OpenClinica Web Services Tutorial Videos

OpenClinica’s web services layer provides a powerful mechanism for programmatic data interchange between OpenClinica and other systems. Below are the first two videos in a series of tutorials on working with web services. The videos are created by Hiro Honshuku, including the background music! Thanks Hiro!





The OpenClinica Platform – Developer Round Table Discussions

OpenClinica is a clinical trial software platform that aims to provide data capture, data management, and operations management functionality to support human subjects-based research. It can be used for traditional clinical trials as well as a wide variety of other types of human subjects-based research.

Our vision for the product is to provide data capture, data management, and operations management functionality out-of-the-box, in an easily configurable, usable, and highly reliable manner. The underlying platform should be interoperable, modular, extensible, and familiar – so users can solve specific problems, in a generalizable way.

This past spring, the development team here at OpenClinica, LLC held a series of round table discussions about how this vision is reflected in the product. Our goals were to learn critical standards and information models needed for our technology to truly reflect this vision, to develop a consistent, shared vocabulary for the problem domain and the OpenClinica technology, and identify the most urgent opportunities to put these lessons into practice in the product and the community. In particular, we spent a lot of the time in these discussions about how OpenClinica’s use of the CDISC Operational Data Model helps enable this vision.

The discussions were invigorating and thought-provoking. We’ve recorded them to share with the greater community of OpenClinica developers, integrators, and others who want to better understand how the technology works, the design philosophy behind it, and where we’re going in the future. The videos are embedded below.

But before getting to the videos, here’s a bit more background on how we think about OpenClinica as a product and a platform.

First, OpenClinica functionality should be ready out-of-the-box, easily configurable and highly usable. Some of the most important features include:

  • Data definition and instrument/form design with no or minimal programming
  • Sophisticated data structures such as repeating items and item groups
  • Support for a wide variety of response types and data types (single select, multiple choice, free text, image)
  • Data management and review capabilities (including discrepancy management and clinical monitoring) with flexible workflows
  • ALCOA-compliant controls and audit history over all data and metadata, including electronic signature capabilities
  • Patient visit calendar design with management of multiple patient encounters and multi-form support
  • Reporting and data extract to a wide variety of formats (tab, SPSS, CDISC ODM)
  • Ability to combine electronic patient reported outcome (ePRO) data with clinically reported data using common form definitions (write once, run anywhere)
  • Deployment via multiple media, mobile or standard web browser

Many of these things have already been implemented, and more are under development.

The core concept around which OpenClinica is organized is the electronic case report form (CRF). In OpenClinica, a CRF is a resource that is essentially a bunch of metadata modeled in CDISC ODM with OpenClinica extensions. It doesn’t (necessarily) have to correspond to a physical or virtual form; it may represent a lab data set or something similar. An OpenClinica Event CRF is that same bunch of metadata populated with actual data about a particular study participant. Thus, it combines the metadata with the corresponding item (field) data, with references to the study subject, event definition, CRF version, and event ordinal that it pertains to. In this conceptual view of the world, CRFs (as well as CRF items, studies, study events, etc.) are resources with core, intrinsic properties and then some other metadata that has to do with how they are presented in a particular representation. Built around these core resources are all the workflow, reporting, API, security, and other mechanisms that allow OpenClinica to actually save you time and increase accuracy in your research.

Second, OpenClinica should be interoperable. The ultimate measure of interoperability is having shared, machine readable study protocol definitions, and robust, real-time, ALCOA-compliant exchange of clinical data and metadata that aligns with user’s business processes. It should be easy to plug in and pull out or mix-and-match different features, such as forms, rules, study definitions, report/export formats, and modules, to transport them across OpenClinica instances or interact with other applications. Establishing well defined methods and approaches for integration into existing health data environments is a key goal of interoperability.

Third, OpenClinica should be modular and extensible. OpenClinica already provides some of the most common data capture and data management components and aims to have a very broad selection of input types, rules, reports, data extracts, and workflows. However OpenClinica developers should also have the freedom to come up with their own twist on a workflow, module, or data review workflow and have it work easily and relatively seamlessly with the rest of OpenClinica. User identification, authentication, and authorization should be highly configurable and support commonly used general purpose technologies for user credentialing and single-sign-on (such as LDAP & OAuth).

