The Lab Manager INFORMATICS RESOURCE GUIDE

Things to Think About Before Buying a Lab Informatics System BY RYAN ACKERMAN

Considering the Cloud BY JOHN JOYCE, PhD

LIMS: Flexible Data Management BY MIKE MAY, PhD 20 To LIMS or Not to LIMS? 17 BY ANGELO DEPALMA, PhD

Product Focus: Electronic Laboratory Notebooks BY ANGELO DEPALMA, PhD Informatics Resource Guide 2017

Things to Think About Before Buying a Lab Informatics System Modern informatics systems come in a variety of different types and configurations to suit any researcher’s needs

By Ryan Ackerman

A LABORATORY INFORMATICS INTEGRATION TIP When integrating a new informatics solution into your lab, one thing you’ll want to make sure of is that the variety of instruments in your lab will be compatible with the new software. Make a list of your lab’s equipment and do your research to make sure it will work with the new informatics platform before you start.

How does the scale (size, people, and processes) How will increases in scope or scale determine affect the ideal informatics set-up? which informatics system should be used?

Modern informatics systems come in a variety of different types and Increases in scope or scale can bring up many fears for most configurations to suit any researcher’s needs. If you are part of a small laboratories. Failing to meet compliance, having a system which is research lab that works out of a single location with only a few tests, no longer fit for the purpose, or having an informatics system which using a hardware-based solution may be best. This allows you to more can no longer handle the amount of data are a few. Researching to easily troubleshoot the hardware and keep the data safe on-site. For see if the system is capable of being customized or upgraded to much larger laboratories which incorporate more processes, business accommodate these changes is important. lines, and employees in a global setting, there are a variety of options available, including software-based platforms. Many vendors can offer customizable solutions for a laboratory’s needs, such as the ability to translate between languages.

How will the need for significant travel or accessibility influence which informatics system is best?

As the needs for laboratories to connect with each other across great distances increases, many researchers are finding that the need to travel has also grown. As a result, having 24/7 access to your informatics systems has become crucial. With the advent of cloud- based data storage, this has become easier than ever. Many informatics systems offer such storage options, even allowing the informatics system to be completely web-based. With this option, you can access all of your research data anywhere an Internet connection is available.

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Considering the Cloud Despite all the hype being tossed around, the cloud is a logical evolution of previous systems.

By John Joyce, PhD

When considering the cloud to host the data system for either a clinical or a chemical laboratory, there are additional factors that you must consider:

• First, and perhaps most important, is the laboratory you are attempting to automate one that is required to conform to GXP regulations? If so, you must consider how these regulations affect your ability to take advantage of the cloud. Exactly which regulations are relevant depends on your type of laboratory, the objective of the laboratory, where it is, and where it ships products. Additionally, this evaluation must be done before signing a contract and implementing a system, or you are just begging for an inspector to start issuing citations.

Data Protection, System Maintenance, and GXP • How is your data acquired? Do you anticipate controlling Compliance Are Just the Beginning instruments through this cloud system? Is this control time- sensitive? The term “cloud computing” reputedly came from the common use on flowcharts of a cloudlike symbol to represent the Internet. • How is validation of your system maintained? This issue is In common usage, “the cloud” is a very loosely defined term. The tightly coupled with the issue of how change control is handled cloud can be used to store data, as a backup medium, as a processing and who handles it. platform, and in any number of other ways. The National Institute of Standards and Technology has a much more specific definition • How do you go about auditing this cloud data system? Can you of what cloud computing is, but many people use the term much gain access to the data center to perform the audit— or even more broadly—and actually, a significant portion of people do not determine where the data is actually stored?1 understand it at all. One of the cloud’s main features is its elasticity. This simply means that as your memory or processing needs change, A very good introduction to these issues, particularly regarding the system can automatically adjust its resources to your requirements. the regulatory impact, can be found in the writings of Dr. R. D. McDowall,2 a highly respected expert in the field of automated Despite all the hype being tossed around, the cloud is simply a logical laboratory system validation. In his evaluation, McDowell eliminates a evolution of previous systems. Because of its elasticity, it is frequently variety of unsuitable cloud configurations, but concludes that a SaaS preferred for processes during which the computing or storage system—where each customer is running its own instance of the demands can change significantly and suddenly. With the cloud, application with its own database, in its own virtual machine—does you have to pay for only the resources that you actually use. You do have advantages for the customer. Cloud latency can be addressed not have to purchase hardware capable of handling your maximum using a local interface box to actually collect data and control processing or memory load. This frequently allows you to launch instruments. prototype projects for evaluation that you would never get approved if you had to purchase all of the equipment. You will frequently find One of the major factors you have to accept when using the cloud, the cloud used with so-called big data projects, but other applications no matter your purpose, is that your data is passing outside of your using the cloud include Gmail and similar services. control and you must trust your cloud provider to protect it. For some

