labdb Resources

ABOUT

labdb is an advanced database-driven web software package to manage biological and chemical resources in a laboratory. It has been written in PHP language and relies on MySQL relational database system.

labdb is a modular program consisting of a standalone engine (i.e., core package) and modules/plugins. The core package is needed to run the modules. Each module enables management of a unique resource and can be added (or removed) easily without affecting the rest of the system.

Six modules are currently available. These are staffdb (for personnel details), wormdb (for nematode/worm strains), plasmiddb (for plasmids/fosmids/DNA constructs etc.), oligodb (for oligos/primers), chemdb (for chemicals), and refdb (for references/publications). Additional modules, such as microdb (for microbial cultures) and celldb (for cell lines), are planned in the future.

labdb has been developed and maintained by Gupta Lab (McMaster University). It is available for use in research labs. Please contact by email (admin@labdb.net) for more information. 

CURRENT VERSION

GUEST AND REGISTERED USERS

At least one user account (administrator) is required to manage software and databases. Additional user accounts (manager and general/standard) can also be registered. Any one visiting the site without validating credentials is considered guest and given free access to certain resources. Access privileges follow the following order:

Admin > Manager > General > Guest

Users belonging to Admin, Manager and General categories need to log in order to use enhanced features. The ability to search, browse, and make changes to database records varies depending upon access settings. An administrator has full control over all features including modification of user accounts. Guest users cannot make changes to database tables.

SHARING

You are welcome to use labdb. Contact us by email (adminATlabdbDOTnet) for assistance with an account for your lab/group. Depending upon your needs some customization may be made. If you wish to have the software installed on your own server then we could provide a copy to you. In this case, a PHP-driven web server and MySQL database will be required.

THINGS TO DO

• Allow power users (manager and admin) to alter notepad access settings via the Setup script.
• Improve Setup script. It should be able to scan new module folders for installation and update existing modules, table structures, module-specific messages and other things.
• Administrator portal needs to be fully developed.
• Allow multiple module records to be searched simultaneously.
• wormdb module:
  - Number of records in List option needs to be modifiable.
  - Storage box labels should be optional.
  - Dropdown menu categories should be customizable.
• plasmiddb module:
  - Allow an overview option for plasmids along with enhancer/promoter/reporter.
• oligodb module:
  - Allow addition of new storage boxes and assignment of tube locations.
• chemdb module:
  - Allow user-based customization of display fields for browsing records.
• refdb module:
  - Allow sharing of reference libraries between users.
  - Allow automated retrieval of records through PubMed ID.
• Develop other modules: celldb (cell lines), microdb (microbial cultures), protocoldb (protocols and methods).
• ...and many more.

KNOWN BUGS

• (Jan 9, 2019) Attempting to add a record in refdb via NCBI PubMed query does not always work, yet the output message is shown as if query was successful.
• (Jan 7, 2019) Search functionality in refdb is not working.
• (Jan 7, 2019) Record field values need better filtering in refdb to escape errors caused by special characters in some text.
• (Jan 3, 2019) Browsing records of plasmiddb via 'jump to page' tool does not work.

VERSION HISTORY

July 26, 2022 [Core package 0.9.9, Module: chemdb 0.2.1, oligodb 0.2.4, plasmiddb 0.2.2, staffdb 0.1.2, wormdb 0.8.5]

• MySQLi driver has been implemented.
• Scripts have been cleaned up. Modularity is improved and they are documented better.
• Log in session function was accidentally broken in the previous release. It has been fixed now.
• Minor enhancement in oligodb module.
• refdb module has been removed from this release as it needs much more work.
• Logfile functionality has been greatly improved. It will record major changes in the base package database table and module tables made by users.

January 3, 2019
[Core package 0.9.8, Module: wormdb 0.8.4, oligodb 0.2.3, refdb 0.2]

• Global messages have been updated.
• Minor changes in wormdb to handle an issue specific to the external hosting server that was preventing entry of new records.
• Fixed a bug in oligodb that was related to one specific option for the 'purpose' category of records.
• The module refdb has been updated. It is now possible to enter new records using DOI.

