Public Access to Chado

A forum for discussing Power User related features of FlyBase such as using Chado, GFF, FASTA files, etc...

Public Access to Chado

Postby Josh Goodman » Thu Feb 07, 2008 2:01 pm

FlyBase is pleased to announce direct read only access to our Chado database.

hostname: flybase.org
port: 5432
username: flybase
password: no password
database name: flybase

e.g. Using the PostgreSQL client
Code: Select all
psql -h flybase.org -U flybase flybase


The release available via this method will match the current version displayed on our web site. Prior to each release there will be a planned database service outage of ~5 hours while the new data is loaded. These will occur approximately once a month. Please check back here for updates on when outages will take place.

Also, if you would like a local copy of our database you can always download our PostgreSQL dumps from: ftp://ftp.flybase.net/releases/current/psql
Josh Goodman
Site Admin
 
Posts: 64
Joined: Mon Nov 26, 2007 2:39 pm

Re: Public Access to Chado

Postby jpltanis » Tue Jan 26, 2010 12:47 pm

Hi Josh,

I am from the GrainGenes.org and currently doing research on Chado schema. We are hoping to adopted it for use in our system. I like to use the public access to do some performance comparison. What protocol is needed to access the DB? I tried - ssh, http - with no success.

Thanks,
John
jpltanis
 
Posts: 1
Joined: Tue Jan 26, 2010 12:28 pm

Re: Public Access to Chado

Postby Josh Goodman » Tue Jan 26, 2010 1:19 pm

You need to install the PostgreSQL client for your operating system. See http://www.postgresql.org/. There are also many database GUI clients that support the PostgreSQL client protocol (e.g. http://squirrel-sql.sourceforge.net/).

Using this service for exploring Chado or for moderate usage is fine. I would absolutely not use it for a performance comparison for several reasons. One, this is a shared public service so any number of other users can impact your benchmarks at any time. Even if there are no other PostgreSQL users, that machine handles a variety of other services that may or may not be in use. Two, the hardware that runs this service isn't top notch. Three, network access is almost always slower than direct local access. The amount of network traffic in between you and our servers will have a significant impact on performance.

If you want to benchmark performance I suggest you download our PostgreSQL Chado dumps and run your tests locally.

ftp://ftp.flybase.org/releases/current/psql/

Cheers,
Josh
Josh Goodman
Site Admin
 
Posts: 64
Joined: Mon Nov 26, 2007 2:39 pm


Return to Power Users

cron