Access Keys:
Skip to content (Access Key - 0)

Bar coding in a breeding program or laboratory

Shawn Yates, Agriculture and Agri-Food Canada (shawn.yates@agr.gc.ca)

With increasing amounts of information and data being generated in breeding programs, the need to implement tools and protocols to improve efficiency and quality controls has become vital.  One aspect of achieving this is through proper tracking of laboratory samples and field material.  Depending on the size and resources of each breeding program, bar coding may or may not be a feasible way to improve efficiency and quality controls.  The following highlights some of the considerations that need to be weighed by each breeding program looking to incorporate bar coding into their workflow, as it is not a "one-size fits all" approach.

Bar coding is essentially the practice of putting an optical, machine-readable symbol onto labels or envelopes which can be read by a piece of hardware, the Bar Code Reader, connected to a handheld device or computer.  These optical symbols contain information about the samples that can be translated by the software on the device connected to the bar code reader.  This information could be as simple as some sort of Germplasm ID (which links to accompanying information in a database), or the plot number in the field.  Each step in this process has a cost, whether it is due to equipment and materials or related labour costs, and needs to be evaluated by the individual breeding programs.

Potential Bar Coding Uses in Field Operations

One problem when taking phenotypic notes in the field is the potential for errors during the process.  While human error will always have to be taken into consideration when looking at collected data, breeders are always looking to develop methods and practices to improve the efficiency and accuracy of collecting data.  Bar coding field material could be one way of improving quality controls during plot rating and harvest tasks.

With field material, labels with bar codes on them are placed around a plant in each plot.  In a typical example, the person doing the rating would carry a bar code reader (corded or wireless) and/or a handheld device which would scan each label so the system would automatically find the correct plot, thus eliminating the problem of having a mix-up in the field and ratings being accidentally interchanged.  This approach could also save time, as the person rating does not have to double check their field maps if they lose their place in the field.  For more generic ratings, the person could carry a sheet of barcodes which represent each of the rating choices.  They would scan the plot and then scan the correct rating to help diminish typos.  There are some considerations to these examples, however.  First, the costs of weatherproof bar code labels are usually more expensive than normal labels.  Also, there is a labour component involved with the time it takes to put labels on every plot in the field, and the time it takes to develop protocols to insure that the labels are put on the plants in the correct order.  The breeder will need to determine whether these extra labour and material costs will result in improved efficiency over the cost of having plots in a sequential grid system, where the plot order is on the hand held device and the person taking the notes can keep moving without having to bend down and scan each label. The number of bar code readers and hand held devices required also make a huge impact on the cost as well.  Does each person need one, or can a few be shared among the group?  As mentioned in later sections, the weight and durability of the hardware is also a concern for the workers carrying the equipment to the field. 

                Another scenario where bar coding has prospective use is during the very busy harvest season.  By bar coding samples as they are harvested, an immediate inventory can be taken which may help tremendously during processing activities in the laboratory. Bar coding harvest bags is usually quick and easy, since labels are generally produced to put on the bags anyway and protocols are already in place to verify that labels are placed on the correct bag.  In most cases, basic bar code labels can be used since the harvest bags will not be exposed to the weather over extended periods.  While bar coding may help with keeping track of incoming harvest samples, it may not improve efficiency depending on the process that harvest samples go through.  For example, if culling is done post-harvest on specific plots and the samples are not in any order, it may still take excessive time to find those samples, regardless of being bar coded or not.  Whether or not this approach is more efficient will depend on the amount of samples being harvested and the type of processing that takes place.     

