The EnzymeTracker is a web-based laboratory information management system for sample tracking.

In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from versioning or sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone as data do not undergo any validation process. The EnzymeTracker is a flexible and user-friendly alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples, from their basic functional annotations to their complete enzymatic activity. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management.

Overview of the features and the data flow in the EnzymeTracker

Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. It also features a number of tools to visualize and annotate experimental data, and export customizable reports.

Screenshots

Interface overview GUI customization Filters Filter types Report designer Clones Transformants Vectors Plate assays Liquid assays E-PAGE annotations Charts Login window Data history Connexion logs User management

Note: As part of confidentiality agreements with our collaborators, all IDs and sequences were scrambled on the screenshots.

Download

The EnzymeTracker is distributed under the GPL v3.

The EnzymeTracker may be downloaded by clicking on the red button below. The package contains the database schema and all the files necessary to run the EnzymeTracker. Installation instructions are detailed in the online documentation.

You may also download sample data. The sample data correspond to real data. However, for privacy reasons, all IDs, names and sequences were scrambled.

Licence and Legal Notice

The EnzymeTracker is developed, hosted, and maintained by the CSFG team at Concordia University, and as such it is offered to the scientific community under the usual terms and conditions stated by Concordia University.

The EnzymeTracker is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License version 3 as published by the Free Software Foundation. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

To facilitate evaluation by laboratories, we also configured a virtual machine image for VirtualBox that comes with everything that is needed to run the EnzymeTracker in a few clicks. See instructions below to run the image under VirtualBox.

Documentation

Data Entry

The spreadsheets are the primary means to enter data in the EnzymeTracker. All data entries are logged for future reference. On specific pages (in the screening section in particular), more advanced tools are provided to annotate E-PAGE gels or microplates.

Note: You must have the write permission to create/edit/delete data.

How to create an entry?

Simply click on the [ Add] button in the toolbar. A new blank entry will be inserted at the top of the spreadsheet.

How to create an entry?

To edit an entry, double-click on the corresponding row in the spreadsheet. You can press [Tab] or [Shift]+[Tab] to move to the next/previous column if your browser supports custom keyboard shortcuts. Each column is associated with an editor that depends on the data type of the column. References to data from another spreadsheet can usually be entered using a drop-down menu: an item from the list must be selected to enforce referential integrity. Editors may also be associated with a validator to ensure that data follows certain rules. In such a case, the entry must satisfy the rules to be validated and saved in the database. An error message explaining the expected format will otherwise be returned to the user. For example, pH entries are expected to be entered as numbers ranging from 0 to 14. Any other value will throw an error. Similarly, DNA sequences

Once the record is properly edited, press [Enter] to validate the last entry. Don't forget to click on the [ Save] button in the toolbar after you are done!

Note that automatically computed columns (e.g. sequence length, molecular weight...) are not editable.

How to delete an entry?

Click on the [ Remove] button in the toolbar. Note that when "deleted", the record is internally flagged as obsolete but is not actually deleted. If needed, sysadmins can therefore retrieve data inadvertently deleted.

Data-Mining

Each spreadsheet in the EnzymeTracker is fully searchable. Towards that end, each column is associated with a flexible filter that depends on the type of data the column represents. Five different kinds of filters are possible:

• Full-text
• Numerical
• Calendar
• Boolean
• Multi-selection

How to add a filter?

The screenshot below illustrates how to use filters (in red):

• Move the cursor over the column to filter
• Click on the down-arrow that appears
• Move the mouse over Search in the drop-down menu and click in the text field

You can define several filters at a time, which makes searching the EnzymeTracker very efficient.

How to delete a filter?

To remove one filter, simply deleted the content of the search box(-es) or tick Search (in the drop-down menu) off. To remove all the filters at once, click on the icon shown in blue in the above screenshot.

What is the scope of the queries?

The EnzymeTracker remotely searches the database. Hence, any query will return any entry in the complete table that matches the filters, regardless of the page of data currently loaded and displayed. Hence, a query is likely to return results that were not currently displayed.

To search for data on the current page only (local search), press [CTRL]+[F] on the keyboard.

Filter types

The EnzymeTracker features 5 types of filters, depending on the type of data in the column:

• Full-text: This is the default filter. It will retrieve records such that the filtered column contains the query string as substring.