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users this is untenable; others find ways to live with it. This is one of mundane things such as who is responsible for backing up the system, the reasons you want to vet your cloud supplier very carefully and to how the system is backed up, and how the company confirms that validate its procedures as much as possible. Two critical procedures to this backup has been done and is functional. Note that while some start with are the way data is transferred and the way the application existing SLAs might cover availability to the application on the virtual program interface (API) works, as this is your portal into the cloud. If machine, they don’t necessarily guarantee access to the data or accept your data is not encrypted while being transferred, it’s time to look for liability for any data lost.1 another vendor immediately. The API should also be secure, requiring identity verification before executing any process. When the data is There is one additional issue you should be aware of when making not actually being used, the best practice is to keep it encrypted. the decision as to which type of cloud to use, if any. This issue doesn’t actually address whether your data has been exposed or not—just When considering, implementing, or using a cloudbased data system, whether you are aware of it. While your cloud provider might encrypt it is expedient to be on good terms with your organization’s IT group, all of your data and pledge not to release the encryption keys, thanks as they can supply vital input into items to consider when generating to the Patriot Act (with the obvious inference that anybody who a service level agreement (SLA) and contract for the system. To be objects to it is unpatriotic) and associated laws, the federal government blunt, this can sometimes be a ticklish interaction that may put your needs only to send your provider a national security letter (NSL)3 management and negotiating skills to the test. The important thing is demanding whatever they want, even if it is your entire database: that the intent of both sides is to successfully implement the project, “They do not require prior approval from a judge, only the assertion not to make it something that they can leverage others with. that the information demanded is relevant to a national-security investigation.” 4 Even better, this letter usually includes a gag order For IT to be willing to trust that everyone involved knows what that makes it a crime for the cloud provider even to admit that it has they are talking about, it helps if you have personnel with sufficient received an NSL, let alone to notify the affected customer. This makes computer expertise and, ideally, experience working with the IT it possible to siphon off your data without your even being aware of staff. It is also important to get the IT team involved early in the it. Admittedly, the government could send the letter to you directly, process, as they generally control the network infrastructure and the but then you would know what they were doing. Even the Justice organization’s interface with the Internet. This interaction is important Department’s Inspector General has found serious FBI abuses of the for several reasons. As some types of instruments generate GB-size NSL power. A similar scenario based on older laws5 is currently being files, the IT staff must ensure that its infrastructure is capable of used by the U.S. government in trying to acquire data from Microsoft handling such a load. This might require them to upgrade network that is stored in Ireland. If you don’t like this approach, a good place to switches and cabling or to contract for a higher data rate connection start is to write your congressman. to the Internet so that your operation doesn’t effectively lock up the entire organization’s network. It is for this reason—so that cloud providers couldn’t release your information even if they wanted to—that developers are working on In addition to the IT group, it is prudent to have someone from your a scheme that would allow the customer to hold all of the encryption legal department on the team drafting the SLA and the contract. keys. Do keep this in mind when deciding where to store your data. While many cloud providers go out of their way to maximize the uptime of your operation, some are not quite as straightforward. These are not all of the things to consider when deciding whether You need the legal team to ensure that all of your requirements to use a cloud service, but hopefully this article has highlighted some are explicitly covered in either the SLA or the contract, including concerns for you to start thinking about. when the SLA kicks in and what the vendor will do in the event of a system failure. This should include not only how the system will be configured, but details of how change control is handled. For References 1. McKendrick, J. 9 Questions to Ask Before Signing a Cloud Computing Contract. Forbes. 2013; systems requiring regulatory validation, the upgrade of a driver or published online Jan. 14. http://www.forbes.com/sites/joemckendrick/2013/01/14/9-questions-to-ask- DLL without your knowledge can void the entire validation. Another before-signing-a-cloud-computing-contract/ (accessed Sept. 15, 2015). 2. McDowall, R.D. Is Cloud Computing Right for Your Laboratory... or Are You Living in Cloud reason to have your legal department on board is that currently it is Cuckoo Land? Spectroscopy Online. 2012; published online April 1. http://www.spectroscopyonline. still unclear which nation’s laws apply, as the data may be stored in com/cloudcomputing-right-your-laboratory-or-are-you-living-cloud-cuckoo-land (accessed Sept. 15, 2015). multiple places around the globe. That is more than a bit worrying, as 3. ACLU. National Security Letters. Am. Civ. Lib. Union. 2015; published online July 30. https:// some nations’ laws could be construed as being in conflict with others’. www.aclu.org/national-security-letters (accessed July 30, 2015). 4. Bustillo, M. What It’s Like to Get a National-Security Letter. New Yorker. June 27, 2013. http:// www.newyorker.com/tech/elements/what-its-liketo-get-a-national-security-letter (accessed July 31, Another thing the SLA should cover is how the company will protect 2015). 5. Gould, J. US Effort to Grab Data from Microsoft in Ireland Should Frighten All Firms Using the your data. This might include such things as who has access to the Cloud Overseas. Nextgov. 2015; published online Aug. 20. http://www.nextgov.com/technology- encryption keys and how the company’s people are screened to news/tech-insider/2015/08/us-effort-grab-data-microsoft-ireland-should-frighten-allfirms-using- cloud-overseas/119264/ (accessed Sept. 15, 2015). help eliminate the possibility of in-house data theft, as well as more