Potential Bar Coding Uses in the Laboratory

                A laboratory is another place where bar coding may help to increase quality controls and efficiency.  Labs are generally quite structured and have routines to help ensure high quality through-put of data, but when lab technicians are dealing with a vast amount of samples in a short period of time, errors can occur.  In many cases, labs will work with a large number of accession lines and the tracking of these accessions could be handled quite easily with a bar code system.  By simply scanning the label on the sample, not only can the technician be assured that they have the correct material but save time by skipping the step of manually inputting it into a computer (assuming the samples are not already in the same order as listed in the spreadsheet).  Also, in laboratory analysis where generic results are expected, technicians could use bar codes to enter these results into the databases. For example, if a seed colour test is being conducted, the technician could simply scan bar codes that give the resulting color instead of manually entering them.  This could create a level of standardization that could help for sharing of analysis across labs.  Bar coding could also help laboratories in tracking their inventory of chemicals. When some volume is taken from the container, the technician could scan the barcode and enter how much they are taking and the system could generate a message when it is time to re-order.  Bar coding would also be useful when running experiments in the lab, where large numbers of samples are being observed (i.e. sprouting tests in Petri dishes done over a period of time with many intervals) and the samples are in random order.  Instead of always having to place the samples in order or having to manually find the sample in the spreadsheet, the investigator simply scans the bar code and enters the observation.

A major factor to consider about the implementation a bar code system in a laboratory is whether the number of samples or inventory going through the lab is high enough to warrant such a system? Can the software be connected to the tools and databases of the Integrated Breeding Platform?  Also, it is important to think about how much disruption implementation and training may cause initially, and whether it will create any downtime for the lab.

Bar Coding Uses in a Genebank

                In many ways, bar coding practices in a genebank seems to make perfect sense.  There may be large numbers of accession samples coming in an out of the genebank on any given day, and to manually enter all these transactions can be a very time consuming practice, when a label could just be scanned instead.  As always, the cost of starting up a bar code system is a concern, especially if there is downtime while the system is being set up.  However, inventory tracking and control represents the main usage of bar coding systems throughout the world, so many existing software systems could be immediately adopted to keep track of sample inventory.  The main consideration in this case would be how to modify these existing systems to connect to the Integrated Breeding Platform.  Some providers may be able to help create links between their software and existing databases.

Bar Coding Systems

Essentially, all that is needed to set up a bar code system is a label printer, some software to create barcodes, a bar code reader, and either a computer or handheld device to run the software.  However, each breeding program will have specific uses and needs for bar coding which may influence the type of hardware purchased.

   Bar Code Printers

Most bar codes in field operations would typically only need to store a few items of information so a 1-dimensional bar code would suffice.  However, labs and genebanks may want to look at the more complex 2-dimensional bar codes, which may require more expensive printers to ensure first-scan readability, but can store up to 1800 characters of text in a single code.  Genebanks, for example, could store passport information within a single barcode.  In order to print these barcodes to a label, the type of printer to purchase is dependent on the environment in which these labels will be used and the quality desired. If barcodes are only going to be used inside a laboratory, a Direct Thermal Printer could be used.  These printers generally use less expensive labels and do not require any extra ribbons or toners.  The downside of the Direct Thermal labels is that they cannot withstand heat, direct sunlight, chemical vapours or moisture.  If the end use is for field material or higher quality labels, then it would be best to use a Thermal Transfer Printer which carries a much higher cost for the labels and ribbons needed.  Both of these printers may come with or without printing software already included, which also affects the cost.   For very basic needs, a dot-matrix printer could even be used, but it is important to recognize that low end printers, while keeping the cost of implementation down, may print low quality bar codes which affect the ability of the bar code reader to scan the label in one read.  Poor bar code readings may result in the user having to manually stop and enter the information into the computer, wasting time.   Laboratories and Genebanks would typically look for a wide-carriage printer, as they have the ability to print multiple bar code types on a single line and can allow to customization of the labels.  Narrow carriage printers would be the best choice for creating simple labels, such as plot labels.

