2019 INFORMATICS RESOURCE GUIDE

Questions to Ask When Buying Cloud Computing for the Laboratory Laboratory Informatics Using LIMS to Address Core LIMS Meets the Modern Laboratory Labs’ Workflows

LIMS: Flexible Data Management Selecting a SaaS LIMS Informatics Resource Guide

Questions to Should I invest in a cloud-based system? Many potential users have concerns about security when storing their valuable lab data in the cloud. However, vendors who offer Ask When cloud-based LIMS have many security measures in place and are continually monitoring and acting upon potential threats. Cloud-based solutions might end up being more secure than Buying storage on your lab’s in-house servers. In addition to security, cloud-based systems offer automated and flexible backups to ensure that you never lose your data. Storage capabilities of Laboratory cloud-based systems can also be expanded as the data needs of the lab grow.

Will I need to purchase specific instruments Informatics to integrate them with my LIMS? aboratory information management systems (LIMS) are computer programs used to facilitate laboratory Many laboratory instrument manufacturers are teaming up with Loperations. They can be used for sample management, LIMS programmers to integrate their instrument monitoring instrument integration and monitoring, data collection, into LIMS platforms. However, other manufacturers continue to compliance, quality assurance, experiment documentation, develop proprietary instruments that require their own software and many other tasks. LIMS form a central database where solutions. In other cases, monitoring devices can be added to lab members can access all laboratory information, increasing instruments, allowing for integration of instrument monitoring transparency and efficiency within your lab. for multiple units into a single interface. Consult with the LIMS vendor to determine if your instruments will be compatible with How do I know if an adaptable LIMS is the software. Before purchasing any new instruments, check right for my lab? whether they will be compatible with your LIMS.

LIMSs can be purchased as out-of-the-box solutions designed to work for your lab with complete functionality. However, many PURCHASING TIP vendors also offer adaptable LIMSs that can be configured to When purchasing a LIMS, look for software that is highly the users’ needs and can be changed in the future as the data configurable. When implementing the system, you’ll want management needs of the laboratory change. These systems to be able to tailor the software to your needs and workflows eliminate unnecessary functions, simplifying the software for rather than being confined to its pre-set capabilities. Over the end user. The right system will depend on the complexity time, configurable software will be able to adapt as your needs of the functions required. If your needs are simpler, an adaptable change without having to implement a new system. solution might be a better fit for your lab.

Lab Manager 2 Informatics Resource Guide

research, to cover both lab samples and processes. For decades, LIMSs focused on the former, while electronic LIMS Meets laboratory notebooks (ELNs) handled the latter. When first developed, LIMSs and ELNs were built the Modern independently and their functions didn’t meet unless the customers wanted both types of software. At this point, the vendors would try to figure out how to make the software Laboratory packages work together. The latest trends in laboratory information Today, through mergers, acquisitions, and technology management systems acquisition, most major LIMS developers incorporate at least some aspects of laboratory execution software (LES), ELNs, By Angelo DePalma, PhD database, or supervisory functions into their LIMSs.

aboratory information management systems (LIMS) One goal of both ELNs and LIMSs is elimination of nonvalue- have evolved toward greater accessibility, functionality, added laboratory activities, of which paperwork is a substantial Land interconnectivity, to a degree that could not be but seemingly entrenched component. Many lab workers foreseen (or have been possible) when LIMSs were first still use paper notebooks, even when they have high-level introduced. In the early 1980s, when LIMSs first emerged, information systems in place. Thus, the elimination of programmers were working with small mainframes or paperwork became a common driver for adoption of both ELNs minicomputers and didn’t have Oracle databases, Windows, and LIMSs, which further drove their integration. or microcomputers. The challenge was sample management, and that’s what LIMSs were designed to handle. Another idea, that individual lab processes were part of a larger organic whole, made integration of LIMS and ELN products At the time, the pharmaceutical industry was just even more appealing. LIMS should not exist in silos as this adopting large compound libraries for drug discovery software is highly interrelated and can leverage common and combinatorial chemistry to probe active molecules functionality. In addition, customers want a single vendor for all within those molecule collections. As more drug discovery their software, so it makes sense to have LIMS, ELN, and LES organizations adopted these tools, labs became inundated available under a single software platform. with samples, sometimes needing to process thousands of unique samples per week. Democratizing complexity