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LIMS: Flexible Data Management

The adage of “adapt or die” applies to a laboratory information management system (LIMS) just as it does to evolution.

By Mike May, PhD

In many ways, adaptable means personalized. “We can configure our LabVantage 8 to work the way you want to work,” says Ralph Goldberg, product manager at LabVantage in Somerset, New Jersey. For many users, that will be one of the key aspects of adaptability. Raj Maitra, another product manager at LabVantage, puts it all in perspective: “When something is easy to configure and change, it’s less of a headache.” That could be a mantra for an adaptable LIMS—fewer headaches.

Create your own flow

“An adaptable LIMS will not lock its users into a rigid workflow but will Adaptability in a LIMS can mean adjusting it for the way a researcher handle and track any workflow,” Zolnai says. As an example of how to works or accommodating changing needs in a lab, such as handling data do this, he says, the software can allow “the objects that are handled by from new devices added to a workflow. “In order to be accepted and the LIMS to be linked to each other [with] no restriction, and it will welcomed— especially in R&D-type environments—a LIMS has to also allow these objects to be used independently [of] each other.” He be able to handle projects that command innovative solutions and quick adds that this lets “the LIMS be phased into a lab incrementally and development,” says Zsolt Zolnai, head of the Sesame LIMS developed independently of the workflow.”Abbott at the University of Wisconsin–Madison. When looking for a LIMS, Zolnai proposes high expectations. “An An adaptable LIMS can also save money and reduce the risk of being adaptable LIMS should fit [more easily] into laboratory operations, and out of compliance. Waters Corporation in Milford, Massachusetts, its introduction should not be a disruptive event.” developed the NuGenesis Lab Management System (LMS), and principle product manager Garrett Mullen says, “With an adaptable Mullen points out that scientists can use the “Smart Builder” feature lab management system, a company or lab can use fewer systems, to set up the NuGenesis LMS. “You just drag and drop saved building which reduces the cost of managing and of overall maintenance of blocks—like an instrument selection or sample measurement—to set systems in the lab.” If a company or lab works on projects in a regulated up more complex procedures,” he says. environment, such as developing new medicines, an adaptable LIMS can reduce regulatory risk. “If you can use one system—instead of Other vendors also create development methods, such as the having several to keep certified and updated—it can reduce risk when LabVantage Connect tool. “It lets you communicate with instruments the regulator comes to look at data records,” Mullen explains. through drivers,” says Goldberg. “We have a number of drivers to handle the output from various instruments, and we can add more.” Some systems are aimed at specific uses. As an example, STARLIMS Users of LabVantage 8 can even design the user interface the way they from Abbott in Abbott Park, Illinois, “provides labs with the cumulative want it. “Anyone going into the system can choose the view they like,” analytics and data management tools that are needed for health care Maitra says. environments,” says Jacqueline Barberena, director of global marketing and communications for informatics. This system, says Barberena, So when you think “adaptable” in a LIMS, decide what you want to be helps “laboratories worldwide optimize data accessibility, integrity, and able to control or change—now and over time. Then you can select the analytics.” option that delivers the control you need to keep your research evolving instead of going extinct.

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To LIMS or Not to LIMS? Assessing Needs, Avoiding Pitfalls

By Angelo DePalma, PhD

Just a few years ago, lab information products were sold and operated in stand-alone mode. Next came interoperability and data exchange. The convergence and overlap of major laboratory IT products have been followed by a blurring of terms. Thanks to a consensus decision by ASTM, an ELN for QA/QC is now referred to as an LES (laboratory execution system). By no means is that the limit of integration. Thermo Fisher includes an SDMS (scientific data management system) within the same platform as its LIMS/LES. “LES is the correct way to think of and refer to an ELN in a QA/ QC environment because you’re executing predefined processes versus designing and executing experiments as you’d do in an R&D organization,” Meek tells Lab Manager.