Bar Code Readers

Within a breeding program, a bar code reader is typically a scanner that has to be moved over the bar code on the label to read it. There are many different types of bar code readers but the most common are wands or light pens and can range from less than a hundred dollars for lower-end, 1-dimensional readers to a few thousand dollars for 2-dimensional readers.  Light pens are relatively inexpensive compared to other readers, and can come as either contact or non-contact styles.  They also require very little, if any, special programming to scan the bar codes.  Scanners, which are several times more expensive, have the added advantage of needing no direct contact with the bar codes and being able to scan from some distance away, which means the user does not have to always align the bar code a certain way to read it.  Scanners also work well on uneven surfaces, such as full harvest bags. Some points to consider when purchasing bar code readers for field operations could be the weight of the readers and how durable are they.  Obviously, bar code readers that will be used in the field will be under much harsher conditions than readers used in a laboratory.  For laboratories and genebanks, the question may be about which type of reader is most efficient for their needs.  Many of these answers can be found by reading reviews about the various makes and models on manufacturer's websites.

Computers and Hand Held Devices

Finally, there is the consideration of the device that will run the software for the bar code reader and collect the data.  In a laboratory or genebank setting, a desktop computer or laptop would generally be used to collect data, so it would make sense for the bar code reader and software to run on it as well.  However, in the field it is generally more efficient to carry a battery-powered handheld device to attach the reader to.  This discussion will not cover laptops or desktop computers, as they are generally in use already; they only need the software installed.    

Handheld devices are becoming more powerful and compact all the time.  Some carry versions of spreadsheet packages which are already in use for collecting field data.  The introduction of bar coding allows the user to combine quality control with the electronic raw data files.  The same approach should be taken when looking for a handheld device as is taken when looking for a computer; there should be enough RAM and computing power to run the software in an efficient manner and enough storage to hold all the files until it is docked and uploaded to the workstation computer.  They should also have enough battery capacity to go a whole day in the field or lab without having to be recharged.  There are some considerations to think of when purchasing them.  For example, does the device have an imbedded keyboard or external keyboard? Touch-screen keyboards are not always useful when taking notes in the field and can lead to mistakes. How does the bar code reader connect to the device?  Some devices may have input jacks that corded bar code readers can connect to, but others might use wireless connections such as Bluetooth. How heavy and durable is the handheld device?  Users will not want to carry a heavy handheld device and bar code reader through the field while taking notes and these devices will more than likely be exposed to sunlight, heat and moisture in the field.  Also, the display on the device has to be large enough and be clearly seen in direct sunlight.  Many of the color screens on handheld devices have very vivid displays indoors but are completely useless in the bright sun.  Reading the reviews on manufacturer's websites can give good clues to the model and make of a sufficient handheld device to purchase.

Commercial Bar Coding Packages

One of the challenges of implementing bar codes into a breeding program is finding system that contains the hardware and software that can run efficiently, be intuitive to cut down on training costs and sources of errors, and also connect to existing databases.  Currently, there are many different options for users who wish to purchase a commercial system that comes with the hardware and software ready to go. Companies, such as Aurora (http://www.aurorabarcode.com/), Code Soft (http://www.code-soft.com/), Dynamic Bar Code Systems (http://www.dynamicbarcode.com/) or ABS A1 Barcode Systems (http://www.a1barcodesystems.com/)  offer complete bar coding  systems, but the focus of many of these systems are mainly geared towards inventory activities, and may not work well with breeding program requirements.  Many of these companies can offer their clients some degree of customization to the software to meet their needs, for a fee.  An advantage to purchasing a commercial bar code system is the elimination of deciding what type of hardware and software to buy; a consultant generally will outfit their client with appropriate equipment based on their requirements.  Maintenance and software updates may be easier to assimilate through a company, rather than by manually searching out the latest updates to your hardware drivers and software.  Some basic level of training and support is often provided with these packages as well. The downside of these systems is that they may cost several thousands of dollars to implement and still not meet all the requirements needed by a breeding program.  There may also be a cost associated with continued support of the system, and it may be hard to use new hardware devices that are not company-compliant. Other labour costs will still be involved due to the continuing need of staff to develop and follow quality-control practices when printing and distributing labels to the samples.  When purchasing a commercial system, it is important to not only relay the current requirements, but also the future goals to ensure that the system will handle expansion and changes in the future

Radio Frequency Identification (RFID)

An alternate approach to bar coding the use of Radio Frequency Identification, a system that uses microchips instead of printed labels and the readers use radio waves to access the information.  This method of tracking allows the user to detect samples from further distances and without having to have a direct sight line of the chip.  This system may be useful in genebank inventories, where information from the RFID tag could be accessed without having to manually locate the package. 