To this day, a great deal of the effort in lab automation, As LIMSs began losing their exclusive focus on samples, particularly on the software side, attempts to manage such they also underwent what this column has termed (with

Lab Manager 3 Informatics Resource Guide respect to instrumentation) “democratization”— reduced LIMS are also able to connect to ELNs to provide a complete complexity leading to improved usability and accessibility picture of quality data and how it is acquired. ELNs track each by ordinary users. step in the process so that if a product is out-of-specification, the manufacturer can track back to the specific production lot as well This new class of products, or “lean” LIMS, provides an as how the product was tested. alternative to the traditional pharmaceutical LIMSs, which are highly loaded and require significant investment. The traditional Modern LIMSs have a good deal of ELN functionality already software also has many modules and stacks required for built in, but some customers, prefer a dedicated ELN. functionalities, which can scare many users. A LIMS should be intuitive to use. Into the cloud

Cross-functionality—to a point The question of whether to host a LIMS (or any data-intensive application) locally, at or near the point of use, versus keeping Integration with third-party laboratory and process software it in the cloud has pretty much been settled. Drug companies, has long been a goal for LIMS companies. Early on, developers which churn out thousands of patents per year and with a keen were constrained by computing power, limitations in supervisory sense of intellectual property ownership, were at one time software, and the proprietary nature of such products. Those reluctant to let their data “out.” Today, the preference is for limitations are disappearing as interface standards emerge and cloud-based data repositories. suppliers recognize that staying in business requires them to accept the reality of multi-sourcing for laboratory information Cloud-based LIMSs offer better performance, better disaster products. recovery, greater redundancy, superior security and data integrity, and easier scaling with very little capital investment. LIMS are also becoming more tightly integrated into In addition, using the software-as-a-service model means that instrumentation and non-LIMS information management vendors are increasingly involved, and labs are able to subscribe to systems such as ERP (enterprise resource planning) and SAP software rather than purchasing, which can help when budgeting. (systems applications and products).

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Lab Manager 4 Informatics Resource Guide

In many ways, adaptable means personalized. Vendors can LIMS: configure your LIMS to the way you want to work. When something is easy to configure and adapt, it leads to less headaches for the end user. That could be a mantra for an Flexible Data adaptable LIMS—fewer headaches. Create your own flow

Management Adaptable LIMS can handle and track protocols without locking users into a rigid workflow. For example, the software The adage of “adapt or die” applies to can allow the objects handled by the LIMS to be linked to a laboratory information management each other with little restriction and can also allow these system (LIMS) just as it does to evolution objects to be used independently. This ability allows the LIMS to be phased into a lab incrementally and independently of by Mike May, PhD a workflow. An adaptable LIMS should fit seamlessly into a laboratory’s operations and implementation should not be daptability in a LIMS can mean adjusting it for the disruptive for the lab. way a researcher works or accommodating changing A needs in a lab, such as handling data from new devices Drag and drop configurations can make it easy to set up more added to a workflow. In order to be accepted, a LIMS needs to complex procedures. Vendors are also creating development be capable of handling projects that require innovative solutions methods that let you communicate with instruments using and quick development. drivers and design the interface the way you want.

An adaptable LIMS can also save money and reduce the risk of So, when you think “adaptable” in a LIMS, decide what you being out of compliance. Adaptable platforms allow companies want to be able to control or change—now and over time. Then or labs to use fewer systems, reducing the cost of managing and you can select the option that delivers the control you need to maintaining LIMS in the lab. Using a single, adaptable system – keep your research evolving instead of going extinct. instead of having several systems to keep updated and certified – can reduce the regulatory risk when working in a regulated environment, such as pharmaceuticals.

