Advanced users can intall Bionemo locally and explore the Bionemo data in a greater depth. We provide a PostgreSQL Dump of the latest version of Bionemo and an Perl API to facilitate its access.

You will need a computer running PostgreSQL. PostgreSQL will run on almost any hardware and any modern Unix-compatible platform should be able to run PostgreSQL. It also runs natively on Microsoft Windows NT-based operating systems like Win2000 SP4, WinXP, and Win2003. Please check the PostgreSQL WebSite for additional information and installation instructions.

To install Bionemo:

1. Download the Bionemo PostgreSQL Dump (Attention! 11.5 MB)

2. Uncompress it

bzip2 -d bionemo.pgdump.bz2

3. Create a PostgreSQL database to load Bionemo in it

createdb however_you_want_to_call_bionemo

4. Load Bionemo dump

psql -d however_you_want_to_call_bionemo -f bionemo.pgdump

If you want to use the Perl API you will need to need to install the DBI and the DBD::Pg Perl modules. You can donwload the Bionemo API here and read the documentation here

We also provide a fasta file containing the 1101 protein sequences contained in Bionemo (note that 6 proteins are Bionemo are actually "generic" proteins, such us sigma factors, and so they have no real sequence). Obtaining sequences from this file could be more convenient to some users than getting them form the SQL Database.

Downloads:

Bionemo PostgreSQL Dump	(Attention! 11.5 MB)
API	compressed file including installation instructions and documentation (392 Kb).
Bionemo Sequences	1101 Protein sequences in a Fasta format file (392 Kb).