Phytotracker, an information management system for easy recording and tracking of plants, seeds and plasmids
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A large number of different plant lines are produced and maintained in a typical plant research laboratory, both as seed stocks and in active growth. These collections need careful and consistent management to track and maintain them properly, and this is a particularly pressing issue in laboratories undertaking research involving genetic manipulation due to regulatory requirements. Researchers and PIs need to access these data and collections, and therefore an easy-to-use plant-oriented laboratory information management system that implements, maintains and displays the information in a simple and visual format would be of great help in both the daily work in the lab and in ensuring regulatory compliance.
Here, we introduce ‘Phytotracker’, a laboratory management system designed specifically to organise and track plasmids, seeds and growing plants that can be used in mixed platform environments. Phytotracker is designed with simplicity of user operation and ease of installation and management as the major factor, whilst providing tracking tools that cover the full range of activities in molecular genetics labs. It utilises the cross-platform Filemaker relational database, which allows it to be run as a stand-alone or as a server-based networked solution available across all workstations in a lab that can be internet accessible if desired. It can also be readily modified or customised further. Phytotracker provides cataloguing and search functions for plasmids, seed batches, seed stocks and plants growing in pots or trays, and allows tracking of each plant from seed sowing, through harvest to the new seed batch and can print appropriate labels at each stage. The system enters seed information as it is transferred from the previous harvest data, and allows both selfing and hybridization (crossing) to be defined and tracked. Transgenic lines can be linked to their plasmid DNA source. This ease of use and flexibility helps users to reduce their time needed to organise their plants, seeds and plasmids and to maintain laboratory continuity involving multiple workers.
We have developed and used Phytotracker for over five years and have found it has been an intuitive, powerful and flexible research tool in organising our plasmid, seed and plant collections requiring minimal maintenance and training for users. It has been developed in an Arabidopsis molecular genetics environment, but can be readily adapted for almost any plant laboratory research.
KeywordsDatabase Plant LIMS Software
Growing plants in a laboratory environment creates several logistical and administrative challenges. A system is needed to record and track the various plants and seed stocks from different researchers over time. Seeds can be stored for extended periods and laboratories will accumulate a large number of seed stocks which require careful and consistent documentation. Furthermore, national regulations require research groups to maintain records of genetically modified seeds and plants.
Laboratory Information Management Systems (LIMS) are designed to support a modern laboratory and often include a range of integrated features. Some of these have been specifically aimed to store information about plasmids, microarrays, and even plants[2, 3, 4, 5]. Furthermore we found LIMS which focus on plant breeding and field trials[6, 7] and we know that some labs work with systems that are not publicly available. The previously reported solution PlantDB offers a broadly similar solution, but being built in Microsoft Access, it is not cross-platform, less readily adaptable, and differs somewhat in the workflow conception. It also lacks the ability to link to details of plasmids encoding transforming DNA. Therefore, after evaluation of the existing options available to us, we could not find a simple, inexpensive yet adaptable system that can organise and track the operations involved in growing plants in a research facility. The system described here called ‘Phytotracker’ is designed to be easy to use and can be readily implemented in any laboratory without specialist computer knowledge. Phytotracker has been designed specifically for the end user and has been refined using regular feedback over a five-year period in a modern plant research laboratory.
The Phytotracker package has been developed in the commercially available database client FileMaker Pro. SQL-type web-based and free database systems such as MySQL were considered but FileMaker Pro was chosen because for the non-expert it is easier and faster to build a relatively small system in FileMaker Pro than in SQL-based systems. As a commercial package, Filemaker Pro is continually updated and supported and has extensive documentation (http://www.filemaker.com). Although there are costs associated with FileMaker Pro, discounts normally apply to academic users, and we felt it allows for an intuitive and flexible interface that is highly scalable as systems grow and easily modified by non-experts. FileMaker Pro can be installed on both PC and Mac computers or on a server and works well in a mixed PC/Mac environment, and offers modification of fields and other features together with inherent FileMaker features such as report generation and searching. To facilitate simple labelling of seed bags and plants, cost effective DYMO label printers were used, but the label layout can be adapted for any printer. Phytotracker consists of 5 related tables containing the information of plants, trays, seeds, seed stocks and plasmids. Further technical details about the tables can be found in additional file1.
