Portfolio

Though I have done other writing, editing, teaching, and researching work outside of LIMSwiki and LIMSforum (I can provide examples upon request), a majority of my efforts in the last 13 years has involved those two sites, as well as two others. Over the years I have used a variety of publishing tools for this content, including MediaWiki, WordPress, Moodle, LearnDash, and TiddlyWiki, as well as the Microsoft suite of applications. Most of that content has landed on LIMSwiki, and to a lesser extent LIMSforum. I've developed and maintained other MediaWiki installations for the same client as well over the years. Sites include:

LIMSwiki, the laboratory, health, and science informatics encyclopedia and knowledge repository;
LIMSforum, a WordPress-based site for the laboratory, medical, and scientific informatics community (I only add/import a subset of content on this site);
CannaQAwiki, a wiki for cannabis-related science, particularly as it relates to laboratory testing (its content has since been imported to LIMSwiki and is no longer maintained); and
LIMSpec.com, a wiki for the laboratory informatics specification document LIMSpec (it was discontinued in roughly 2019 and moved to LIMSwiki, in a new format).

Finally, I can't overstate enough that a majority of this content has been developed in MediaWiki, which I've been using extensively for nearly two decades, beginning with Wikipedia. While most of my experience is on the front-end use, maintenance, and upgrading of MediaWiki, I've slowly picked up a thing or two about the back end of maintaining the software. As such, I have plenty of experience in adding, managing, moving, and updating MediaWiki-based content and styles. My WordPress skills are still quite good, though I'm a bit rusty on Moodle and LearnDash. I've recently become more intrigued by a specific implementation of TiddlyWiki, which is described later.

The rest of this page provides examples of my work over 13 years with my laboratory software client.

Guides and white papers

Note that the year indicated is the year the content was last updated, not necessarily the year it was first researched and written. An attempt has been made to update these guides within two years of the last publication. However, due to time constraints and the numerous projects from the client over the years, it hasn't always been easy. In at least one case (the COVID-19 testing guide), an upper-level decision was made to not put more work into maintaining it.

You may notice numerous red links in these items. The immensity of the work associated with many of these documents can't be understated. Numerous encyclopedic and vendor articles help support the content, and it is beyond my available time to import every page linked throughout these documents. As always, a link to the original object at LIMSwiki is included in the top header information should you want to see the original version in its entirety.

Researched, written, and revised by me

Choosing and Implementing a Cloud-based Service for Your Laboratory (2023): This guide looks at the specifics of cloud computing and applies them to the world of laboratory software. It includes appendices of cloud and security service providers, as well as request for information (RFI) questionnaires.
Clinical, Health, and Scientific Informatics Programs in Higher Education (2021): I was requested to seek out as many relevant clinical, health, and scientific informatics programs in higher education as possible, research and develop a university page for each entity, and then detail in tabular form all the programs for easier comparison. Note that for this portfolio, none of the 272 university pages are loaded; a link to the original showing the full extent of the work is included on the intro page of this portfolio version.

