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FREQUENTLY ASKED QUESTIONS
(Please remember to visit our User Forum and subscribe to our mailing list for discussion and further advice)
Installation

How do I get started with OpenFreezer?

What is the username and password for my first login?

Can I install OpenFreezer on a Windows server?

General Layout

What is the general layout of OpenFreezer?

Users and Labs

Can multiple labs share OpenFreezer?

Reagent Tracking

What kind of reagents can I track in OpenFreezer?

How do I add a reagent to OpenFreezer?

How do I share my reagent information with other OpenFreezer users?

What if I want to track a property for my reagent that is not currently available in OpenFreezer?

How do I add new reagent types to OpenFreezer?

Can a reagent type be its own parent?

Why is the cDNA Insert shown separate from other vector information?

Is it possible to easily duplicate cell line information, for example when you create a new stable cell line from a parent cell line?

Location Tracking

How do I add a location for my reagent preps?

Is there a way to give read-only access to someone for reagent details but not the location of that reagent?

Is it possible to add triangular dimensions for liquid nitrogen stocks?

Additional Tools

What tools are available in OpenFreezer?



Q.  How do I get started with OpenFreezer?

A.  Please refer to the Download section of the website for instructions on how to download and install OpenFreezer. Technical Documentation is available for programmers in the Documentation section. A detailed User Guide is provided in the Documentation section. A database startup guide, called OpenFreezer Database Notes.pdf is included with the source code distribution. Please visit the User Forum for discussion and further advice.

Q.  Once OpenFreezer is installed, what is the username and password for my first login?

A.  Please refer to the OpenFreezer Database Notes.pdf document included with the source code distribution.

Q.  Can I install OpenFreezer on a Windows server?

A. OpenFreezer has been developed and tested on Linux. Since OpenFreezer is not a standalone desktop application but a composite client-server system, a Unix-like platform would be the preferable environment for operating it. Thus, the source code archive is not a Windows installable. Therefore, if you have a Unix server in your lab, we would encourage you to install OpenFreezer on it. However, you are most welcome to go ahead and set up OpenFreezer on your Windows server and share your experience with us. The installation procedure would be similar to Unix, with minor changes for Windows specifications.

Q.  What is the general layout of OpenFreezer?

A. OpenFreezer is divided into three modules. In the Reagent Tracker, all reagent types (i.e, Vector, Oligo) are defined, and details on individual reagents are stored. In the Location Tracker, the location and properties of physical preparations of these reagents are stored. In the Administrator module, users, laboratories, and projects are stored.

Q.  Can multiple labs share OpenFreezer?

A. Yes. In the administrator module, a user designated as an administrator can add multiple labs and multiple users per lab to OpenFreezer. All reagents in OpenFreezer are assigned to a Project, and the Project defines which users have read or write access to reagents.

Q.  What kind of reagents can I track in OpenFreezer?

A.  Four reagent types are pre-loaded into OpenFreezer - vector, insert, oligo and cell line. An administrator of OpenFreezer can add another reagent type through the Add Reagent Type function. Prior to adding the reagent type, you need to identify the properties that you wish to track for that reagent and their corresponding categories.

Q.  How do I add a reagent to OpenFreezer?

A.  On the sidebar menu, go to ‘Add Reagents’ under ‘Reagent Tracker’ and select the type of reagent you wish to add. Populate the form with your reagent properties to create the reagent. If you are making vectors or cell lines from pre-existing reagents, you will need to know the OpenFreezer IDs for those parent reagents. Batch upload of reagents is planned for a later release of OpenFreezer.


Q.  How do I share my reagent information with other OpenFreezer users?

A.  Before you enter reagent information, you will create a project for your reagents. You can add any OpenFreezer user to your project either as a reader (view only) or writer (view and modify). You may also make your project ‘public’ so all OpenFreezer users may view it.


Q.  What if I want to track a property for my reagent that is not currently available in OpenFreezer?

A.  Contact your local administrator. The properties that are tracked for a reagent type (Vector, Cell Line etc.) are modifiable through Reagent Type Detailed View and new properties can be added.


Q.  How do I add new reagent types to OpenFreezer?
A.  Contact your local administrator. Addition of new reagent types is described in detail in the User Manual.


Q.  Can a reagent type be its own parent?
A.  Yes. As an example, a Vector can easily be used to generate other vectors. To make a reagent type its own potential parent, at reagent type creation check the ‘Include reagent type in progress’ checkbox below the parents list.


Q.  Why is the cDNA Insert shown separate from other vector information?

A.  The cDNA Insert is defined as its own reagent type. It was set up this way so that the insert (the physical preparation created during the cloning process) could be stored as its own entity. In addition, we track a fair bit of information about the insert (i.e., external identifiers) so it made sense to give it its own page.


Q.  Is it possible to easily duplicate cell line information, for example when you create a new stable cell line from a parent cell line?

A.  You can create Stable Cell Lines using a parent Cell Line and Vector, in which case some of the properties of the original cell line (i.e, species, morphology) are duplicated.


Q.  How do I add a location for my reagent preps?

A.  Locations for physical preparations are tracked in the location tracker module. Select ‘Search Containers’ from the sidebar menu. Select the appropriate container type (ie Glycerol Stocks) and the actual container to which you want to add the prep. Select the specific well or slot from the container and fill in the relevant information. Links between the reagent detailed view and the preps of the reagent are automatically created.


Q.  Is there a way to give read-only access to someone for reagent details but not the location of that reagent?

A.  Not at the moment, as access to locations is restricted by project - i.e. if users can view a reagent, they can naturally view the location associated with it.


Q.  Is it possible to add triangular dimensions for liquid nitrogen stocks?

A.  No, OpenFreezer only supports storage of rectangular containers.


Q.  What tools are available in OpenFreezer?

A.  Tools are continually being added to OpenFreezer to assist with workflow centred on reagents. For instance, Primer Design allows a user to create inserts and accompanying PCR primers automatically starting with the protein translation of a cDNA as a template. As another example, during vector creation, the sequence of a child vector is automatically constituted from the parents and sequence features are remapped.


For any questions regarding the website or the software, please contact openfreezer.admin@lunenfeld.ca