April 29, 2018
[Core package 0.9.7, Module: wormdb 0.8.3, staffdb 0.1.1, plasmiddb 0.2.1, refdb 0.1]

• Searches of module records no longer output errors if the module table is missing.
• This release includes a new module refdb that allows management of published articles and books. Users can create, view and delete records, write notes, and attach PDF documents.
• Fixed bugs in staffdb and plasmiddb related to editing and viewing records. Also, staff listing has been altered such that current members are shown first.
• Made few changes in the core package to secure variables

April 10, 2017
[Module: wormdb 0.8.2, oligo-0.2.2]

• Fixed two bugs related to record search output and modification in wormdb. There is a new option to rectify the box series of records that were previously entered incorrectly.
• Enabled searches of oligos in oligodb using sequence as input.

January 22, 2017
[Core package 0.9.6, Modules: wormdb 0.8.1]

• Setup script was modified to avoid banned users from being assigned as module curators.
• Fixed few bugs related to the maintenance of user accounts. Administrators cannot ban themselves!
• 'About' and 'Guide' page links have been modified.
• wormdb module now queries the custom species list created by the administrator and updates the database table accordingly.
• Entries placed in a wrong box series in wormdb module are now color coded for easy identification.

January 3, 2017
[Core package 0.9.5]

• Fixed a bug related to administrator toolkit 'user management' that was affecting user list and URL link.

February 2, 2016
[Core package 0.9.4]

• The 'About' and 'Guide' links of individual labdb accounts point to pages at labdb.net site.

January 28, 2016
[Core package 0.9.3]

• Backup of database tables is now possible. It no longer exits with an error. Two formats, SQL and CSV (comma separated), are provided. The output can also be downloaded. For security reasons the table containing registered user details is excluded from this operation and requires manual backup.

January 17-21, 2016
[Core package 0.9.2]

• The main landing page format has been updated.
• Logfile output table width can be adjusted by the user.
• Fixed few errors with scratchpad. It is now accessible to module curators and above.

April 23, 2015
[Core package 0.9.1]

• Minor update in the core package - added a log file to track user access.
• Fixed a bug related to secure access of log file.

April 21, 2015
[Core package 0.9, Modules: chemdb 0.2, oligodb 0.2.1, plasmiddb 0.2, staffdb 0.1, wormdb 0.8]

• Numerous enhancements have been made in the core package and modules. A new 'Guide' page describes software operation and access privileges. Admin options are integrated in the default index.php page.
• Setup script has many new features. It allows fine control of user access to modules. It integrates better with module-specific settings.
• The manager and administrator can lock the website temporarily if needed.
• A new ADMIN interface has been created. This allows backend access in the event of website lockdown.
• Database backup feature is greatly improved.
• Several new functions have been written to visualize database records.
• Notepad uses Javascript WYSIWYG Editor tinyMCE. It is visible to all registered users and can be modified by Admins, Managers, and module record Curators. The notepad contents are stored in a database table.
• Each module now includes a brief description of its features.
• wormdb module includes an expanded search feature for registered users.
• plasmiddb module has an option to save DNA sequences. The module accurately displays box and slot locations of records. It is now possible to add new storage boxes and assign tube locations.
• A new module staffdb has been created. It can be used to list laboratory personnels along with their contact and work info.

May 7, 2013
[Core package 0.8, Modules: wormdb 0.7.2]

• Fixed a bug in SETUP to show all users in the module section.
• Fixed the expanded search option link in wormdb module. It was broken.

December 6, 2012
[Module: chemdb 0.1.1]

• A minor enhancement in chemdb module to show MSDS links while browsing records.

December 2, 2012
[Module: oligodb 0.2, chemdb 0.1]

• oligodb shows improved display of search records.
• A new module chemdb (Chemical Inventory) has been included in this release.

April 4, 2012
[Module: wormdb 0.7.2]

• This is a bug fix release. It addresses two issues related to species category and species name in the wormdb module. The species category was unmodifiable whereas species name was being dropped while editing a record. Both issues are now resolved.