Lab Manager 5 Informatics Resource Guide

2. Preventing loss of the data (asset), either through the data being removed from organizations through improper means Cloud or information becoming no longer available. Computing A strategy to deal with large data sets Data volumes are increasing, and organizations are looking for flexible data storage that can continue to meet business for the needs. The amount of data that is being created, and consequently Laboratory stored and used securely within organizations and laboratories, is increasing. One of the reasons for this Using data in the cloud-what it means for increase in data storage is the fact that many laboratories data security are now using electronic data management solutions, which make it easier to capture and analyze data efficiently. Such by Stuart Ward solutions include electronic laboratory notebooks (ELNs) and laboratory information management systems (LIMS). he pharmaceutical market continues to grow and organizations are looking for innovative ways to These systems have changed the end user’s behavior Tmanage the ever-increasing amount of data. For from capturing the minimum amount of data for a given many laboratories, the data collected from experiments and experiment (because it is time-consuming to insert the data processes performed is the most valuable asset they have and into a paper-based document), to capturing all of the data underpins the business decisions they make. Therefore, it is available. An electronic solution streamlines data capture and crucial that the data is collated and stored in a manner that analysis, since many of the processes are automated. This also keeps it secure, but also allows it to be efficiently used to means the end user, whether they are a scientist or a researcher, support the various business objectives. can perform their responsibilities in a more effective and efficient manner. It’s a win-win for organizations as well as For the purposes of this article, the concept of security covers the users. In addition, it’s widely accepted that electronic data the following broad areas: management solutions, which are integrated into corporate user identity management systems, provide a high level of security for 1. Data collected is a true record of what has been performed an organization’s most treasured asset: their data. and has not been tampered with. This is very important when the data is being used to make decisions and/or being used to Many of these electronic-based data management systems back up submissions to regulatory authorities. are deployed using an organization’s infrastructure; for

Lab Manager 6 Informatics Resource Guide example, using servers that are hosted within an on-premise or decreased as organizational needs change; for example, the data center. This has meant that as the amount of captured, increase or decrease of users on the system or the volumes of analyzed, and stored data increases, so does the need for data being stored. more infrastructure, such as servers. The processes that many laboratories and organizations need to go through to obtain Providing this same level of flexibility, security, scalability, and this extra infrastructure can be extremely time-consuming. resilience for an organization’s on-premise deployed system is Subsequently, the ability to quickly adapt to the changing extremely costly and time-consuming. So, organizations are business requirements can be lost. In addition, if laboratories turning to cloud technology, and in many cases using software as then stop the program of work that requires this extra resource, a service (SaaS), to further reduce their operational burden and the organization is left with this infrastructure not providing drive increased efficiency. any benefit to their business. So, laboratories and organizations are now turning to technology providers that can deliver How does SaaS help customers deliver infrastructure and/or software in a flexible way, which can adapt their business objectives faster? to the ever-changing business needs and/or the desire to capture and use increasing amounts of data. Many data management software solutions are now provided as SaaS. This is because organizations are focusing on the The answer for many laboratories is to use the cloud to provide capabilities of what the software provides—does it meet the this flexible infrastructure and, in many cases, software business need? SaaS products also tend to be quicker to deploy resources. The pharmaceutical cloud computing market is since setting up and maintaining the infrastructure to run the expected to grow at a Compound Annual Growth Rate (CAGR) software is the responsibility of the vendor providing the service. of 20.9 percent between 2018 and 2022, reaching an impressive Another advantage of SaaS is that there’s a clear separation of $12.1 billion. Clearly, cloud technology is here to stay. responsibilities between the customer using the software and the vendor providing the service/software. This approach adds a However, many laboratories and organizations are asking, “Is layer of security in that it would require both the vendor and the the use of the cloud secure?” Is it the right place to store such customer to conspire to tamper with the data. The likelihood of an important asset, especially when the data is going to be used that is extremely small. The vendor is focused on ensuring that for regulatory purposes? One reason for this is that some people the software/service is running to provide the best experience are not confident with what the cloud, especially “public cloud,” for the customer, and that the data is captured and stored in a means and provides. secure and resilient manner. This means that the customer can focus on their business needs and adapt or change as required. “Does using the ‘public cloud’ mean that my data is available to For example, the ability to easily increase or decrease their use everyone?” The short answer to this question is no! The data as business objectives change and keep the organization nimble is not available to everyone. The public cloud just means that and competitive, while keeping their data secure, always. the service the public cloud vendor is providing can be made available to everyone. How to choose the right SaaS solution

