LII:The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies

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Title: The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies

Author for citation: Joe Liscouski, with editorial modifications by Shawn Douglas

License for content: Creative Commons Attribution-ShareAlike 4.0 International

Publication date: April 2021

Introduction

The purpose of this piece is to introduce people who are not intimately familiar with laboratory work to the basics of laboratory operations and the role that informatics can play in assisting scientists, engineers, and technicians in their efforts. The concepts are important because they provide a functional foundation for understanding lab work and how that work is done in the early part of the twenty-first century (things will change, just wait for it).

Who is this intended for?

This material is intended for anyone who is interested in seeing how modern informatics tools can help those doing scientific work. It will provide an orientation to scientific and laboratory work, as well as the systems that have been developed to make that work more productive. It’s for people coming out of school who have carried out lab experiments but not corporate research projects, for those who need to understand how testing labs work, and for IT professionals who may be faced with supporting computing systems in lab environments. It’s also for those who may be tasked with managing projects to choose, install, and make informatics tools useful.

Figure 1 shows the elements we’ll be discussing in this piece. The treatment of the technical material will be on the lighter side, leaving in-depth subject matter to other works. Instrument data systems will be covered lightly, as any serious discussion becomes lengthy and discipline-specific very quickly; additionally, that material has been covered in other works.


Fig1 Liscouski AppInfoSciWork21.png

Figure 1. Elements we’ll be covering

Types of scientific and laboratory work

Science is about seeking truthful answers to questions. Sometimes those questions are open-ended without any idea where they will lead you in answering them (e.g. “Why does water ice float?”). Others are very specific, concerning material composition or properties (e.g., “How much lead is in this drinking water?”, “How much does a butterfly weigh?”). Still others may take some effort before you determine the best approach to working on them. The approach someone uses to address these questions depends on the nature of the question; some are destined for research, while others are addressed using specific test methods.

There are two types of research: basic and applied. Both can include field work, observations, experiments, models (mathematical, computer, and simulation), etc. Applied research is also done in testing or service laboratories, as with, for example, the development of new methods of analysis.

Basic and applied research

Basic research is open-ended, as you are looking into something without any idea of where the work will lead. It is often funded by grants through universities or government institutions; continued support depends on the perceived value of the research. Projects can range in size from the work of a single individual to a small team to large-scale groups studying astronomy, high-energy physics, engineering, the life sciences, or a number of fields.

Applied research, on the other hand, is directed toward a goal. That goal could be a cure for a disease, the development of a COVID-19 vaccine, or work towards artificial intelligence (AI). As with basic research, the work may begin with a single individual or a small team until some early goals have been reached, and then the project scales up. The effort may be broken down into a set of more narrowly focused efforts, whose results will be combined as the development proceeds. Since applied research is goal-directed, funding will depend upon who benefits from those goals being met. Projects of national interest, including security, may be wholly or partially funded by the government. Projects with a commercial interest tend to be funded by corporate interests, including individual companies in their own laboratories or through contract research organizations with expertise useful to the program. Where there is interest from a number of corporate and/or government groups, consortiums may form to distribute the cost and share in the results.

Both basic and applied research can be found in government institutions (including military groups, research and development agencies like the Defense Advanced Research Project Agency [DARPA], and task-specific institutions such as the National Institutes of Health [NIH]), public and private non-profit groups, corporations, consortia, and contract research organizations.

The research process

The research process begins with a question. Any question will do, including “why is the sky blue?” We’ll bypass Greek mythology[a] by asking more questions and planning how to proceed to answer them. For example, “Is the sky always blue?”, “When is/isn’t it?”, and “What other colors can it be?” Once the process begins, it can include a number of steps, the choice and direction depending upon the nature of the research and the mindset of the researcher:

  • Observations: This includes basic note-taking with support material (text, photos, drawings, charts, and scanned material). Research (e.g., as with basic astronomy, field biology) can be as simple as looking something up on Google or as complex as understanding how a virus works. Research is about asking questions and looking for answers, which often leads to more questions. It’s a little like my granddaughter who always asks “why?” no matter how well I answer the previous question (or at least how well I think I did).
  • Enhanced observations: This includes interacting with items under observation, as well as non-directed interactions, preliminary data gathering, and behavioral analysis.
  • Experiments and information gathering: This includes organized experiments that are planned, directed, and purpose-driven, as well as data and information gathering.
  • Team building: This includes the creation of teams or networks of people working on the same or similar projects.
  • Analytics and reporting: This includes data and information analysis, data modeling (e.g., mathematical, computer algorithm, and simulation), information synthesis, and knowledge creation.
  • Technology acquisition: This includes gaining access to public, commercial, remote, and other types of databases to assist the research.

Pinning down a “typical” approach to research isn’t possible because the routes people follow are as individual as the researchers and their area of work are. However, this is generally not the case with testing labs.

Testing laboratories

In addition to research labs, there are also testing or "service" laboratories. Service labs carry out specific test routines on samples and specimens; you may be familiar with them as quality control labs, clinical labs, toxicology labs, forensic science labs, etc. They are called service labs because they support other organizations, including research organizations, and they have similar modes of operation and work organization, running different tests depending on their area of specialization.

Contract testing labs are another flavor of service laboratories, acting as independent labs that do testing for a fee. These labs can offer capabilities and expertise that their customer doesn’t have, either because the equipment is specialized and not frequently needed or because the customer is looking for a second opinion on an analysis.

Regardless of the type of service lab, they all have one thing in common: the way they function. For a moment let’s forget about science and think about something else. Take for example a company that does graphics printing as a service to graphic designers and marketing groups. The company could offer a variety of printing services:

  • business cards
  • stationary (e.g., envelopes, letterhead, etc.)
  • postcards
  • brochures
  • signs
  • graphics for trade shows (including mounting of an image on backing, lightboxes, etc.)
  • postal marketing services

In this scenario, customers can come into the shop and drop off work to be done or place orders online (the company website provides a good description of their services and products). One of their biggest concerns is workflow management: what work is coming in, what is in progress, what is in quality control, and what is ready for delivery. Many activities may be associated with this workflow.

  • Order acceptance: Log the job into a log book, the go-to reference for work orders. Add the corresponding work order to a binder of work orders; work orders can be removed from the binders as needed (for example, when people are working on the job) and returned when completed. Comments are made on the work order and referenced to an individual’s notebook for details. Work orders shouldn’t be duplicated since people may not be aware of the duplicates and information may be lost. This does add some inefficiency to the process if a work order contains multiple components (e.g., brochures and trade show graphics); if someone needs to work on a task and someone else has the work order, they have to find it. Work orders contain the names of graphics files and their location. Then a check is made to ensure all the needed information is there, notifying people if something is missing. This includes checking to see if the graphics files are available, in the correct format, etc. The priority of the work is determined with respect to other work. Then the customer is notified of the work order status and the expected completion date.
  • Scheduling: The work order is assigned to one or more individuals for completion.
  • Performing the work: This is where the actual work is performed, including task coordination if an order has multiple components.
  • Customer service: This includes answering customer questions about the work order and addressing inquiries on completion date.
  • Draft review: This involves obtaining customer sign-off on a prototype stage if required, making adjustments if needed, and then proceeding to completion.
  • Quality control: This is where projects are reviewed and approved for completion.
  • Delivery: This involves shipping the material back to the customer or notifying the customer the order is ready for pick-up.
  • Billing: After satisfaction with the completed work is acknowledged, the work order is billed to the customer.

When the shop has a large number of projects going on, such a manual, paper-based workflow is difficult and time-consuming to manage. Projects have to be scheduled so that they get done and don’t interfere with other projects that might be on a tight deadline. And then there is inventory management, making sure you have the materials you need on hand when you need them. There is also the occasional rescheduling that occurs if equipment breaks down or someone is out sick. A simplified workflow based on the above is shown in Figure 2.