Variable but remarkably similar needs When implementing laboratory informatics systems, managers should consider both current and anticipated workflows, says Trish Meek, For Garrett Mullen, manager for NuGenesis Lab Management director of product strategy at Thermo Fisher Scientific (Waltham, Systems at Waters (Milford, MA), companies should base LIMS MA). “They need complete agreement and buy-in from business purchase decisions on key business drivers—the need to create and owners and IT. Managers should consider the agility their business manage inputs and make sound decisions based on them. requires, for example, when bringing in a new product or instrument.” “Those high-level requirements then push down into laboratories and She cautions to avoid, for example, LIMS that must be recoded for the information they generate and use,” he says. every new feature. Labs must absorb programming themselves, call the vendor back in, or outsource coding to third-party software firms Needs vary for different industries and laboratory sizes, for regulated that lack sufficient familiarity with the package. and unregulated businesses. Many LIMS are designed for food or environmental testing. Some are traditional sample management “People treat a LIMS deployment like the end of a race,” Meek says, tools, and others integrate with electronic laboratory notebooks “but the process is more like buying a house, where you redo the or supervisory software, while others take on the functions of a kitchen one year, replace the roof the next year. You’re constantly laboratory execution system. extending your LIMS implementation because your business keeps changing.” LIMS should be flexible and support those changes. So what would trigger undertaking a LIMS deployment? Mullen rejects the notion that workflows, sample volumes, or company size Rate-limiting steps should dictate.

Since one goal of lab informatics systems is to reduce human error, LIMS options and opportunities for small to mediumsized labs have potential purchasers should examine the flow points or rate-limiting never been better. Quality and traceability options are in no way less steps within their workflows and see to it that their LIMS can execute critical for these customers than for multinational corporations. “They those tasks. Tasks may be as simple as documenting which materials also need to manage sampling, register samples, allocate work, manage are being weighed and the numerical value, or as complex as routing results capture, measure standards, and create reports,” Mullen says. an out-ofspecification value to the correct manager for action. Today’s LIMS can be designed specifically for tasks that small labs

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need to manage, and at a level that suits them.

This leads to the most common mistake lab managers make when embarking on a LIMS project, what Mullen refers to as “boiling the ocean.”

Personnel managing a LIMS installation usually create a wish list of capabilities they’re seeking. That’s natural. But insisting that the LIMS plug all sample management and data holes, and do so from day one, is unreasonable. Projects that begin in that manner too often have unpleasant consequences, sometimes extending beyond the tenures of key personnel, through mergers, and after the original mission no longer applies.

“Consider a phased approach,” Mullen advises. “Don’t try to solve every single problem. Your lab may not need a full-blown LIMS.”

With luck you may eventually “boil the ocean,” but the odds of success are greater if you approach the problem one bucket at a time.

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Product Focus: Electronic Laboratory Notebooks Although the electronic laboratory notebook (ELN) market is mature, it has undergone several cycles during the past three decades. This existential back-and-forth has centered on whether ELNs should primarily serve as direct replacements for paper notebooks or something more.

By Angelo DePalma, PhD

technology should be easy to use,” Weiss says, “and products that are easy to use ultimately have a lower cost of ownership.”

Originally, IDBS ELNs were based on a Microsoft Windows and Java operating system. This platform limits how and where laboratories could tap into ELN resources. Thus, IDBS and other vendors have moved entire installations to the Web, making many ELN features accessible through tablets and other mobile devices. Computer platform neutrality capabilities improve accessibility by allowing users to work remotely on the device of their choice and by freeing access and operation from any particular computer operating system.

De-siloing

Simpler implementation, more accessibility Early ELNs were industry-specific to the point where chemical, environmental, and biology labs sourced their products from Today, the marketplace demands that in addition to serving as different vendors with reputations for particular industries. That electronic repositories for intellectual properties, ELNs should foster is no longer true, says Leif Pedersen, senior VP of marketing and collaboration within business units or research silos of large R&D product management at Biovia (San Diego, CA). “Out-of-the-box organizations. implementation makes it easier to adopt new software releases, integrate with other software, and derive other values.” “Many vendors are promoting the idea that ELNs foster a collective, collaborative experience that allows sharing of insights, information, ELNs have matured to the point where all leading products serve and knowledge,” says Scott Weiss, director of product strategy at all fields equally well. Leading stand-alone ELNs of 2014 should IDBS (London, UK). register novel intellectual property from biology labs as easily as from chemistry labs, a capability that required extra work with ELNs of a Early on, ELNs followed development paths similar to that of decade ago. laboratory information management systems, where installations catered to one type of work, for example, analytical chemistry. Related—perhaps enabling the trend in versatility— have been Modern ELNs incorporate modules that handle numerous workflow vendors’ efforts at creating modular ELN components, for example, types and “allow deep verticalization that supports sharing,” according for quality, data mining, data capture, recipe, and procedure to Weiss. management modules sitting atop the ELN platform.