Phytotracker, like any FileMaker database can be run on a server, shared or run as a stand-alone application. In our group we are running Phytotracker on a FileMaker Server, which allows the system to be available throughout the local network for any computer with FileMaker Pro installed. We have chosen the networked solution because researchers can access Phytotracker from their desks, and having dedicated computers with label printers in the growth rooms and potting area greatly facilitates harvesting and sowing plants, as labels can be printed on site.
Results and discussion
In principle, information can be entered in any table, however initial input into the database is usually via the Seeds table. When seeds are sown and the information is entered into the Seeds table, content is passed on to the Plants table which contains details of all plants that are currently growing or were grown in the past. Each plant record in this table has a unique ID number and refers to an individual plant in the growth room or glasshouse. When seeds are harvested from these plants, Phytotracker automatically generates a new unique seed record passing on the information from the parent plant and indicates the plant as harvested and removed from the growth facility. In this way, users can backtrack their plant lines and keep track of their plants growing at the moment. The Trays table can be simply seen as a collection of plants that are grown together, usually physically grouped in a pot(s) or a multi-compartment tray. This makes it simpler and quicker to enter and track information about similar plants grown at the same time, and is flexible in the number of plants in a “tray”, which can be set to 1 or any other value.
Seeds and Seed Stock tables
The Seeds table contains information about batches of seeds stored. Phytotracker allocates a unique number to each seed batch that is used throughout the system to identify plants originating from this seed batch. When seeds are harvested from a plant that is already in the system, information about the parent plant such as its name and ID number is stored in the seed record. A special type of seed record is a cross between two different parents, and in this case the information of both parents are stored. The ‘show ancestors’ button in the Seeds table will perform a search to find all the (female) antecedents of the seed record being browsed. This makes it easier to track the origin of a seed batch. If a seed batch is particularly useful for the lab, the user can copy the information into the Seed Stock table. This table is a valuable tool, representing that subgroup of seed lines of particular importance in a research group, for example, it can contain homozygous mutant combinations and transformants that are used by multiple researchers. The advantage is that the Seed Stock table can be browsed and searched more easily than the Seeds table, which, since it contains all seed batches ever harvested, makes it somewhat unwieldy for finding frequently used stocks. An additional advantage in having a Seed Stock is the ability to have a selection of curated seed batches. The Seed Stock table can contain more detailed information about the seed batches such as reference to journals, images and a field to record to which other research groups the seeds have been sent. It is important to note that a record in the Seed Stock is directly linked to the seed record such that the seeds will always keep their unique seed ID from the seed table in addition to the Seed Stock. This is necessary to keep track of the lineage of parent plants and their offspring.
Pots and trays table
Filemaker has a built-in user and password management system which allows to assign specific privileges to users, for example whether they are permitted to delete or modify records. In our research group, only the system administrator is allowed to delete records, but users are allowed to modify. Every change in a record is logged and can be accessed in the ‘Change log’ layout in each table.
Our aim is to provide a helpful tool to the plant community, which can be adapted to the specific needs of plant laboratories. Phytotracker is available through sourceforge.net, which is the leading open source software repository. On the dedicated project page, users have various options including a discussion forum and a possibility to upload their own version of Phytotracker.
As any live software product, Phytotracker will be subject to ongoing improvement. We plan to add more features such as a sample database linked to the plant and seed database, a better way to explore the progeny and parental lines from a particular plant or seed batch, barcode labelling, and a version of Phytotracker for mobile devices. The online forum will be helpful to interact with users and discuss further developments.
Phytotracker was designed for facilitating the task of keeping record of growing plants, seed stocks and plasmids in molecular genetics labs. Ease of use and minimal user input were primary considerations during the design of the system. It is known that users should be involved in the development of a software product and indeed our group has used and refined the system for over five years and it has helped us to manage thousands plants and seeds generated by many different users. The empty database can be downloaded from the link provided, along with a populated example. This site also provides a forum for user comments or improvements.
Availability and requirements
Project name: Phytotracker
Project home page:http://sourceforge.net/projects/Phytotracker
Operating system(s): Windows XP or higher, Mac OSX 10.5 or higher
Other requirements: Filemaker Pro 8 or higher for standalone computer or for networked systems FileMaker Pro Advanced 8 or higher or FileMaker Server 8 or higher. FileMaker Pro 12 requires OSX 10.6. Dymo Labelwriter 450 or 450 Twin Turbo printers were used with Dymo 99017 for plant or seed labels and Dymo 11352 for tray labels.
License: GNU GPL
Any restrictions to use by non-academics: none
We thank members of Jim Murray’s lab for useful suggestions and testing the database.
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