In reality, security is at the forefront of everything that a public The selection process of a SaaS solution should not vary cloud vendor does since it would be very detrimental to the significantly from any other software purchase: the software third-party vendor if the security of any data that was stored must be able to meet the business need(s) it’s being selected in their public cloud was compromised. Therefore, public for. Other considerations, if not one of the primary needs, cloud vendors have large numbers of security professionals should be the flexibility the software will provide so that it can and systems, compared to organizations’ on-premise setups, address the anticipated future needs and deliver a seamless end which are continually monitoring and acting upon perceived user experience. For example, can the SaaS solution be easily security threats in addition to actual threats. This also includes integrated with other systems and business processes to make it keeping the systems up to date in terms of infrastructure and easy for end users to perform the work? It should be, as this will software updates. Therefore, the systems that the cloud vendor help drive adoption and maintain usage. is providing are always in top condition and ready to adapt to a customer’s needs. Since SaaS solutions are generally licensed using a subscription- based module, the other important consideration and question On top of this “secure” platform, a cloud-deployed system to ask is: what happens to the data when the contract to use the can also provide organizations with an automated and flexible software is terminated? SaaS solutions generally have interfaces backup process, which generally includes the ability to back that enable customers to extract their data when the software up in different locations, to ensure that the risk of data loss due is no longer used but it’s worth confirming this. to system issues is extremely small. The cloud also provides a scalable infrastructure resource that can easily be increased

Lab Manager 7 Informatics Resource Guide

Historically, software deployed on-premise offered “one-size- fits-all” solutions, sometimes denying users the level of flexibility their businesses required. Choosing the right technology means catering to organizations’ unique needs, challenges, and strengths, while increasing efficiency across all teams. SaaS solutions, underpinned by cloud technology, have the ability to address industry concerns and provide the flexibility to adapt to ever-changing business needs, while providing the necessary security for the most valuable asset: the data.

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Lab Manager 8 Informatics Resource Guide

formats so that information flowing into the LIMS of requesting labs is understandable and accessible. This traceability is Using LIMS necessary, especially when a lab is running many experiments under multiple requests. For large core labs, performing tests, to Address moving data, and maintaining quality are not trivial. Although LIMSs are often viewed as a solution for errors introduced via manual manipulation and data entry, perhaps Core Labs’ the greatest benefit arises in labs that are completely automated or nearly so—the case with most NGS and diagnostics labs. Data quality and interchangeability aside, the sheer volume of Workflow data generated by these core labs becomes the paramount issue, and the need for LIMSs more compelling. In a 2014 Clinical Core labs for medical testing and next- Biochemist Reviews article, Richard Jones of the Yorkshire generation sequencing (NGS) are Centre for Health Informatics at the University of Leeds (Leeds, apparently here to stay UK) notes that despite extensive computerization, the 152 National Health Service laboratories in the UK send six million by Angelo DePalma, PhD pieces of paper annually to one another, at a cost of 300 person- years. By contrast, Britain’s National Pathology Exchange, based hile the democratization of big-ticket on LIMSs, is virtually paperless. instrumentation has made some research center W core laboratories obsolete, core labs for medical In the clouds testing and next-generation sequencing (NGS) are apparently here to stay. Cloud operation and integration with conventional data platforms such as electronic laboratory notebooks (ELNs) But despite these shifts, most substantial laboratory enterprises are significant trends in LIMSs generally that serve core labs rely on the core lab concept to some degree, which presents in particular. Cloud-based systems allow instant access from unique challenges for data management. Laboratory information anywhere while shifting the burdens of data storage and security management systems (LIMS) have, as a consequence, evolved to companies that do it best. to address the special needs for data integrity, ownership, accessibility, and integration with local computing, data, and The democratization of LIMS through cloud services is evident instrument systems. from android apps available from the Google Play store, many of which appear to have built-in ELN features and full access via a Core facilities execute work requests from multiple labs while tablet or phone. documenting all processes and data securely and in standardized