• Numerical: This filter is used for numerical data. It is particularly useful one the enzyme characterization spreadsheets with columns like pH, temperature or activity. For instance, one can easily retrieve enzymes with a high activity when the pH is comprised between 4 and 6.

• Calendar: This filter is used when the data corresponds to dates. Using this filter, it is for example possible to retrieve samples that were sent between March, 1st 2010 and April, 15th very easily.

• Boolean: This filter is used with boolean data (true/false data). It is particularly useful for the screening pages as it makes easy to find plates where some activity has been detected (activity=true) for instance. It is also very useful to displayed only starred records.

• Multi-selection: This filter is most useful when the underlying data comes from a well-defined list of items. For examples, it is possible to filters only those liquid assays that were performed by one or more people.

Reports

The screenshot below illustrates the tool to design complex report in a few clicks. The panel on the right (B) lists all pieces of data that may be inserted in the configuration of a report (panel C) using drag-and-drops. The list can be filtered so that one can quickly search among the numerous fields. Corresponding SQL queries are automatically generated using a graph representation of the database. The resulting report is automatically displayed for preview (panel A) when configuration changes (can be disabled to avoid long refresh delays in case of complex queries).

In the configuration panel, it is possible to define filters on selected columns (e.g. cellulase here) as part of the template. After the report template is created, regular mining tools can be used to further query the database. The latest queries are not part of the template.

In addition, various functions can be applied to the columns, e.g. to get the length or the molecular weight of a sequence. Data can also be aggregated to generate some statistics.

Advanced users can use flags to refine the SQL query: left/inner joins, distinct values, all/active records.

Installation Procedure

Requirements

To install the EnzymeTracker, you need a server or a workstation running a web server that supports PHP and a MySQL database. Any server running a flavor of Linux, Apache, MySQL and PHP 5 should work fine.

The EnzymeTracker is an online tool, hence your computer must be connected to the Internet. It is compatible with Windows, MacOS X and Linux systems and may be accessed using any recent good web browsers, in particular:

• Mozilla Firefox v3.5+ (recommended)
• Google Chrome
• Apple Safari v4+

Note: Internet Explorer (all versions) is not supported at this time. There are also number of display issues when using Opera.

Procedure

The EnzymeTracker is implemented in PHP and requires very little configuration to run. It should be installed on a server running a web server (Apache for example) and a MySQL server. This documentation assumes that Apache and MySQL are up and running. For help with the installation and configuration of your server, please look at the abondant literature available on the web.

1. Download the full EnzymeTracker package

2. Extract and copy the content of the package in the Apache www folder

3. Create a new database enzymetracker

4. Import the database schema in that database:

   mysql -u username -p enzymetracker < enzymetracker.sql

   The above command also creates the EnzymeTracker administrator account.

5. The EnzymeTracker should be available at: http://your-domain/enzymetracker/index.html. You may login using the administrator account:

   User name: root
   Password: root

   Note: We recommend you change the administrator's password for security reasons.

Virtual Machine Configuration

To facilitate evaluation by laboratories, we also configured a virtual machine image for VirtualBox that comes with everything that is needed to run the EnzymeTracker in a few clicks.

Warning: Please note that virtual machines run slower than dedicated servers. A virtual machine setup should therefore not be used to evaluate performance or response time, but features only.

Requirements

To run the virtual image, you need first to download Oracle VirtualBox, which is available on all major operating systems (including Windows, MacOS and Linux).

Note: The virtual machine is configured to be allocated 1GB of memory. Please make sure you run the virtual machine on a computer with at least 2GB of RAM to ensure performance remains acceptable.

Procedure

1. Download the virtual machine image of the EnzymeTracker

2. Extract the content of the archive

3. Open the file EnzymeTrackerDemo.vbox. VirtualBox will open and automatically prepare the virtual machine so that it is ready to run.

4. Once imported, start the virtual machine by right clicking on its name in the main window of the VirtualBox interface. Then click on "start".

5. The virtual machine should automatically login the administrator account. If not, use the following login information:

   User name: enzymetracker
   Password: enzymetracker

6. You may now start the EnzymeTracker by clicking on its icon on the desktop. Username and password are the default one mentioned above, ie:

   User name: root
   Password: root