Friday, March 09, 2007

reinstalling drupal, preparing for live & dev sites

Ok, I'm archiving my current dev install of drupal (which is bloated with modules, some of which have altered the mysql database) and starting with new install of 5.1. Once I have just the right constellation of modules locally, I'll copy them over to our live site ( Here are the mysql commands I used to reset the database for my new drupal install:
  • mysqldump -u username -p --databases drupal >/tmp/drupal.sql
  • drop database drupal;
  • create database igem2007;
    ON igem2007.*
    TO 'drupal'@'localhost' IDENTIFIED BY 'foopass';
Then I grabbed drupal 5.1 and followed the install instructions to unpack the files and move them into my webserver's base directory. So, from the terminal:
  • cd /Library/WebServer/Documents
  • rm -rv *
  • curl -LO
  • tar -xzvf drupal-5.1.tar.gz
  • mv drupal-5.1/* drupal-5.1/.htaccess ./
  • rmdir drupal-5.1
  • chmod 777 ./sites/default/settings.php
    - this part isn't actually mentioned in the install.txt; see my earlier post
  • visit the drupal site root via web browser and supply database info
  • chmod 644 ./sites/default/settings.php
  • mkdir files
  • sudo chown www:admin files
  • sudo chmod 755 files
That's it! Drupal 5.1 has been restored to virginal status. I'll post the modules I decided on and the configuration details next.


Thursday, March 08, 2007

An Open Scientific Future (or, an email to OWW)

"If you had five minutes on stage what would you say? What if you only got 20 slides and they rotated automatically after 15 seconds? Would you pitch a project? Launch a web site? Teach a hack?"

Check out Deepak Singh's presentation at Ignite Seattle, An Open Scientific Future.

I liked his observation that scientists already have pretty good access to information via tools like ncbi, but to use sites like that you really have to know what you're looking for quoting (he showed a quote by Jon Udell: "Effective search depends on reservoirs of tacit knowledge and conscious skill. Some people possess much deeper resevoirs, and/or can tap into them more effectively, than others. That makes them valuable.")

He then said "I do know what I'm looking for but I can't share that information with the rest of the world, it's limited to me. And that's the challenge, and that's why science needs to get open. Because historically it resided inside us completely." He then talks about some current examples of systems that allow the community to share that expertise in finding data.

Also, Austin and I just checked out his blog and noticed his post about OWW and that OWW has now got a technorati tag. Also also, I just noticed that someone named pedro is mentioned on deepaks blog as interviewing Jason, so Jason, is this all old hat to you?