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lims-V1

by Mathieu Dandonneau

Description

  • an open source LIMS type teamlab project management web server

  • 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

  • .....