Diary of Mr.ZAM

September 8, 2007

Install PostgreSQL on Ubuntu

Today I just install postgresql on ubuntu feisty complete ... T_T. Sure I install PostgreSQL v8.2 by using the following command:

$sudo apt-get install postgresql-8.2

Then I install the following package - phppgadmin pgadmin3 pgadmin3-data using command:

$sudo apt-get install phppgadmin pgadmin3 pgadmin3-data

After this, I need to reset the password for the 'postgres' admin account for the server, so I can use this for all of the system administration tasks. Type the following at the command-line (substitute in the password you want to use for your administrator account):

$sudo su postgres -c psql template1
template1=# ALTER USER postgres WITH PASSWORD 'password_you_want';
template1=# \q

Then, from here on in we can use pgAdmin to run the database server.

Finally, I need to open up the server so that I can access and use it remotely - unless you only want to access the database on the local machine (The guidelines here are for opening up your server on a secure LAN - if you are not on a secure LAN you may want to look into adding SSL authentication before proceeding with these steps).

To do this, first, I need to edit the postgresql.conf file:

$sudo gedit /etc/postgresql/8.2/main/postgresql.conf

Now, to edit a couple of lines in the 'Connections and Authentication' section...

Change the line:

#listen_addresses = 'localhost'


listen_addresses = '*'

and also change the line:

#password_encryption = on


password_encryption = on

Then save the file and close gedit.

Now for the final step, I must define who can access the server. This is all done using the pg_hba.conf file.

$sudo gedit /etc/postgresql/8.2/main/pg_hba.conf

Now add the following lines to the file:

# Allow any user on the local system to connect to any database under
# any user name using Unix-domain sockets (the default for local
# connections).
# Database administrative login by UNIX sockets
local all all trust


# "local" is for Unix domain socket connections only
local all all md5

# IPv4 local connections:
host all all md5
# IPv6 local connections:
host all all ::1/128 md5

# Connections for all PCs on the subnet
host all all [ip address] [subnet mask] md5

and in the last line, add in your subnet mask (i.e. and the IP address of the machine that you would like to access your server (i.e. However, if you would like to enable access to a range of IP addresses, just substitute the last number for a zero and all machines within that range will be allowed access (i.e. would allow all machines with an IP address 138.250.192.x to use the database server).

That's it, now all you have to do is restart the server and all should be working!

$sudo /etc/init.d/postgresql-8.2 restart

September 5, 2007

Web Services for Bioinformatics

Sine June 2006, I am interesting about Web Services for Bioinformatics. The first that I interested was Sharing genome data using web services from independent database sources.

From the following below are url of articles that talk about web services for bioinformatics:
  • http://webservices.xml.com/pub/a/ws/2002/05/14/biows.html
  • http://www.ibm.com/developerworks/webservices/library/ws-bioinfo.html
  • http://www.ibm.com/developerworks/webservices/library/ws-bioinfo2.html
  • http://radar.oreilly.com/archives/2006/08/web_services_for_bioinformatic.html
  • http://psb.stanford.edu/psb04/tut_jensen.html
  • http://www.bioinfotool.org/
Many of applications that I study usually use perl programming (I'm java programming) sometime use java, so I can study from java programming only T_T.

Oh, and then, many of Web Services for Bioinformatics usually use for sharing application sometime sharing data from databases. Then I'd like to study ws (web services) for sharing data from databases first, after this I'll study ws for bioinformatics applications. :)

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