The CRF-centric model allows us a great deal of flexibility and extensibility. We can support multiple modalities, with different representation metadata for rendering the same form, or perhaps the shared representation metadata but applied in a different way (i.e. web browser vs. mobile vs. import job). We can address any part of the CRF in an atomic, computable manner. This approach has been successfully applied in the Rule Designer, which takes the ODM study metadata and allows browsing of the study CRFs and items, with the ability to drag and drop those resources to form rule expressions. Features such as rules and report/export formats are represented as XML documents. These documents define how the features behave in standardized ways so that one rule can, say, be easily replaced with another rule without having to modify all the code that makes use of the rule.

Finally, OpenClinica aims to be familiar in the sense of allowing data managers, developers, statisticians to work in a design/configuration/programming environment that they already know. Programmers don’t all have the same experience, and it would be somewhat limiting to force OpenClinica developers to all use the same language (Java) that OpenClinica was written in. We are constantly looking at ways to make it possible (not to mention reliable and easy!) for users and developers to interact with and extend OpenClinica in a programmatic way. This can mean anything from data loading to more meaningful integrations of applications common to the clinical research environment. As proponents of open, standards-based interoperability, our starting point is always to develop interfaces for these interactions based on the most successful, open, and proven methods in the history of technology – namely the protocols that power the World Wide Web (such as HTTP, SSL, XML, OAuth 2.0). They are relatively simple, extensively documented, widely understood, and well-supported out of the box in a large number of programming and IT environments. On top of this foundation, we rely heavily on the wonderful work of CDISC and the CDISC ODM to model and represent the clinical research protocol and clinical data.

Session 1:  from 30-March-2012 (start at the 5 min 20 sec mark)

Session 2:  from 06-April-2012 (start at the 1 min 25 sec mark)

Session 2a:  from 20-April-2012

Session 3:  from 27-April-2012

Session 4:  from 11-May-2012

OpenClinica Exhibiting at DIA China Conference (May 20-23, Shanghai)

OpenClinica is exhibiting at the Drug Information Association’s 4th Annual China Meeting, May 20-23 at the Shanghai International Convention Center.

The environment for clinical research is rapidly evolving in China. This theme of this year’s event is “collaboration and innovation in China.” Sessions features numerous topics related to China and global pharmaceuticals.

Stop by the OpenClinica booth to learn about how OpenClinica is leading the way for modern, more effective clinical research in China.

OpenClinica at Society for Clinical Trials Annual Meeting (May 20-23, Miami)

OpenClinica will be both exhibiting and presenting at this year’s Society for Clinical Trials Annual Meeting, May 20-23 in Miami. Come by the OpenClinica booth to introduce yourself and learn about the many exciting things happening within the OpenClinica software and community! On Wednesday, May 23, OpenClinica’s, CEO, Cal Collins, will lead a presentation showcasing an innovative new OpenClinica mobile data capture technology. The session is titled “Electronic Patient Reported Data for Risk Screening in Primary Care Clinics using OpenClinica and CDISC ODM.”

Breaking Barriers: Forging a New Model for Clinical Development

Could the principles of open source and open innovation transform the future of clinical research? Come hear thought leader and innovator Dr. Tomasz Sablinski deliver the keynote presentation titled “Breaking Barriers: Forging a New Model for Clinical Development” at the 2012 OpenClinica Conference on April 23rd in Boston.

The world has shown that it is possible to harness the power of crowds to deliver incredibly successful innovation and services (think Facebook, Wikipedia, Linux). However, this style of innovation is relatively absent within the domain of clinical research. Sablinski believes the time may be ripe to borrow from the principles of open source and telemedicine in order to create a new, more effective model for clinical development.

Dr. Sablinski’s ideas have profound implications. However, while bold and thought provoking, they are more than academic. He puts his money where his mouth is–Sablinski’s start-up company, Transparency Life Sciences, has set out  to increase the efficiency of clinical development leveraging open principles that turn much of the current way of thinking on its head.

