lims-V1

by Mathieu Dandonneau

Description

• an open source LIMS type teamlab project management web application

• designed originally for the URMITE laboratory http://www.ifr48.com/spip.php?article9

• to facilitate safe data storage, data sharing among collaborators, and tracability of the lab microbiology genomic projects

• coded in Ruby on Rails

• include a :

  • CRUD DBMS ( create/read/update/delete databases management system) for tables related to genomic projects
  • Devise-based authentication system
  • Cancan role-based administration system
  • Intuitive and ergonomic interface designed with twitter bootstrap
  • Forms have been designed with Formtastic

• screencast : http://www.youtube.com/watch?v=C9C6babXuXQ&feature=relmfu

• this project management system is particularely adapted to biology laboratories projects

• i believe it is rather easily modifiable for your own need .. it is basically needed to replace the element tables with your own

• it represents a lighter and more simple alternative to open-source project management projects such as Redmine or Teambox

Installation Instructions

-install Ruby 1.9 and Rails 3

-Clone the repo :

git clone git@github.com:matoeilD/lims-V1.git

-create a database.yml file in config folder and fill as a start with:

# SQLite version 3.x
#   gem install sqlite3
#
#   Ensure the SQLite 3 gem is defined in your Gemfile
#   gem 'sqlite3'
development:
  adapter: sqlite3
  database: db/development.sqlite3
  pool: 5
  timeout: 5000

# Warning: The database defined as "test" will be erased and
# re-generated from your development database when you run "rake".
# Do not set this db to the same as development or production.
test:
  adapter: sqlite3
  database: db/test.sqlite3
  pool: 5
  timeout: 5000

production:
  adapter: sqlite3
  database: db/production.sqlite3
  pool: 5
  timeout: 5000>

-run bundle install

-run bundle exec rake db:migrate

-run rails s

-navigate at http://localhost:3000/

Signing up as administrator (initial step)

-in app\controllers\user_controller.rb

remove these lines of code

      #helper from devise
      before_filter :authenticate_user!

      #helper from cancan
      load_and_authorize_resource>

-start the server again , sign up , click on user , edit button , assign to admin

-put back lines of code above corresponding to authentication and administration helpers

you are now ready to use the application

few guidelines on how to use the application

• as administrator , attribute different roles to the users, which will restrict access to the databases and tasks

• these access can be modify in ability.rb ( see Cancan documentation )

• create a project

• add elements to it to choose between the following tables :

  • culture
  • extraction
  • library
  • EM_PCR
  • sequencing
  • submission
  • data
  • genome
  • metagenome
  • 16s_pyro
  • RNAseq
  • mass_spectro

that's pretty it !

gimme feedback at dandonneau@yahoo.com

Contributor guidelines

• find ways to make this app more generic so that it serves any needs and not only biology projects

• do code refactoring

• ameliorate ajax that is ( partially ) fonctional at this stage only for elements index view

• add a metasearch system

• add a log system

• add a undo system

• .....