PIANA distribution contains several directories and files compressed in a tar.gz file. Source code and documentation files are included in the distribution. If you want to use the limited piana database we provide, you'll need to download as well the mysql dump of pianaDB_limited.

PIANA code is under GNU General Public License By downloading the code you agree to the terms of that license.

Attention! We are planning to release a major revision in a short time. Apart from updating parsers (so that they can parse the once-again changed formats for some DBs) we are going to modify PIANA to acept new protein codes (eg. GeneID) and accept interactions others than Protein-Protein interactions. Subscribe to the announcement list if you want to hear from us when we release PIANA 2.0.
Until then, we will continue to correct any bugs that we/you find in PIANA 1.2

file name	size	description	date
piana_v1.47.tar.gz	5MB	latest revision of PIANA v1.4	Jul 19 2007
pianaDB_limited.v1.4.mysqldump.gz	632MB	PIANA limited database populated with piana v1.4 (it is compatible with PIANA v1.4)	Jul 02 2007
piana_v1.22.tar.gz	5MB	latest revision of PIANA v1.2	Nov 24th 2006
piana_v1.11.tar.gz	4.8MB	last revision of PIANA v1.1	Mar 29th 2006
piana_v1.038.tar.gz	4.8MB	last revision of PIANA v1.0	Feb 21st 2006
pianaDB_limited.v1.037.mysqldump.gz	512MB	PIANA limited database populated with piana v1.037 (it is compatible with PIANA v1.1 and v1.2)	Feb 21 2006

Software versions description

• PIANA v1.4
  Parameters and commands available in this version are described in this file
  • Much more data can be parsed than in previous versions
  • Much faster than previous versions
  • Many new protein identifier types are accepted
  • New database design: old PIANA databases do not work with this version. However, the performance (space allocated, speed, ...) gains are huge.
  • Many performance tricks implemented: memory, speed, ...
  • New command to find the interacting motifs of a protein (see paper on PLoS Comp Bio)
  • New parameter to control the memory usage
  • Many minor bugs corrected
  • Important: read this to learn more about PIANA v1.4 with respect to PIANA v1.2

PIANA v1.3 was a internal release

• PIANA v1.2
  Parameters and commands available in this version are described in this file
  • New parameter allows the use of the PIANA database through a different MySQL port (v1.22)
  • Corrected bug in command expand-interactions (v1.22)
  • PIANA now outputs information in Cytoscape format (sif, noa and eda) (v1.2)
  • Added parameter use-secondary-db to piana_configuration_parameters.py (v1.2)
  • Added parameter piana-db to PIANA commands add-protein and add-proteins-file (v1.2)
  • Changed run_piana_protein_by_protein to run_multiple_pianas. Now, multiple piana.py can be executed for many input files in a directory (v1.2)
  • Multiple bugs fixed (eg. PIANA was halting for certain cases with proteins with multiple names) (v1.2)
  • Added PIANA commands match-proteins-to-pathways and match-proteins-to-gos (v1.2)
  • Improved documentation, mainly on PIANA outputs and command usage (v1.2)


• PIANA v1.1
  Parameters and commands available in this version are described in this file
  • Added PIANA parameter use-self-ints: allows the user to avoid using self-interactions (v1.11)
  • method PianaDBaccess.get_all_interactions has been removed: use instead get_all_partners (v1.11)
  • Added documentation on how to populate the PIANA database with the human interactome published on Nature and Cell (v1.11)
  • Corrected bug in pianaDB tables: embl accessions were truncated to 8 chars (Thanks to C. Winter) (v1.11)
  • Added PIANA command find-shortest-route (v1.1)
  • STRING parser modified to allow a faster execution and avoid ambiguities (v1.1)
  • Improved documentation, mainly on PIANA outputs and command usage (v1.1)


• PIANA v1.0 was the first public release of PIANA
  Parameters and commands available in this version are described in this file


• PIANA v1.038 is the latest revision made to v1.0
  
  • README.pythonpath corrected (directory for CirGraphCluster was incorrect) (Thanks to J. Huerta) (v1.038)
  • Added indexes to psi databases (increases parsing speed) (Thanks to C. Winter) (v1.038)
  • Root connectivity and number of neighbours information is now correctly printed to interaction tables (v1.037)
  • added index to column proteinDescription in table proteinDescription (v1.037)
    without this index, parser psi2piana.py is too slow
    if you have a PIANA database created with a version previous to v1.037, you should create an index on your database by doing:
    mysql> use your_pianaDB
    mysql> create index proteinDescription on proteinDescription (proteinDescription);
  • modifications made to psi2piana to make it faster. (Thanks to C. Winter) (v1.037)
  • there was a missing class in the previous release: ClusteredGraphGenerator (v1.036)
  • some documentantion has been added, mainly to README.piana_tutorial (v1.035)
  • corrected bug in psi2piana (bug was halting the parsing) (v1.033)
  • corrected bug in genpept2piana (bug was incorrectly getting the name of the protein) Thanks to W.K. Kim and C. Winter (v1.033)
  • corrected bug in nr2piana, pdbaa2piana and swissprot2piana (proteinSpecies table was not being updated) (v1.033)

• pianaDB_limited v1.037 is the PIANA limited database that has been populated using parsers from piana_v1.037
  The contents of this version are described in this file