Learn about OpenFreezer : Events : G-SIN

Date: Thursday, October 06, 2011

Venue: Webinar

The Ontario Genomics Institute (OGI) hosted a 1 hour web conference/webinar about OpenFreezer - a free, open-source, web-based software application that maintains detailed and standardized documentation on common laboratory reagents and provides useful tools for their manipulation.

The software was recently featured in Nature Methods (http://www.nature.com/nmeth/journal/v8/n8/full/nmeth.1658.html) and is accessible at http://openfreezer.org. Open Freezer can be useful to researchers in all sizes and types of labs and the webinar will be appropriate for all levels from graduate student to principal investigator.

The webinar covered how to use OpenFreezer, including:

Defining reagent types (e.g., vectors, antibodies)
Entering and modifying individual reagents including using workflow support tools such as automated plasmid sequence construction and primer design
Entering and modifying locations for reagents
Software architecture overview and installation requirements

The presentation was given by Marina Olhovksy, Software Engineer, Mount Sinai Hospital, Toronto.

Click here for the slide presentation.

Click here to access a recording of the webinar.

Q&A

Is there any standard workflow for cloning non-coding inserts, such as promoters, spacers, IRES etc., or combining multiple inserts, e.g. gateway recombination?
Currently, Primer Design only works with inserts that have a translated sequence. However, non-coding inserts such as promoters can be cloned using OpenFreezer. Add the sequence to OpenFreezer as an Insert with intact restriction enzymes and then add the resulting insert to a parent vector using the 'non-recombination vector' subtype option. For gateway recombination, select the applicable Gateway vector subtypes (entry, expression) during 'Add Reagent'. There is no standard workflow for multiple inserts (including Gateway). One workaround would be to create one insert that combines multiple inserts into one sequence (if possible) before adding it to a parent vector. Alternately, you could create an intermediate vector that has the first insert and then add the second insert to this intermediate.
Is there a barcode scanner input option?
There is no barcode scanner input option at the moment. Users should contact us if they are interested in contributing this feature to OpenFreezer.
Is it possible to import reagents into the database from Excel?
An ability to upload reagents in batch is our most frequent request. Currently, there is no user interface that will import reagents directly from Excel sheets but we are planning to implement a batch upload feature in our next release of OpenFreezer. In the meantime, reagents can be parsed directly into the database from excel sheets by a programmer familiar with the MySQL database structure.
Can we access OpenFreezer remotely?
OpenFreezer is a web-based application, so it is accessible through a web browser. Depending on the network security setup at your institute, you may or may not require a Virtual Private Network (VPN) connection to access an installation of OpenFreezer behind a firewall at your institute.
Primer design: 1. Does Melting Temperature (Tm) calculation account for primer and Mg concentration? 2. Does it check for the false priming, dimers, and hairpins?
The Primer Design assumes standard conditions of 50 nM primer, 50 mM Na+, and pH 7.00. It does not check for false priming, dimers or hairpins. We have used Primer Design extensively at the Samuel Lunenfeld Research Institute (SLRI) and for the vast majority of templates, the primer design in OpenFreezer is sufficient. If more analysis of your primers is needed, then you can use an alternate primer design program to create your Oligos and add your Insert to OpenFreezer through the standard 'Add Reagent' option rather than through Primer Design.
Can we populate a 96-well plate using a spreadsheet?
In our next version of OpenFreezer, we will provide a user interface to batch upload location information into OpenFreezer. In our current version, a user can highlight the entire plate and then select 'Create New Wells'. Attributes (if the same) can be added quickly by selecting a column heading and auto-populating the entire column with one entry. Alternately, the location of reagents can be parsed directly into the database from excel sheets by a programmer familiar with the MySQL database structure.
Although it was designed/tested on Unix/Linux, are there any plans on providing installation instructions for Windows-based platforms?
We have established a user forum on SourceForge (http://sourceforge.net/p/openfreezer/discussion/openfreezer/) for users to share their experience with installing OpenFreezer on either Windows-based or Mac-Based platforms. We encourage any user who has successfully installed OpenFreezer on one of these platforms to share their knowledge so that other users may benefit. We also encourage any user who has had issues with installation on these platforms to post their concerns so that other users may assist them.
We have a lot of existing reagents. Let's say I have created a new reagent that fits our needs and then I want to feed in hundreds of entries. Will there be a possibility for batch import let's say from an excel sheet that contains the fields...
Batch uploads is our most frequent request (see answers above to questions 3 and 6).
Would there be a way to write the data into the SQL database over phpMyAdmin which supports excel import or are there too many things to watch out for...
The OpenFreezer database is highly normalized (3NF). To properly record information on one reagent, including general properties, sequence and features, location and parent-child associations, several tables need to be populated. For this reason, we have not relied on phpMyAdmin at SLRI to populate the database. Python scripts have been used to read data in .tsv or .csv format (generated from Excel) and insert the information into the appropriate tables.