of every page.

But there is a simple and more eficient way. Bionemo implements a simple search interface that allows simultaneously querying all the biological entities contained in it. The results are shown categorized by tabs representing classes containing the entity types (reactions, complexes, etc). Please note that the system will search for anything that matches your query so, for instance, searching for "benzoate" will match "benzoate" but also "2,3-Dihydroxybenzoate" or any other word containing your query.

To help you find your query in the result pages you can highlight the matches by clicking on the button at the right of the query

Let us use the example of benzoate to navigate through Bionemo. Just from the results page you will be able to see all the reactions in which any of the 24 compounds found take part, either as product or substrate or as inducer, as shown in the figure above. You can also find which complexes, and which genes are encoding them, perform reactions related to benzoate or any derivative of it,

and all the reactions and pathways in which those compounds are involved.

If you click on the benzoate pathway (Benz2), a graphical representation appears that is also conveniently clickable. A link to the original source in UM-BBD and clickable connections to alternative pathways are also displayed in this page. Compounds, reactions and regulators included in the graph are clickable as well.

Transcription Regulation, when available, can be exposed on top of the pathway by clicking in the button that reads "Display regulation". Note that this button will only appear when transcription regulation information is available.

Clicking on the halobenzoate 1-2 dioxygenase link will take the user to the page displaying that reaction information.

You can now select a gene, cbdA from Burkholderia sp. TH2 in our example, and access its page. There, links to several external databases are offered, including GenBank for DNA sequences containing the gene and GenePep and/or Uniprot for the protein sequence expressed by the gene. All external links are displayed as orange boxes and are opened in new windows.

In addition, if the protein sequence contains domains included in Pfam, these are shown and properly linked to Pfam. Clicking the domain name will retrieve the list of all proteins in Bionemo containing that domain.

Finally, when available, links to resolved 3D structures in PDB are also provided.

Now, we can continue the exploration of the system by taking a look at some of the information on transcriptional regulation contained in it. In the example, the transcriptional information available for the cbdA gene is displayed at the transcriptional unit (the cbdABC operon) that controls the expression of the gene. There you can know which transcription factor regulates the gene, CbdS in this case. The transcription unit page also contains a schematic representation of the operon and its promoter region, including the coordinates of the transcription factor if known, the type of promoter that drives its expression, the type of regulation actiong on it (activation or repression) and the molecules that serve as inducers to the system.

By clicking on the CbdS transcription factor link you will be transfered to its page, where in addition to the available molecular information on it (links to external sequence, domain and structure databases and relevant articles) the list of other target transcription units and the molecules that act as effectors are shown.

The best way to know Bionemo is to use it. Just type some queries in the search box and click around to get the most of it