Dr. Sablisnki’s assessments of the current state of clinical development are based on over 30 years in the field, as a practicing physician, basic researcher, drug developer, investor,  and now, entrepreneur. He has served as a researcher at Harvard Medical School, a Medical Director at Parexel, VP of Clinical Development at Novartis, and Head of Development and Managing Director at private equity firm Celtic Therapeutics.

We look forward to hosting Dr. Sablinski at this year’s OpenClinica Global Conference!

– Ben Baumann
Chair, OpenClinica Conference Committee

Setting up an OpenClinica User Group

This past November I gave a presentation about OpenClinica at the Association Francaise de Data Management Biomedical (“DMB”) annual conference in Paris. DMB is essentially the French equivalent of the Society for Clinical Data Management here in the U.S. The event was well run, full of useful content, and had about 200 attendees.

I was particularly impressed to see a strong level of OpenClinica interest and usage among both attendees and exhibitors. Some people I met there voiced interest in forming a French OpenClinica users group and asked me what I thought. Naturally, I think the idea is an excellent one! Such a group could be useful in a number of ways, such as for sharing tips and best practices, stimulating collaboration, and identifying service providers.

If you are interested in forming a user group, go for it! You certainly don’t need anyone’s permission, but we’d be happy to publicize it and help in other ways where possible. I believe our community is most productive when we empower our colleagues to do things like this. In addition to being geographically based, a “user group” could be defined along other lines, such as type of research, etc. Groups could meet virtually, face-to-face, or both.

Have an idea for a users group? Looking for potential user group members? Post your comments and feedback here. Also, a great place to carry on this discussion is in the OpenClinica users email forum (users@openclinica.org).

All the Best,
– Ben Baumann
OpenClinica, LLC

Three Things I Learned About Export Job Performance From My Uncle Paulo

1. “Realize you can try to do it all…but you’ll do it slowly, very slowly.”

It’s understandable that there may be a desire to export every single dimension, for every CRF in your study, for all time. However, if that export takes 15 hours, then a job starting during off-hours may impact users the next business day, or worse, users in an alternate time-zone who may just be starting their work day.

It’s better to first get a sense of how long a small subset (e.g. reducing the temporal scope to a month) of data will take, manually, and take the elapsed time for the export to complete and multiply by the scope quotient (i.e. estimated total scope divided by reduced scope) to figure out a rough estimate of how long your export may take.

2. “Those temporal scope fields are your friend.”

If you don’t choose a temporal scope for your dataset, you will get data for a wider timeframe than you’re likely to be alive. This is may be fine for a dataset with a few dimensions, or if you happen to be looking for specific data you aren’t sure you may capture accurately with too narrow of a time scope.

However, if you KNOW what the scope is, you should specify this. This is more important with very large dataset. Breaking the dataset down into smaller scoped datasets will give you the flexibility of manageable chunks of data to schedule for export.

3. “Let your jobs breathe.”

You wouldn’t schedule two appointments, one after the other, if you didn’t know what time the first appointment would end, would you? The same idea applies to scheduled export jobs. While there’s nothing inherently wrong with scheduling one job after the other, you can only get away with this when you have a clear sense of when the first job may end. If you don’t have any idea when the first job may end, while the first job may complete successfully, the second will not if it is overrun by the first. When in doubt, give your jobs enough time to complete, by spacing them out.

Remember, it’s better to measure twice, and cut once. (My uncle Paulo didn’t actually say this last one.)

– Tope Oluwole

Growing the Community

A recent discussion on the OpenClinica users mailing list centered around making OpenClinica more optimal for small, low-budget academic research studies, and how open source community participation is helping OpenClinica to meet those users’ needs.

Regarding OpenClinica’s target audience: OpenClinica is used in a tremendous variety of studies and organizations. Many of these are paying customers of OpenClinica LLC (f/k/a Akaza Research) who are running large GCP compliant, multi-site clinical trials. Clearly we as a company have an obligation and incentive to support them and provide software that fits their needs.