Lab Manager 9 Informatics Resource Guide

are significant trends in LIMSs generally that serve core labs in particular. Cloud-based systems allow instant access from Selecting a anywhere while shifting the burdens of data storage and security to companies that do it best. SaaS LIMS The democratization of LIMS through cloud services is evident from android apps available from the Google Play store, many of Price, access, reliability, and more which appear to have built-in ELN features and full access via a must be considered tablet or phone.

by John Joyce, PhD Under the NTIS definition, a cloud computing offering must meet the following requirements; otherwise, you are running efore you can start deciding on which LIMS to get, just a hosted service. you first have to determine what type of LIMS you B want. By type, I am referring to whether you obtain • On-demand self-service a classic LIMS, where you license the software from the • Broad network access vendor and install it on a server in your facility, or you select • Resource pooling a system that is provided to you as a service. • Rapid elasticity In the latter case, there are a pair of sub options as well. You • Measured service can go with a provider that basically sets up a classic LIMS, with the exception that you access it over the Internet. This So, other than semantics, what’s the difference and why does type of system is frequently referred to as a hosted LIMS it matter? The difference is that with an ASP, you are basically or an application service provider (ASP) LIMS. Alternately, getting a classic LIMS, just with someone else handling the you can go with a supplier that provides software as a service maintenance. With SaaS you get much more. Because of the (SaaS) access to a LIMS. A hosted service can be running on a resource pooling and rapid elasticity of the cloud, as your system standard server hosted at the supplier’s data center or as a service demands change, whether in memory, storage, or processing in the cloud. A LIMS provided as a SaaS typically runs in the power, the cloud adjusts to provide it. The only way to change cloud. The difference can be confusing at first, particularly as the resources available on a hosted server is to physically salespeople frequently misuse the technical terms. For example, swap out the server. In general, the SaaS system is also more many people refer to any service provided from outside their redundant. If a particular server were to crash, processing would firewalls as being in the cloud. However, the National Technical be taken over by another node. Information Service (NTIS) has a much more stringent definition.Cloud operation and integration with conventional Another difference is that a hosted LIMS is dedicated to your data platforms such as electronic laboratory notebooks (ELNs) application, so only your group can use it. The corollary to this is