Fig2 Liscouski AppInfoSciWork21.png

Figure 2. Simplified print shop workflow, with some details omitted for clarity

Let's say our print shop has seven people working there. The owner manages the overall operation, and an administrator logs in work orders, notes the location of files that will be used on those orders, and does the final checkout of work, shipping, and billing. The remaining five people—staff, although everyone is at the same organizational level—take care of the actual production work; everyone is cross-trained, but some are more adept on some tasks than others.

Imagine you worked in this shop; how might your day go if you were one of the staff? The admininstrator will have prioritized the work depending on urgency and grouping similar work orders (or partial orders if there is request for multiple services) together. This is just a matter of efficiency: if you are using a particular piece of equipment and it has to be set up, calibrated, and cleaned when finished, you may as well make the most of that effort and run as many similar jobs as you can. Tracking down copies of work orders is an issue if someone is already working part of the order as there is only one copy so that notes and comments don’t get lost. Each staff member has a notebook to keep track of work, any settings used on equipment, and comments about how the work progressed. These notebook entries are important and useful in case questions come up about a job, how it was run, and if any issues were encountered. As one set of jobs is completed, you move on to the next set. Inventory has to be checked to make sure that the needed materials are on-hand or ordered; if something is missing work has to be rescheduled. The workflow is a continual, organized mix of tasks, with people scheduling time on equipment as needed.

You can begin to appreciate how difficult the manual, paper-based workflow in a shop like that is to manage, particularly when it depends upon people communicating clearly. It is the same workflow as any service-oriented business, from a florist to a repair shop. What differs is the size of the organization, the complexity of the work, and the education needed to perform the required tasks.

Now let's get back to the service laboratory. The print shop workflow is much like the structural workflow of such a laboratory. In the end, it’s the nature of the tasks; the complexity of equipment, instrumentation, and electronic systems used; and the education needed to carry out the work that sets the service laboratory apart from other service operations. However, there is one other, critical aspect that sets it apart: most service labs have to meet federal or industry regulations (e.g., the ISO 9000 family of standards) for their operations.

As noted earlier, there are many different types of service laboratories. The basic workflow is the same (see Figure 3 for one perspective on the commonalities of research and service laboratories), but the nature of the testing separates one from another. A water testing lab uses different test procedures than a toxicology lab does, or a clinical lab. Those working in different types of labs have to learn how to run different tests, and they also have to learn about the materials they work with. After all, people's observations about the material tested will differ depending upon how much experience they have with different kinds of materials.


Fig3 Liscouski AppInfoSciWork21.png

Figure 3. This diagram represents one perspective on the relationship between laboratory types. This is a bit simplified, particularly on the roles of research labs. Large research facilities, or those in which waiting for test results impacts the progress of research work, may incorporate a “service lab” function within their operations; the same workflow, just a merger of boxes. The downside of doing that is the loss of independent verification of test results, as people sometimes see what they want to see. This can be addressed by having critical and random samples analyzed independently.

While workflows vary between research and service labs, there is one consistent factor that cuts across both: record keeping.

The laboratory notebook

The laboratory notebook has been a fixture in scientific work for centuries. The laboratory notebook is essentially a diary and can contain text, drawings, pasted photos, illustrations, charts, and so on. Historically, at least until the mid-1970s, it was a paper document that has evolved as legal and regulatory considerations have developed. Figure 4 shows part of Dr. Alexander Graham Bell’s notebook.


AGBell Notebook.jpg

Figure 4. Pages 40-41 of Alexander Graham Bell Family Papers in the Library of Congress, Manuscript Division, Public Domain

The format of today’s paper notebooks has changed somewhat, and the process of using it has become more rigorous. Take for example Scientific Bindery Productions, a modern manufacturer of professional laboratory notebooks. The description for their duplicate lined notebook includes the following elements[1]:

  • table of contents
  • instructions page, for how to use the notebook and address patent protection
  • headers and footers, with legally defensible language
  • headers that include title, project number, and book number fields, as well as a "work continued from page" section
  • footers that include signature, date, disclosed to, and understood by fields, as well as a "work continued to page" section

The details of some of these points are called out in Figure 5, courtesy of Dr. Raquel Cumeras.


