How a Busy Research Clinical Laboratory Deploys OpenClinica as a Laboratory Information System (LIS)

Here at Geneuity Research Services, we do laboratory tests for clients
conducting clinical trials. We are a one-­stop shop, handling everything
from routine clinical assays to esoteric molecular analyses. We use
OpenClinica as an in-­house LIS to keep track of work­flow and to help
with administrative tasks like billing and specimen archiving. This isn’t
exactly what the developers of OpenClinica had in mind originally. The
application was designed from the point of view of trial sponsors, not their
subcontractors. But it works very well for us nonetheless. In this article,
we briefly describe how we do it.

As everybody who uses OpenClinica knows, defining your event x
CRF matrix is the most important step in configuring a trial. When a
client comes to us with a new trial, we do just that. We are careful
to reproduce the anticipated flow of events and patient groupings
just as designated by the trial’s specifications. “Why bother?”
you’re probably asking. “You’re just a subcontractor. That’s not your
concern.” But it is. Invariably, specimens get mislabeled and
inappropriate tests get ordered, and we’re able to detect many such
mistakes by doing a quick visual inspection of OpenClinica’s patient
x event dashboard with its easy-­to-­take-­in iconification. We feel
that this double-checking is part of our service to the sponsor.

CRF design is our next consideration. In this case, we don’t
try to reproduce everything required from the sponsor’s point of
view. Instead, we design a set of CRF’s that reflects just our role
as a contract clinical laboratory. This means that our CRF’s are far
more narrowly focused and less complicated. But it also means we
include some unique types of fields for pricing, specimen archiving
and the like, items that a trial sponsor usually doesn’t need to
address in their CRF’s but which are very helpful to us.

We are very careful how we name our items when crafting our
CRF’s. Specifically, we use the same terminology across our trials
whenever possible. For instance, the field for a specimen’s accession
number is always named ‘accession_number‘. Likewise, we consistently
use the names ‘freezer‘, ‘received_date‘, ‘price‘, ‘shipping_deviation
and ‘%assay_date‘ (where % is the wildcard string).

Using such a controlled vocabulary is vital in our case because
we use a separate installation of OpenClinica for each study and
employ the postgresql contrib module ‘dblink’ to federate their
attendant databases for querying. A helter­skeleter vocabulary would
render the latter problematic, to say the very least.

For example, we wrote a federated database procedure we call
accessions(). When executed, it consults the accession_number field
in all our installations and returns the number of accessioned
specimens broken down by trial name. This table lists some of the
federated procedures we’ve developed and their functionality.
Collectively, they provide us with a real­time, global snap­shot of
our work­flow and freezer contents.

Because OpenClinica is web­-based and has finely grained user
roles, our clients can remotely log into their respective
installations at our site with read­-only privileges and see the
status of their specimens whenever they want. Conversely, when we
think a specimen has been mislabeled or have some other issue, we can
call a client and direct them to a particular URL displaying the
pertinent information and seek clarification. OpenClinica thus
becomes a shareable laboratory notebook between us and our clients.

The bottom­line: OpenClinica works for Geneuity. Because
OpenClinica is open source, elegantly designed and well documented,
we are able to tailor the application to our needs. In the spirit of
mutual collaboration and aid fostered by OpenClinica’s lead
developers at Akaza Research, we’re making our federated procedures
freely available. They can be downloaded here.

OpenClinica 2.5 is Here!

It is with great excitement that I can finally say the production release of OpenClinica 2.5 is here! It took a lot of hard work and dedication not just from our developers, but our testers and community contributors as well.

Please go here to download the latest and greatest offering of the preeminent open source application for electronic data capture and clinical data management. You will need to have an account on to download it.  If you don’t have one you can register for one.

In the download package you will find installation scripts for both the Oracle and PostgreSQL databases on both the Linux and Windows operating systems. In addition, for folks currently using version 2.2.1 or 2.2.2, there are scripts to upgrade your instance to OpenClinica 2.5.

Everyone will be able to experience the robust new features of the application including Bulk Data Import, Improved Query Management and Resolution, Cross Form/Cross Field Edit Checks, and Editing/Copying Datasets. Also, we have removed the need for a nightly data warehouse script to run and now you can extract data in real time.

Please join Akaza Research on October 7th for a free webinar introducing OpenClinica 2.5. You can sign-up here:

Webinar @ 19:00 – 20:30 (GMT -5:00)
Webinar @ 9:30 – 11:00 (GMT – 5:00)

Of course we’d highly recommend attending a training course so you too can become an expert user of OpenClinica. Our first open enrollment training on OpenClinica 2.5 is being offered October 15-17.

