BIANA: Biologic Interaction and Network Analysis

Frequently Asked Questions

• Installation
  • How do I check whether python package is installed properly?
    • Execute python interpreter and try to import the package as below. If you interpreter prompts "BIANA>" string, is installed properly.
      

      \\$> python >>> import biana

      If not, revisit the installation instructions and make sure that python package is installed properly.
  • What to do if Cytoscape gives package import error while starting plugin?
    • Make sure that you configured PYTHONPATH environment variable to include directory where python package is installed.
    • Restart your computer (to make sure that Cytoscape sees the changes you made to PYTHONPATH).
  • What should I do if I get "can not connect to MySQL database" error?
    • Check that MySQL server is running properly and (re)start it if necessary.
    • Check that database host and user information you provide is correct.
    • If you are MySQL server in your local host try using "127.0.0.1" instead of "localhost" as host name.
• Database population
  • Is it normal that populating a takes more time than expected?
    • population time will depend on multiple factors that can produce differences in parsing between different computers: parsed database, disk free space, disk access speed, network speed if MySQL server is in other computer... can have two distinct states: Running and parsing. When parsing, state is in "parsing" mode, and when starting a Session it changes automatically to "running" mode.
  • Why does not recognize, a new parser I have created?
    • Make sure you copied your new parser into _Installation_ path/bianaParser. Then, should recognize the parser and it will appear in the graphical interface as well. If you are not sure where was installed, execute python interpreter and try the following.
      

      \\$> python >>> import biana >>> biana.__path__
• Data Unification
  • What is the best unification protocol to use, do you have any suggested unification protocols?
    • Create & use a unification protocol that suits best to your needs (specific to your problem). You may want to check proposed unification protocols section to have some ideas.
• BIANA Execution
  • Why does the message "Optimizing database..." appear during a long time, when I start a Session?
    • This message only appears the first time you start a Session in a after adding a new external database in it. This process creates all necessary indices in the database to increase performance while running, and it is done after populating database in order to increase parsing performance. Depending on the Database size, this process can take from few seconds to a couple of hours.
    • If it takes too long, check your disk space where Database is stored is not full!
  • I do not have any entries when I create a new user entity set, what could be the reason?
    • If you created a unification protocol using only promiscuous databases, it is normal that you do not have any user entities. Data coming from promiscuous databases added to (multiple) user entities that contain at least one entry coming from a non-promiscuous entry.
    • There may not be any entry associated with your query, try to refine the attributes and values you have used.
  • Is it normal that creating networks takes too much time?
    • Huge and very connected networks can take some time. Be patient. Be sure you are doing the network you want to the correct level. If you don't want interactions between elements at the last level, don't add them!
    • If you are using the graphical interface as a Cytoscape Plugin, it usually slows down the process significantly. Execute the same process by command line. A trick is to create the set with Cytoscape, start the network at level 0 without relations at the last level, then save the commands into a file, then edit manually the file to set the correct level and finally execute the script.
  • Database connection has been lost when using Cytoscape plugin. Should I restart the plugin?
    • MySQL server usually closes connection after some time the connection has not been used (this time will depend on your MySQL server configuration). It is not necessary to restart the plugin, right-click in the Biana Session and select the option "Reconnect database".
  • When I execute Cytoscape plugin, it is very slow or Cytoscape exits suddenly.
    • When executing as a Cytoscape plugin, it consumes more time and memory than executing it as a command line application. You have different options:
      • By default, cytoscape.sh uses a maximum memory limit of 512Mb. If the program exceeds it, it will automatically exit without saving anything. You can increase this memory limit by modifying the parameter -Xmx512M when executing cytoscape.
      • If you are creating a huge network and you are not interested in visualizing it but only in getting the data, use scripts: it will be faster and it will require less computer resources. You can use the following trick to create the script you are interested in:
        1. Run Cytoscape plugin, create the network at level 0 and perform all the operations you are interested in.
        2. In the Session Popup Menu (right-click on Session), select the option "Save commands history".
        3. Modify the saved script by changing all the parameters you want and execute it from command line.
• Citing
  • How should I cite BIANA in my manuscipt?
    • Javier Garcia-Garcia, Emre Guney, Ramon Aragues, Joan Planas-Iglesias and Baldo Oliva, BIANA: A Software Framework for Compiling Biological Interactions and analyzing networks, in preparation.
    • Please cite original data sources as well as BIANA in your manuscript