Fig5 Liscouski AppInfoSciWork21.png

Figure 5. A lab notebook example, courtesey of Dr. Raquel Cumeras, Science 2 Knowledge blog, 2019

Over the years, several guidelines have been published about the use of laboratory notebooks. Examples include:

  • Good manufacturing practice (GMP) and good laboratory practice (GLP) recordkeeping, from David West, St. Louis Community College, Center for Plant and Life Sciences[2]
  • NIH scientific recordkeeping guidelines, from the National Institutes of Health[3]
  • General laboratory notebook guidelines, from Science editor Elisabeth Pain[4]

A Google search of "guidelines for maintaining laboratory notebooks" or something similar will provide more examples, including those developed by leading universities.

At this point, you’re probably wondering why we’re spending so much time on this. The point: good record keeping is the foundation for documenting scientific work regardless of the media, be it paper or electronic. Yes, the laboratory notebook has an electronic equivelant: the electronic laboratory notebook (ELN). These ELNs and other laboratory informatics systems have to support everything paper systems do or they will fail in ensuring the integrity of documented work.

Using laboratory records

Laboratory records, whether in laboratory notebooks or some other format, can be acted upon in many ways. Laboratory personnel interact with them by:

  • recording observations, results, instrument data output, photos, and charts
  • describing research processes, goals, and results
  • ensuring the authenticity of laboratory work
  • planning and collaborating on experiments
  • extracting information for reporting
  • backing up data
  • querying data
  • sharing data
  • publishing data
  • archiving and retrieving data
  • securing data

Everything on that list can be done with paper records; however, those activities are easier, faster, and less error prone with electronic systems. Paper records aren’t going away anytime soon, for example when when needing to record comments and information that may not have been provided for in electronic systems. This is particularly true as a project team expands from one person to more people. The need to have shared access to information becomes a limiting factor in productivity when we rely on paper-based systems. Paper-based systems also depend upon the proximity of people working together, something that became problematic during the COVID-19 pandemic. Social distancing requirements made sharing paper-based notebook pages more challenging, requiring scanning and emailing. This was perhaps feasible for small amounts of physical materials, but less so for large projects with significant paper-based records.

That brings up another important point concerning ownership: whose data is it? When people are handed a notebook, they are told “this is your notebook, a place to write down your work and observations, and you are responsible for it.” Depending upon how employment or consulting contracts are written, the content that goes into the notebook belongs to whoever is paying for the work. When I worked in a lab, the notebook I used as mine was referenced by others as “your notebook” (it even had my name on it) even though it wasn’t mine but rather the company’s property, and when it was filled they took possession of it and archived it. This concept of ownership has become a stumbling block in some organizations when they deciding to install an ELN or laboratory information management system (LIMS), particularly if there are people who have been working there for a long time and have ingrained behaviors. Those people become concerned that someone is going to see their work in an incomplete state before they’ve reviewed and completed it. It’s their work and they don’t want anyone to look at it until it’s done. While the true owners of the work have always had that right, they may not have exercised it, respecting people’s privacy until the work is complete. If you’re considering an informatics system, does it address that concern about ownership?

Bringing informatics into the lab

So far I've hinted at the implications of adding laboratory informatics systems into the laboratory, but now it's time to discuss it further. Deciding how and when to bring such systems into the lab depends on a number of factors.

1. What is the lab's budget? If an informatics implementation can't be properly funded, don’t start that implementation until it can be. The cost of a laptop computer is trivial compared to the total cost of implementation.

2. Do we have in-house access to educated and experienced IT support? That staff should understand that laboratory operations are not just another PC- or Microsoft-dominated arena, but rather an environment which has needs for informatics solutions beyond the business office. For example, laboratory instruments need to be connected to computers, and that data integrated to make it more actionable.

3. Are laboratory staff ready to use the technologies and take responsibility for the things that go with it? Staff must be trained in more than how to operate an instrument. Can they back up data? Do they understand the security and data privacy risks associated with handling the data?