The evolution from thin, horizontal “paper on glass” ELNs is in direct Why the interest? response to the complexities of modern scientific workflows. Several factors explain the uptick in interest in ELNs. One is the While adding features and capabilities, developers have made realization that ELNs are truly universal tools. Instead of purchasing ELNs easier to use and more accessible. Again, this is a response one ELN for chemistry, a different product for biology, and versions to the reality of lab workers who are computer savvy but resist each for upstream and downstream activities, a pharmaceutical steep learning curves for new software. “They take as a given that company, for example, can make everything work on one platform.

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Second, organizations can now ease their way into ELNs as never to digitize a process for creating buffers or reagents and plug in sample before. Instead of plunging into the software, labs can now take a preparation protocols,” Mullen says. “That’s the all-important lab stepwise approach. The first step can be as simple as creating a data execution level, when the full functionality of an electronic notebook repository that mirrors paper notebooks—paper on glass is the is realized.” operative term. This is the stage where tests and assays are automatically digitized Perhaps the most significant factor is that companies realize that the and users create templates applicable to multiple workflows. “It’s a cost of not using an ELN is simply too high. Issues related to first- lot like Lego blocks,” Mullen says. “You don’t need to create a new to-file, lost data, the ability to categorize and clone experiments, and component each time.” regulatory compliance have essentially rendered paper obsolete. By significantly lowering the learning curve, stepwise deployment has “Software costs are probably not that different from the early days, contributed significantly toward making ELNs more user friendly. but efficiencies are higher,” Pedersen explains. “Large companies now need only one product, not several. And the costs of consulting and Lab managers should avoid technology for technology’s sake, however. implementation have fallen significantly, which has driven down the “Automating because you sense the need to automate is an insufficient cost of ownership.” motivator for installing an ELN,” Mullen cautions. “There has to be a business benefit that improves productivity and quality, safeguards The layered approach your business, and reduces the risk of failing an audit.”

“The world of ELNs is best entered stepwise,” says Garrett Mullen, senior product marketing manager for NuGenesis products at Waters (Milford, MA). That is how best-in-class companies work today, ELNS FOR DECISION SUPPORT particularly with ELN-naïve customers. While ELNs were initially introduced primarily for IP compliance purposes, as several note, the benefits of ELN ELNs that have an SDMS component can capture data from have been extended to global collaboration and workflow networked computers and equipment such as pH meters and support. This puts ELN systems in the position to manage spectrophotometers, manage samples, and at the highest level substantial portions of R&D data in a research organization. participate in lab execution processes such as managing instruments, The consequence of this shift is that an ELN, if properly enabling stability study management, and ensuring compliance. The conceived and implemented, can play a fundamental role in varied deployment levels underscore the need to take things one step decision support. This is a fundamental transformation from at a time. ELN systems in the past, that in many ways functioned more like document repositories such as SharePoint: they could At its simplest implementation, an ELN uses data management be searched, but the data was not structured sufficiently so software to capture, store, and organize metadata within a centralized, companies were forced to maintain separate operational secure repository. The next stage involves building a test execution systems to enable decision-making and analytics. “A key system on top of data storage to leverage that data to create a objective of our approach,” says Michael Swartz, VP of laboratory management system. Business Development at PerkinElmer Informatics, “is to provide functionality that first is very adaptable to different “At this stage you’re ready to implement inventories of instruments research purposes, and secondly makes it natural for and reagents that can manage instrument calibrations, help maintain scientists to structure their data in the course of their work. reagent stocks using volume subtractions, and send notices for This enables the data in an ELN to be easily transferred to reorder,” Mullen adds. At this stage of the business, paybacks become an analytics platform where researchers can decide what to tangible. ELNs also assist with corrective actions. In the case of an do next. Enabling this natural transition from collaboration instrument calibration that may compromise product quality, issues and workflow to decision support is probably the most can now be easily identified and understood. Finally, the ELN moves important requirement for ELN’s today.” toward more complex operations such as assigning tests and managing stability studies.

At what step does this evolving information technology project become an ELN?

“It begins when the system manages test execution, when you’re able

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