But I also am committed to making OpenClinica (the technology) successful and widely used. We want OpenClinica to power as many studies as possible, both small and large. If you’re determined to scratch down some data into Excel I won’t stop you. But since you’re reading this you likely know the arguments against doing so, and want a more robust solution for capturing and managing your clinical research data. We want lots of OpenClinica researchers, entrepreneurs and service providers to thrive in a growing ecosystem. If you are a researcher with no budget and you need OpenClinica to do X, me and my staff are ready and willing to prioritize getting feature X into a release if we have meaningful participation from community members to get that feature designed, coded, documented, tested, etc. Every participant in the OpenClinica community has the ability to make those contributions and/or to mobilize community participation to get their feature defined and developed. It’s not benevolence or volunteer work – with open source software the benefit you get out is proportional to the investment you put in.

There are growing examples of this participation. But more is needed to truly realize OpenClinica’s potential. As a community, we need to ask: (1) How do we grow participation? (2) How do we make it easier to participate? and (3) What can you contribute?

Clinical Trials in the Cloud

I got a phone call the other day from a longtime OpenClinica user about the announcement of our new OpenClinica Optimized™ Hosting. He remarked on how leading companies in the industry (including his) are making big investments in cloud computing products and services, because these technologies provide easy-to-access functionality on an infrastructure that is more redundant, scalable, and cost-effective than you could hope to build or buy on your own.

However, in the clinical research field, putting together such an offering is not for the faint of heart. Though our free OpenClinica Community Edition has been installed and run by users on cloud servers for years, our OpenClinica Enterprise Edition offering (which carries regulatory guarantees) would have to meet rigorous reliability, security, and regulatory compliance requirements. How can this be accomplished if you don’t actually know where your data physically resides at any point in time on the cloud?

Prior to the launch of Optimized Hosting, we offered each hosted customer a dedicated server or two server (application + database) setup. This provided a certain peace of mind from knowing that your clinical data lives on a dedicated piece of hardware, but for many the costs were high and suffered from the inherent limitations of being tied to a physical machine. At the end of last year our data center partner achieved SAS 70 Type II certification for their cloud services, and we decided it was time to begin diligence on a cloud-based offering for OpenClinica.

We have spent the past 9 months listening to our customers’ needs and concerns, a designing and testing a solution. The resulting OpenClinica Optimized™ Hosting is an innovative hybrid architecture that provides the best of both worlds:  the scalability, high availability, and flexibility of the cloud combined with the peace of mind that your data lives in purpose-built dedicated hardware.Clinical Research in the Cloud

In short, OpenClinica Optimized Hosting offers greater fault tolerance, with better scalability and performance, at a lower cost than alternatives. Here’s how it works:

Application

Each OpenClinica application instance is a cloud server cloned from an image that has been qualified according to our exacting installation instructions. We configure the instance according to the customer’s supplied configuration parameters and complete operational qualification (OQ). The instance is typically available and ready for production use within a day or two. Thanks to the cloud, computing resources are instantly scalable on-demand.

Database

Dedicated (non-cloud) high performance database machines are configured in a master/slave relationship to provide instant data replication and fault tolerance. By utilizing multiple slave databases located in different geographic regions, the OpenClinica Optimized Hosting database cluster is designed for zero data loss even in event of nuclear strike. The servers use the fastest hard disk technology available today (Fusion-io®), dramatically improving database performance. For example, in our testing, we commonly see data extracts run up to 10x faster than in the prior environment. Database servers are physically isolated via CISCO ASA firewall to eliminate all nonessential access credentials.

Validation and Compliance

OpenClinica Optimized Hosting provides maximum flexibility and transparency in the area of change control and compliance. It has been constructed around a carefully designed set of controls to ensure all updates are fully tested (and documented) in the environment prior to release, and that customers can have upgrades and maintenance releases applied according to their individual schedules and priorities.

One of the great advantages of OpenClinica is the choice it offers – you can use and extend the open source licensed code, you can choose between OpenClinica Community Edition and OpenClinica Enterprise, you can deploy it locally or choose the hosted option. Or, any combination of the above. The new Optimized Hosting environment enhances that choice by providing a fast, reliable, and cost-effective way to get up and running with OpenClinica.

For more on security in OpenClinica Optimized Hosting, see Clinical Trials in the Cloud – Part II.

– Cal Collins