Thanks again to everyone for making this release a success!

– Paul Galvin

OpenClinica 2.5 – the final countdown!

OpenClinica 2.5 has been going through rigorous testing over the last few months and we are finally getting close to releasing a production ready version of the application.  There are currently 2 betas and 1 alpha available to the community, but shortly we will be having a Release Candidate available that has been subjected to full, rigorous testing procedures.

This Release Candidate will also contain scripts that will allow OpenClinica to run on the Oracle 10g database for the first time as part of a downloadable package.

As you can see below in another post about the release of 2.5, I mentioned it would be on August 29th.  Mea culpa. Clearly, however, it is more important to issue a software product that has been fully tested (and retested) rather then putting a marginal product out just to meet a date. If only Microsoft realized this 🙂

The release candidate will be available to the general public on Wednesday morning, 9/10/2008, and we will be targeting a full production release within the coming weeks.

As we get closer to the production release, please check back for more updates. In the meantime here’s some Final Countdown inspiration from Europe.

Why Open Source is Good for International Health Research (and Everyone Else)

A recent article titled, “Could an Open-Source Clinical Trial Data-Management System Be What We Have All Been Looking For?”, published in PLoS (Public Library of Science) proposes that “international health research organisations combine their efforts and spending power and assist with the development of systems that are open to all.” This is a bold statement with, in my opinion, solid rationale.

The authors, Greg W. Fegan and Trudie A. Lang, manage numerous clinical trials for the Kenya Medical Research Institute–Wellcome Trust Collaborative Research Programme in Kilifi, Kenya. Like many other research organizations in developing countries, their work largely focuses on finding treatments for “neglected diseases” such as malaria, hookworm, and encephalopathies. They clearly communicate the inability for proprietary eClinical software to be a widely useable solution in such settings due to costly and restrictive licensing. 

However, Fegan and Lang define the appeal of open source as something greater than financial savings (although this is a strong motivation). In addition to freedom from license fees, open source clinical trial software built with open components and open standards is more “modifiable and amenable for use with existing software already employed.” Perhaps the most significant point made is that open source can be a more powerful way to promulgate standards and better leverage the collective efforts of disparate research institutions.

Indeed, the authors also point out that the impact of a well designed and supported open source eClinical system “can be beneficial to all clinical researchers” and urge “international health research organisations to combine their efforts and spending power and assist with the development of systems that are open to all and truly fit for purpose.”

The paper closes with the following call to action:

“Research organisations and funders should combine efforts to produce an open-source solution for trial data management. A shared platform could then be easily established, and would bring wider benefits such as electronic submission to regulators, automated sharing of data, and contribution to important public databases such as pharmacovigilance and drug-monitoring registries.

We believe that an open-source approach to a truly designed-for-purpose data-management system for clinical trials is attractive. Such a system would save money by eliminating the reliance on the use of expensive database software systems and their administrators. This would empower and enable a wider variety of people to conduct trials, as the question of capturing, cleaning, and extracting data would not be overly daunting or expensive. This point is significant, as it may encourage more investigators in resource-poor settings to take part in high-standard research that would otherwise be out of reach and beyond their capacity. Surely this would increase the scope and variety of trials that are conducted. Our hope for this article is that it will begin a debate on this topic, and lead to a concerted effort to lobby the international research and donor community to make sure this barrier to trial conduct is understood and addressed.”

I encourage you to read the full article online at the PLoS website.

An open source Elelctronic Data Capture (EDC) system? Really?

Back in 2004, when I would tell people about our open source electronic data capture (EDC) technology and our open source business model, I got a lot of crazy looks and confused reactions.

Fortunately, these days there is a much greater understanding in our industry of what open source software is and for the significance of its ability to solve core problems that proprietary software cannot. However, we still have to try very hard to make sure our users understand what is different about open source and what they should expect. Over the course of my next few posts I’ll explore some aspects of how open source matters in clinical research informatics. Some of the ideas I’ll be exploring include (note this list may change, don’t hold me to it):

  • Validation and Compliance
  • Security
  • Support and reliability
  • Customization
  • Cost

iPhones for Electronic Data Capture in Clinical Trials?

Could it make sense to use iPhones for electronic data capture in clinical trials? On a whim some folks at our office decided to try using OpenClinica from their iPhones. We were quite impressed with the results and found the application works very well as is from this device. See for yourself!