                There are three types of RFID tags; an active tag which requires a battery and sends signals to a receiver, and a passive tag which does not require a battery and is accessed with an external transmitter, and finally, a battery-assisted passive tag, which stay dormant until accessed by a transmitter and then sends signals to a receiver (this chip gives the best first-read capabilities

                Advantages to using RFID tags over bar codes include being able to detect multiple samples at once, instead of having to manually scan each one.  In a harvest situation, all the harvest bags could be accounted for immediately, without having to spend hours scanning each one.  Individual samples could be found easily in a room full of samples by the RFID tag. Bar coding is also a read-only technology, so if information needs to be updated or edited, a new bar code label has to be printed and attached to the sample.  With RFID tags, the information could be updated automatically, without having to physically handle the samples.  In situations where a genebank may wish to track shipped samples en route to their destination, RFID tags could be used to report where in the journey the samples are, and when they arrive at their destination.  RFID tags could even store information about the amount of seed left or how long the seed has been stored – information that could be vital to a breeding program when planning crosses.

                As with all technologies, however, there are some disadvantages to using RFID.  The RFID tags are much more expensive than bar code labels.  The exact cost depends on the purpose; passive tags that only need to be read from a few meters away are much cheaper than active or battery-assisted passive tags, which have longer range and more hardware included. Battery-aided chips may have to be replaced over time as the batteries wear out. Another factor in the cost of RFID tags is whether the user needs read-only, or the pricier read-write tags.   The RFID tags may also have durability problems in long term cold storage or weather exposure.  RFID readers are also much more expensive compared to bar code readers, running into the thousands of dollars for one reader. 

                While RFID offers flexibility and time efficiencies, the price of setting up such a system may be a major deterrent for most breeding programs, laboratories and genebanks.  However, the cost of this technology has decreased rapidly over the years and may one day be a feasible and affordable option to explore.

Training, Support and Maintenance

                As with any type of technology, there is always going to be a financial and labour cost to using the system.  As stated earlier, a commercial system may include some of the training, support and maintenance required, but in most cases this will be minimal at best. Within the work group, there will be time needed to learn the system, someone will be required to train new employees which takes away from their current tasks, and time will have to be accounted for to maintain the equipment whether it is simply cleaning the scanners periodically or installing updates to the software.  Staff  will also have to be continually cognisant of quality controls to secure the integrity of the information on the labels and their distribution onto the samples or plots. This can be classified as on-going costs and should not be overlooked. Generally, the more advanced system that is implemented, the larger these costs can be.   


References

Kasten, Bernard. "Barcoding: The Ideal System". Barcoding: The Ideal System. http://www.eiminc.com/articlemed.htm.  October 19, 2009.

Bonsor, Kevin, Keener, Candace. "How RFID Works". HowStuffWorks. +http://electronics.howstuffworks.com/gadgets/high-tech-gadgets/rfid.htm.+  October 19, 2009.

ZIH Corporation (2008).  Protecting Patient Safety with Laboratory Bar Code Labeling.

"Going electronic with 2D barcodes". eHealth Insider.  http://www.e-health-insider.com/Features/item.cfm?docId=137.  October 20, 2009.

Swedberg, Claire.  "PittsburghHospital Pilots Hybrid System".  RFID Journalhttp://www.rfidjournal.com/article/articleview/1863/1/1/.  October 21, 2009.

Adaptavist Theme Builder (3.3.3-conf210) Powered by Atlassian Confluence 2.10.3, the Enterprise Wiki.
Free theme builder license