October 16, 2011
[Core package 0.8, Modules: wormdb 0.7.1, oligodb 0.1.2, plasmiddb 0.1.1]

• Administrator can take full backup of database records.
• Admin control panel includes a setup script to manage modules, database tables and other website features.
• Improved formatting of records in modules.
• Uploaded data files in plasmiddb module are automatically named after the construct name.

July 29, 2011
[Core package 0.7, Modules: wormdb 0.7, oligodb 0.1.1, plasmiddb 0.1]

• This release of labdb introduces major changes in the underlying structure. The software now consists of two components: core package (base) and modules. A module is an independent unit that can be added to the base to manage a unique resource.
• It is possible to create multiple managers, each responsible for curating one or more resource(s).
• A javascript calendar has been introduced in html forms to enable date selection.
• User management section in Admin control panel has been updated. Several bugs affecting navigation bar and user prefs have also been fixed.
• Management of individual modules can be restricted to specific managers/users.
• The use of lab resources can be restricted to only registered users (i.e., no guest access)
• Worm collection module straindb has been renamed as 'wormdb'. This will avoid confusion with other organism-related modules in the future.
• Plasmid/DNA Collection module plasmiddb is included in this release.

[Version 0.6.3, June 21, 2011]
• This release fixes a bug in straindb module that was causing "species name" to disappear when adding/editing records.
  

[Version 0.6.2, June 17, 2011]
• Another minor release to fix two issues in oligodb module.
  - Enable users to enter new records.
  - Only managers (and above) can delete existing records.

[Version 0.6.1, June 14, 2011]
• This minor release includes two enhancements in straindb module:
  - List category has been merged into Inventory category.
  - Records can be viewed in a storage box format and are hyperlinked to show details.

[Version 0.6, June 11, 2011]
• Oligo Collection module oligodb is included in this release.
• A scratch pad has been introduced to allow curators/managers to write small notes.
• List category in straindb module shows fewer records per page. It is faster, more efficient, and has better navigation options.
• Search feature works for all modules.
• Search output in straindb module is shown in a tabular format, instead of full details of each and every record.
• Many other enhancements throughout the system.

[Version 0.5.1, June 8, 2011]
• A bug fix to enable editing of straindb records.

[Version 0.5, May 1, 2011]
• 'straindb' module is now part of the 'labdb' package along with three other modules (plasmiddb for Plasmids, oligodb for Oligos, and chemdb for Chemicals) to be developed in the future.
• Search feature is limited to straindb records at present. In the future it will include records in other modules as well.
• Fixed the broken inventory link in straindb.
• A four-tier user access approach (admin, manager, general, guest) has been implemented.
• By default, guest access is enabled and can be used to search straindb records.
• Many other small changes and bug fixes.

[Version 0.4, April 27, 2011]
• Navigation is significantly enhanced. It uses a javascript dropdown menu.
• User interface (front page) has been completely redesigned.
• Search feature no longer requires secure HTTP connection and is freely accessible.
• Box locations in straindb module are autogenerated and checked to avoid accidental duplication. New slots are automatically assigned, but could be changed if desired.
• User access and management are fully integrated in straindb. This provides a consistent look and feel throughout.

[Version 0.3, April 2, 2011]
• 'straindb' package has been updated after a long gap. Most scripts have been modified.
• Scripts are modular and cleaner. The search functionality is greatly improved.
• Secure sign in access has been implemented to enable registered users (managers/curators) to make changes in records.
• System administrator can create new accounts and manage the entire system.
• Guest access is enabled by default and can be used freely to perform searches.
• Software requires a secure HTTP (HTTPS) connection to run. (this could be changed in the future)

[Version 0.2, June 12, 2003]

• A basic yet functional set of 'straindb' scripts is in place to manage and search strain records.
• It is possible to view the entire collection page-by-page in a printable format.
• Records of different species can be viewed separately.

[Version 0.1 (beta release), July 22, 2002]

• 'straindb' scripts have been updated and enhanced. It is possible to manage records almost completely via a web browser (front-end). In some cases MySQL command line is still required to edit/fix records in database table.

[Alpha release, July 5, 2000]

• A handful of PHP scripts (straindb) have been written to enable browsing of frozen worm (C. elegans) strains stored in a SQL (MySQL) database. At the moment records can be entered only via command line.