4. Are organizational policies flexible enough to allow practical use of the technology while still keeping security and data privacy risks in mind? The organization should have some sort of network access both internall and externally. Remote access should be possible, particularly given the circumstances surrounding pandemics and the like. A balanced policy on taking an organizational laptop out of the laboratory should be in place. Policies on cameras should also be reasonable, allowing researchers to capture images of samples and specimens for their notebooks. If organizational policies are too restrictive, the technology's usefulness is largely overshadowed.

5. What are the lab's space constraints? The size of a lab and the experiments it must conduct can affect the choice of informatics tools.

6. What is the nature of the lab's operations? Is it a research lab, service lab, or a combination of both? If you are in a service lab situation, bringing in informatics support as early as possible is essential to your workflow and sanity. You want to minimize having to deal with two separate processes and procedures: the old way we did it (paper-based) and the informatics-supported way.

7. Is your lab’s operation governed by external regulatory requirements? If it’s going to be in the future, you may as well start as though it currently is. Note thate everything should be validated, regardless of whether or not the lab is subject regulations. Validation isn't done to satisfy regulators but rather to prove that a process works properly. If you don’t have that proof, what’s the point of using that process? Do you really want to trust what a process produces without proof that it works?

Most of the points above are easily understood, but let's go into further detail. Let's start by looking at a simple case of you and your project, where you are the sole contributor, without any need for regulatory oversight. Your primary need is to record your planning, observations, results, etc. There are tools within the world of computer software to help with this, most notably the word processor. If you have access to one of those, you probably also have access to spreadsheets and other applications that can make your efforts far easier than working with paper. If you search Google for “word processors as lab notebooks” you will find a number of references, including Dr. Martin Engel's guide to using Microsoft OneNote as an ELN[5] and Labforward's 2020 ELN selection guide.[6]

However, simply switching from paper to electronic doesn't mean you're done. There's more to consider, like developing backup policies, addressing witness review, connecting to instruments, and expanding your team.

Backup strategy

You have the electronic documentation tools and the skills to use them, but what else do you need? A backup strategy is imperitive. Imagine a scenario where you are using a desktop computer, laptop, or tablet to do your work and it has one copy of the document you’ve been working on for weeks. You press the power button one morning and nothing happens. However, you are not (completely) worried or panicked but rather largely calm because:

  • you have a local backup on removable media (e.g., flash drive, disk), several instances, in fact, that were backed up at least daily, with backups containing everything on the system you were using (you may have a separate backup of your project);
  • you have a remote backup on your organization's servers (or on a virtual machine);
  • you have a cloud-based backup of at least your project files, and as much of the system files that the cloud storage permits (depending on bandwidth and cost), all secured with two-factor authentication; and
  • depending on the operating system you are using, you may have built-on backup-and-recover abilities, e.g. as with Mac OS X's "Time Machine" functionality.

You've done these things because you've asked yourself "how much is my work worth to me and my organization?"

Wintess review or sign-off

Footnotes

  1. According to Greek mythology (from the E2BN Myths page): "Long long ago, when Queen Athena (Zeus's daughter) was born, Zeus blessed her with two boons for when she came of age. After almost 15 years, Athena was told to think up two things to ask for ... 1) To have a city in Greece named after her (Athens) [and] 2) To have all the people of the world see her face every day of the year (what you are seeing are only her eyes). Thus, The sky is blue, just like the color of Athena's eyes..."

About the author

Initially educated as a chemist, author Joe Liscouski (joe dot liscouski at gmail dot com) is an experienced laboratory automation/computing professional with over forty years of experience in the field, including the design and development of automation systems (both custom and commercial systems), LIMS, robotics and data interchange standards. He also consults on the use of computing in laboratory work. He has held symposia on validation and presented technical material and short courses on laboratory automation and computing in the U.S., Europe, and Japan. He has worked/consulted in pharmaceutical, biotech, polymer, medical, and government laboratories. His current work centers on working with companies to establish planning programs for lab systems, developing effective support groups, and helping people with the application of automation and information technologies in research and quality control environments.

References