Comprehensive Guide to Developing and Implementing a Cybersecurity Plan (2023): This guide examines cybersecurity planning in the scope of several frameworks. "The guide attempts to be helpful to most any organization attempting to navigate the challenges of cybersecurity planning, with a slight bias towards laboratories implementing and updating information systems."
The Comprehensive Guide to Physician Office Laboratory Setup and Operation (2022): This guide holistically examines the current state of the physician office laboratory (POL), with added context post-COVID-19. Testing, equipment, data management, reimbursement, and more are addressed for this somewhat niche laboratory type.
COVID-19 Testing, Reporting, and Information Management in the Laboratory (2021): This was a unique guide in that it was difficult to keep contemporaneous, given the rapidly evolving state of the COVID-19 pandemic, along with trying to meet other work obligations. The first iteration came out in May 2020 as more details were emerging, and multiple updates went into it until September 2021. The client decided to cease updates at that point.
FDA Food Safety Modernization Act Final Rule on Laboratory Accreditation for Analyses of Foods: Considerations for Labs and Informatics Vendors (2022): This mid-length information article examines the U.S. Food and Drug Administration (FDA) Food Safety Modernization Act (FSMA) Laboratory Accreditation for Analyses of Foods (LAAF) rules "and how they affect laboratories that are and want to become LAAF-accredited." It also examines what considerations laboratory informatics vendors might need to take into account for their software.
The Laboratories of Our Lives: Labs, Labs Everywhere! (2022): One of my somewhat earlier works, first appearing in 2017, this guide takes the reader down a path that demonstrates how laboratories intersect our lives at every turn. It looks at a wide swath of industries and points out what types of testing occur within those industries, as well as how how those associated laboratories impact the average person's life today.
Laboratory Informatics Buyer's Guide for Medical Diagnostics and Research (2022): "This guide addresses the medical diagnostics and research laboratories in their myriad forms, as well as how laboratory informatics solutions like the laboratory information management system (LIMS) can benefit them," as well as "the numerous considerations that should be made" before acquiring said solutions.
Laboratory, Scientific, and Health Informatics Buyer's Guide (2023): This mid-length single-page buyer's guide is an extension of work dating back to the late 2000s by the Laboratory Informatics Institute (LII). It provides brief information about acquiring laboratory informatics applications, vendors with public pricing, and other resources for the potential buyer.
LIMS Buyer’s Guide for Cannabis Testing Laboratories (2021): This guide gives cannabis testing laboratories a head start on identifying laboratory informatics solutions that meet the needs of their workflow. Some of the information provides a review of the state of cannabis testing, which is also useful for anyone just learning about the subject. Finally, it includes a customized RFI for the cannabis testing lab seeking informatics software.
LIMS Selection Guide for Food Safety and Quality (2023): This guide examines the current state of the multi-disciplinary food and beverage testing industry. Complex in its roles within society, the guide delves into the nuances of those different roles, while addressing the informatics resources necessary to assist the modern lab with its workflows.
LIMS Selection Guide for ISO/IEC 17025 Laboratories (2023): ISO/IEC 17025 places additional requirements on laboratories seeking to maintain quality standards, and the laboratory informatics solution chosen needs to address that. This guide looks at LIMSpec and the ISO standard, pairing them to requirements as they should apply to vendor software solutions.
LIMS Selection Guide for Manufacturing Quality Control (2023): Quality is a vital aspect of the manufacturing process, for numerous reasons. This guide addresses some of those reasons and how a laboratory informatics solution tailored to the industry helps workflows. It also includes a LIMSpec-driven requirements document for the industry.
LIMSpec 2022 R2 (2022): This guide identifies laboratory informatics functionality requirements for laboratories in general, with some specialty functionality, and presents them in a tabular fashion. Includes a .docx version.
LIMSpec for Cannabis Testing (2023): This guide identifies laboratory informatics functionality requirements for cannabis testing laboratories and presents them using a slightly modified LIMSpec 2022 R2 specification. Includes a .docx version.
Past, Present, and Future of Cannabis Laboratory Testing and Regulation in the United States (2022): Another example of a guide started earlier (2017), this one has seen multiple updates as cannabis regulations have changed regularly over the years. This has in turn affected cannabis laboratory testing, and many other aspects. This guide looks at where the world has been, is, and might be when it comes to cannabis and its testing for quality and safety.

Co-authored by me

Justifying LIMS Acquisition and Deployment within Your Organization (2023): Industry veteran Joe Liscouski addresses the practical considerations of the acquisition and deployment of LIMS and other laboratory informatics solutions in the lab, with many editorial and writing contributions from me, in particular regarding management and stakeholder buy-in.
Starting a Cannabis Testing Laboratory (2023): This mid-length information article examines the various aspects of setting up and running a cannabis testing labs. I address many of the latter topics, while industry veteran Alan Vaughn contributes to the initial discussion on the business plan.

Edited by me, authored by others

The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies (2021): Industry veteran Joe Liscouski takes an introductory look at the "role that informatics can play in assisting scientists, engineers, and technicians in their efforts."
Are You a Laboratory Automation Engineer? (2021): Representing some of his earlier work (originally published in 2006), Liscouski discusses the concept of "laboratory automation engineering," the application of laboratory informatics concepts across a scientific enterprise.
Considerations in the Automation of Laboratory Procedures (2021): Automating laboratories isn't a straightforward task, and in this entry Liscouski gets into the the finer details of transitioning from standard laboratory operations to workflows with automated systems.