CDASH: A new way to standardize data elements

Many people who work with EDC systems have heard of or been impacted by CDISC, Clinical Data Interchange Standards Consortium.  CDISC’s mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare.  They have many different initiatives, but one of their newest ones promises to aid the development and use of electronic Case Report Forms (eCRFs), the foundation of an EDC system.

Clinical Data Acquisition Standards Harmonization, (CDASH) aims to standardize ways of collecting data in a clinical trial.  The current EDC landscape has hundreds, even thousands, of different eCRFs that capture essentially the same information, but with CDASH’s initiative one common data element can be used for each piece of information collected.

The initiative is not being pushed to enforce the way an eCRF looks and feels; rather, it seeks to standardize the way the fields and data on a form map to a database.  Allowing users to create eCRFs with one standard in mind will allow the users to re-use their work again and again rather than having to create new eCRFs the next time they begin a study.

By mapping OpenClinica CRFs to CDASH content standards (element name, definition, and the related metadata) users of OpenClinica can access a basic set of global data collection fields with semantics agreed upon by representatives from Contract Research Organizations (CROs), Academia, Government and Industry.  These CRFs can be found in the OpenClinica Enterprise CRF Library.

Portability: the next frontier in electronic data capture?

Recently, the company Clinical Ink announced their upcoming software release.  Using tablet PCs with proprietary software, they will allow EDC to take place on digital tablets “that retain the look and feel of traditional paper data collection forms.”  This sounds familiar, as we’ve been working on the same thing with our CRF templates to load form metadata into OpenClinica.

Also recently, George Laszlo blogged about the Nextrials Prism system, as seen through the Apple iPhone.   Boston-based PHT is porting their patient diary software to the Samsung Ultra Mobile PC.

Of course, the common thread here is portability.  Everyone wants their electronic data capture app to work in real-time, where the doctor is, where the patient is.  Which is, in effect, changing the game for applications in terms of user interface and the ability to run in a portable environment.

The thing about portability is that it’s not just a closed-sourced game; Apple is releasing their SDK for developers to work on their own apps for the iPhone.  Google is in the process of hyping their Android project together with the Open Handset Alliance, which is an open and free mobile platform.

In short, OpenClinica has several options for becoming a portable competitor to the above; since it runs in Java, its “write once run anywhere” architecture allows it to run on different OSes.  Since it runs through a web browser, users can already set it up to run through a handheld PC running a web browser.  In the future, the challenge to OpenClinica will be to evaluate the open SDKs and determine if there’s room to create a slimmed-down interface suitable for the smaller screens and simpler interfaces of the portable workforce.

Electronic Data Capture (EDC) Spending on the Rise

Health Industry Insights, an IDC Company, recently published a new forecast of the domestic market for electronic data capture (EDC) software. The report titled, “U.S. Electronic Data capture 2006-2011, Spending Forecast and Analysis,” predicts that spending on EDC solutions will total more than $3.1 billion by 2011. This represents an average annual market growth rate of about 15% between now and then.

It is interesting to consider some of the primary factors that are likely driving this trend:

  1. New products to fuel growth. As pharmaceutical companies’ blockbuster drugs run off-patent there is a dearth of candidates waiting to replace them. As a result, many of the large pharma companies will be forced to put their sizeable cash stores to work in the form of increased R&D expenditures and/or acquisitions of smaller firms. Either way, this funding should result in more clinical research. 
  2. EDC is finally a “proven” technology. While once fairly commonplace, stories of failed EDC implementations seem to have become increasingly rare. It seems that EDC is finally delivering upon its promise to enhance the productivity and ROI of clinical studies. With EDC no longer considered a bleeding-edge approach to clinical trials, the level of EDC adoption is starting to look more like an S-curve. According to IDC, “approximately half nearly half of all new Phase I-III studies are now initiated using EDC.”
  3. The globalization of clinical trials. As clinical trial sponsors are driven to control costs and speed discovery, they are partnering with CROs on an increasingly larger portion of their studies. As a result, the CRO industry has been exploding. As competition in the industry increases, these organizations increasingly look towards EDC systems to help make themselves more efficient and deliver higher quality data to the sponsor within a shorter timeframe.

There are invariably other factors driving the growth of EDC, such as the expansion of adaptive trials and increased maturity and expectance of independent standards such as those promulgated by CDISC (Clinical Data Interchange Data Standards Consortium). The intersection of these factors is creating an exciting time in the eclinical industry and 2008 promises to be a dynamic year for new developments and market changes.