Lab Manager 10 Informatics Resource Guide that for other organizations using a LIMS, the vendor would need Another factor relating to LIMS access is the reliability of the to configure another server dedicated to each organization, with server that the application is running on. If you go with an all the setup and configuration work that implies. On the other internal server, do you have it configured with a hot backup so hand, to qualify as a SaaS under the NTIS definition, an instance that in the event of a failure of the primary server, operation of the application must be multitenant. This means that many of the LIMS automatically falls over to the backup? Have you different groups of users might be running on a single instance tested that it works? If you don’t have a hot backup, do you have of the system. The advantage of having many different groups a backup server that you’ll just need to power up? These same running on the same instance of the application is that the vendor questions hold true for a hosted server. If this is important to you, has to install, configure and maintain only a single instance of this should be included in your service level agreement (SLA) the application, greatly reducing their cost and the cost they with the vendor, not just assumed. With a SaaS system, because pass on to you. You will also find that due to the elasticity of the the resources are pooled and shared, the system should be much cloud, you pay only for the resources you use. If you occasionally more resistant to the failure of an individual processing node. In need significantly more memory or processing power, the cloud the event that an instance of the application goes down, the SaaS expands to match the need, so you don’t have to constantly pay architecture makes it much easier to configure the operation to for the maximum resources that you might potentially use. fail over to another instance. Yes, there have been events that have shut down full computing centers, but these are rare. For highly While these definitions might sound esoteric, it is important critical systems, you would not only have multiple instances of that you understand them so that when a vendor talks about the application running, but you also would have them running their system, you will know whether they are using the terms in geographically different data centers to minimize your risk. properly, because the implications of what the system will be Again, this is a detail that would need to be addressed in your able to do hinges on the accurate use of the terms. You must be SLA with the vendor; don’t just assume this is what they do. the guardian ensuring that the terms are used correctly on any purchase orders, as I can guarantee that the majority of people in A related question is how your data backups are performed. With the typical purchasing department won’t know! a local server, that responsibility falls to you. Have you confirmed that they are being backed up? I’ve encountered systems where So what are the different implications for running a LIMS on everyone is certain that backups are being performed, only to a local server, as an ASP or as a SaaS? Let’s start with one that discover when you start asking questions that they aren’t. Policy might be a showstopper. With either of the two latter options, might be to do it, but systems sometimes fall through the cracks. your data is normally moving outside your physical control and Even if your data is being backed up, have you periodically you must rely on the service provider to protect it. Assuming verified that you can restore those backups? If your data is being that standard security practices are applied, the risk of any data backed up, are your IT services willing to restore the backed-up exposure is small, but to some organizations, anything that adds files? Believe it or not, I’ve encountered commercial IT groups an inherent risk is unacceptable. Only you, or the people you that refused to retrieve a set of files from their backup tapes, report to, can make this decision. However, there is an alternative saying that they use the tapes only when they have to restore to keep in mind. Depending on the provider, some will set up a a whole server. Hosted services and SaaS generally have the private cloud or hosted server within your facility. This may still advantage that you can place the burden of performing backups inject a small increased risk of exposure, but it is much smaller on someone else, though that needs to be included in the SLA just than sending the data past your firewall. to minimize any misunderstandings.

The next factor is how important constant access to the LIMS Another question to deal with is whether interfacing analytical is to your operation. If it’s down for more than a few minutes, do instrumentation is supported. This is not just a productivity- you have to shut down operations? How about for hours or days? enhancing feature but also can significantly reduce the Determining which system results in the lowest risk of an outage occurrence of transcription errors. Do you need any special is more difficult to determine than you might think, as it depends hardware, and does this vary with the system type? Even if the on how well people in different departments are following best stand-alone systems directly support instrument interfacing, you practices. At first you might think that remote systems would need to confirm whether the hosted or SaaS provider systems be riskier, as everyone has heard stories of construction crews do. A drawback of a SaaS LIMS is that commonly it is much digging up fiber optic data lines. But consider that a well-designed more difficult to customize the application beyond the vendor’s system would have redundant data lines connecting your facility supported configuration options. to the vendor’s data centers, ideally using totally different paths and providers. Even with internal servers you can face I’m afraid that this article doesn’t answer the question of which this risk if you encounter a power failure or a critical network system type to select, but it should provide you with the switch dies. Are all required switches and servers plugged into questions to consider so that you can make that decision. While uninterruptible power supplies? And don’t forget that a data line you will frequently hear that SaaS systems are much cheaper can be cut as easily inside your facility as it can be outside. than local installations, there are some caveats. Most analyses

Lab Manager 11 Informatics Resource Guide that I’ve encountered indicate that for price, a SaaS LIMS will usually be cheaper for small to midsize organizations and it becomes cheaper to have on-site servers for large organizations. Keep in mind that price is not everything.7 Dealing with some internal IT groups can be very frustrating, and it might be worth the difference in price to work with someone else.

Good luck with your selection.

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Lab Manager 12 Informatics Resource Guide

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