Directions in Laboratory Systems: One Person's Perspective (2021): Here Liscouski provides "one person's perspective on planning for the use of computer systems in the laboratory, and with it a means of developing a direction for the future."
Elements of Laboratory Technology Management (2021): Here Liscouski discusses at length the state of technology management for the laboratory circa 2014.
HIPAA Compliance: An Introduction (2022): Industry veteran Alan Vaughn takes an introductory look at what HIPAA compliance means to a laboratory. First edition released in 2016.
Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering (2020): As Liscouski puts it: "This document was written to get people thinking more seriously about the technologies used in laboratory work and how those technologies contribute to meeting the challenges labs are facing."
Notes on Instrument Data Systems (2020): In this relatively brief missive, Liscouski discusses the instrument data system (IDS) from his years of perspective on its use.
Organizational Memory and Laboratory Knowledge Management: Its Impact on Laboratory Information Flow and Electronic Notebooks (2024): One of his most recent articles, Liscouski discusses the topics of organizational memory, electronic laboratory notebooks (ELNs), and artificial intelligence (AI) mechanisms.
Planning for Disruptions in Laboratory Operations (2022): This article by Liscouski addresses how laboratory operations can be better organized and managed to account for any number of possible disruptions to workflows.
The Practical Guide to the U.S. Physician Office Laboratory (2014): This was one of the first non-encyclopedic articles developed on the wiki, by Dr. Fein. Of course, this makes it one of my earlier editing collaborations.
A Science Student's Guide to Laboratory Informatics (2023): Noting gaps in undergraduate training in the use of informatics applications, Liscouski presents some of the most relevant concerns about the topic in this mid-length article.

Question and answer articles

I've developed more than 30 question and answer (Q&A) articles for LIMSwiki since 2022. These articles roughly have a word limit of 1,200 words, but they exceed that at times when necessary. The general idea here is a question is asked relating to laboratories, industries requiring laboratories, regulations, and more that has a tie-in to laboratory informatics applications like the LIMS. All 34 can be found on LIMSwiki. A representative sample of them are listed below:

FAIR and AI

More recently, I've been researching and writing about the FAIR Data Principles and their touch points with software and artificial intelligence (AI). The FAIR Data Principles, first published by Wilkinson et al. in 2017, recommend that research data and information (i.e., objects) be more findable, accessible, interoperable, and reusable. This concept has since expanded beyond research data objects to all types of objects, including the software used in published (and even proprietary, non-published) research. Through the loading of open-access journal articles on these topics over the years, FAIR and AI has increasingly been on my radar. A couple of recent examples of my writing on the topics are included below; one of them is still in-process as of June 2024:

Why are the FAIR data principles increasingly important to research laboratories and their software? - Completed piece on FAIR as applied to research labs and their software.
What are the potential implications of the FAIR data principles to laboratory informatics applications? - This one actually came before the other, but it was turning into a long-form research piece. As such, it was distilled down to the article prior. This one should be considered an unfinished work-in-progress, with intentions of turning it into part of a larger guide on FAIR and its application to science and industry.

Encyclopedic articles

In addition to all the guides, white papers, journal articles, Q&A articles, etc., I've also had to create from scratch some encyclopedic entries in LIMSwiki. This was done usually because the Wikipedia version was lacking significantly, or there was much more to say than any other wiki article could cover. Over the years, the number of these articles I developed dwindled, due to me being pulled away by my client to work on the other aforementioned projects. This meant an increasing number of articles were getting transcluded (i.e., “mirrored”) into LIMSwiki. In the end, most of the encyclopedic articles I have authored have been software vendor, laboratory, and other company articles, with the occasional topical article being created as well. Most of the non-topical vendor articles were recently moved to their own namespace on LIMSwiki, the Vendor: namespace.

Note: There is a bug on LIMSwiki (and in the greater MediaWiki software) that impacts transcluded Wikipedia (and other wiki) articles that include inline math. I’ve been trying to push to get that bug fixed with the Wikimedia coders since September 2022. You can see the progress on the Phabricator page. Should you see odd gray areas on some LIMSwiki encyclopedic pages with inline math, it’s because of this bug!

Here are some representative examples of encyclopedic articles I've created over the years on LIMSwiki.

Topics

Cloud vendors

Journal articles

I've added an open-access journal article to LIMSwiki on a weekly basis since mid-2015. Each article received soft editing for grammar and readability, with occasional fixes to broken URLs and even missing citations. Occasionally, per the Creative Commons license, an additional contextual modification was made, but only if a critical component was deemed missing, causing confusion to the reader. The culmination of these edited journal articles can be found in the Journal: namespace of LIMSwiki.

