BIANA web server help

BIANA (Biological Interactions And Network Analysis) is a software platform for the creation and analysis of biological networks. BIANA implements sofisticated algorithms to make transparent to the user the recurrent identifiers ambiguities, while mantaining the quality of the data. The Web Server to BIANA allows users to make a limited use of BIANA without having to download any code or do any programming. For more in-depth use of BIANA, users can use the BIANA plugin to Cytoscape (will be published in a few weeks) or directly download the code from the official BIANA web site: http://sbi.imim.es/biana (will be available in a few weeks).

The easiest way of learning how to use the BIANA server is to automatically fill in the formulary with sample data by using the link 'try it using sample data' provided on the top of the server. Once the data has been filled, the user can fill in the email box, click on 'add' to tell BIANA to use the example bioentity to create the interaction network, and then click on the button 'Run Biana!'.

BIANA is similar to other web servers that provide access to repositories of biological interactions. However, BIANA is different in the following aspects: 1) does a real integration of repositories, regardless of the type of identifiers used in the repositories; 2) is not limited to protein interactions and all types of biological interactions can be added; 3) provides users with analysis tools of the integrated networks. Furthermore, the BIANA webserver allows inputting multiple bioentities one by one or from external files, and codified in different identifier types.

Execution process

Provide a name for the experiment, and enter your email (we will send you an email when your results are ready)
Add seed bioentities for your network: these are the bioentities for which BIANA will search interactions. You can add seeds one by one, providing a file with seeds (one id per line, or two columns in each line: first is the id type, second the identifier), or asking for the network of a species. Please, keep in mind that creating the network for a species takes a long time and involves a high load: don't ask for species networks unless you really need them.
- The embedded identifier tags can be the following: uniprotentry, uniprotaccession, genesymbol, geneid, refseq, proteinsequence, cygd, ec, encode, ensembl, flybase, hgnc, ipi, gi, accessionnumber (for NCBI accession number), nucleotidesequence, orfname, pdb (for PDB.chain), pir, sgd, tair, unigene, wormbase, ypd
- One example of file with seed bioentities could be one with the three following lines:
  HDA1_YEAST
  MNP1_YEAST
  HSP82_YEAST
- The same example but embedding the identifier type would be:
  uniprotentry HDA1_YEAST
  uniprotentry MNP1_YEAST
  uniprotentry HSP82_YEAST
Next, you set the output identifier type you wish to use for your outputs. If you select Gene Symbol, all bioentities will be identified with their corresponding gene symbols (if applicable).
Select the depth to which you want to develop the network: a depth of 1 will create a network containing the seeds and their direct interaction partners. A depth of 2 will add to this network the interaction partners of the partners. And so on...
If you want to access to more options (for advanced users), click on 'More Options'.
You can ask BIANA to predict interactions for your seed bioentities, based on interology. Basically, if two bioentities shared a certain feature (that the user can select in the associated select form), BIANA will assumme that they also share interactions.
If you are interested in a certain type of relation, you can fix it by setting the relation type
Set now the BIANA DB release. Leave it to the default version if you are not trying to reproduce a previous experiment: the highest release is always the most complete version of the BIANA database
Choose whether you want BIANA to use all repositories or you are just interested in a few ones
Choose whether you want BIANA to use all detection methods or you are just interested in a few ones
Use the special bioentities section to tag those bioentities that you want to see differentiated afterwards in your results. For example, if you have two files, one with genes that are overexpressed in a microarray experiment and another with those genes that were underexpressed, you can map this information to the network by creating the labels 'under' and 'over'.
Now, tell BIANA which outputs you want to obtain: HTML table with interactions, SIF network and HTML table with information for all bioentities.
Run BIANA by clicking on the button
Wait for an email telling you that the results are ready (with a link to the report)

Useful tips

The input files you provide to BIANA must all follow the same rule: one bioentity per line. Alternatively, you can also have an extra column (separated by a tabulator) where you first specify the identifier type of the bioentitiy. For example, a file with one single bioentity would have one line "uniprotentry[tabulator]ACE_HUMAN". In this case, you will have to set the select box of identifier types to 'embedded'. For all identifier type tags see the above section 'execution process'.

Every input in the formulary has its associated help: just pass the mouse over the text that describes the input and a small window will describe the information that is expected from you.

You can choose which type of relation between bioentities you want to use. For example, if you are just interested in creating a network with physical interactions, you can restrict the network to contain such relation types.

When printing your network you can choose between these options:
- All bioentities and interactions: prints the complete network
- Seeds and linker bioentities: prints seeds, linkers (a 'linker' is a bioentity that connects at least 2 seeds) and interactions between them.

You can ask BIANA to add predictions to the network based on interology (http://en.wikipedia.org/wiki/Interolog). In this type of predictions, BIANA assumes that if two bioentities share a certain characteristic (e.g. COG) then they will also share interaction partners.