Courses and help guides

My client had a website, LIMSuniversity/LabCourses, where they had hosted their training courses for their laboratory software. I was asked to help with a conversion of some of that material to a Moodle installation in 2013 and 2014, as well as develop new courses on laboratory and scientific informatics. You can sort of see the progression here in these archived snapshots:

By 2015, the client decided to shift gears from Moodle to the LearnDash WordPress plug-in, utilized on the client's LIMSforum website. Though the courses I developed are no longer available online (as the client eventually removed them by roughly 2020 or 2021), you can see how they existed here (give the archived page time to load):

November 2018

The LII classes were specifically developed by me, or in a collaboration with others, and included a course on using MediaWiki (001), developing your own courses (002), using OpenEMR (005), and learning about clinical laboratory informatics (006). (An archived look at the 006 class can found on the Internet Archive.) I developed others—though lost to time—plus added additional open-access courses by other entities such as MIT.

Outside of the LearnDash course on MediaWiki, I also developed some training material on LIMSwiki on how to use MediaWiki:

MediaWiki basics (2015): This is a set of guides briefly addressing how to use MediaWiki markdown language on LIMSwiki.
Using the Internet Archive (2017): This brief help article intends to help new MediaWiki users use the Internet Archive as part of their research and citation efforts.

TiddlyWiki and WikiPress content

What is TiddlyWiki? From the guide I developed for using it in conjunction with WikiPress:

TiddlyWiki is described as "a unique non-linear notebook for capturing, organizing and sharing complex information." Initially released in September 2004 by Jeremy Ruston, the open-source software has since grown into its current iteration, TiddlyWiki 5. The publishing "platform" continues to grow and evolve, thanks to the more than 200 contributors who semi-regularly update the source code. Today, the software is fully featured, with support for auto-saving, encryption, keyboard shortcuts, MathML, and much more. A TiddlyWiki instance is quite customizable, and it is also extensible, with a wide array of plug-ins available to expand the capabilities of the platform. TiddlyWiki is also somewhat unique in that the software is a practical Quine, meaning that it can compute and output its own source code when run. As a result, the software is able to independently save changes to itself. The end result is a standalone HTML file that is portable and easy-to-read from practically any modern web browser. As TiddlyWiki puts it:

TiddlyWiki is designed with the long-term needs of its users in mind. Because it is open-source and needs no infrastructure, we can be confident that all we'll need to access a TiddlyWiki file even in the far future is an ordinary HTML browser. If you're starting to use TiddlyWiki at the beginning of your career, you can be confident that it will carry you through to retirement.

This concept is appealing, and my client began to venture into this territory for several years. Very little of it has made it online, however, for unknown client reasons. The idea of using it to publish a guide or book in a tidy HTML file means it's compact, portable, and useable with any browser. Its downsides are that the file can get quite huge the more images that get added to it, and there's a learning curve to using it.

In tandem with TiddlyWiki was the WikiPress effort. Per the guide I developed:

WikiPress takes TiddlyWiki and adds some additional functionality to the platform to make it more user-friendly. This is largely accomplished through a set of plug-ins, the most important being the Summernote Editor ... [t]he ultimate goal of WikiPress is to enable users to integrate content from multiple sources (with MediaWiki sources primarily in mind) in order to develop highly portable and user-friendly electronic books and guides. Summernote Editor adds a certain level of "what you see is what you get" or WYSIWYG editing capability.

Today, there are some problems with the wiki embed plug-in tool that is part of the editor, and I hope to eventually get that sorted out. But even so, it remains a useful publishing tool. Here are examples of me putting this combination of tools to use, not only to develop new material (Diving Into WikiPress) but also to convert some of those guides mentioned at the beginning into the WikiPress format:

Diving into WikiPress (2022) - This example shows a more traditional "open and close on-demand" structure, allowing the reader to view the content how they wish. It's representative of how someone could develop their own long-form guide or short-form book.
Comprehensive Guide to Developing and Implementing a Cybersecurity Plan (2020) - This example demonstrates the importation of a LIMSwiki-based guide into TiddlyWiki/WikiPress. Interfacing with the content works similarly to the prior example. Note: This is the 2020 version of the guide, not the 2023 version posted above.
LIMS Selection Guide for ISO/IEC 17025 Laboratories (2023; partial) - This example is only loaded with the document structure, showing a different way to interact with the content: with it appearing pre-loaded and in-order upon opening it.