OpenClinica 3.1 is Finally Here!

After nearly 20 months, OpenClinica 3.1 is finally ready to meet the world as a production ready application.  You may download OpenClinica 3.1 here.  It has been a long and arduous road, but the final incarnation of 3.1 is the most significant leap forward for the OpenClinica clinical trials software.

OpenClinica 3.1 further accelerates clinical productivity and enhances the clinical trial experience in a number of notable ways:

  • Improved data entry save time and increased performance for accessing large amounts of data.  The architecture around the data entry process in OpenClinica was re-factored to allow more concurrent users accessing the system while conducting more intensive simultaneous processes.  With this re-factoring, page turn times have seen a 10x (and sometimes better) speed improvement.  At the same time, large extracts which had to be broken into smaller subsets in the past can now be executed in a single batch.
  • Skip logic to ensure data entry users only see CRF fields and sections relevant to entering their data.  When a user accesses an eCRF to enter data for a patient or subject, they will only see the fields pertinent to be collected at that time.  Logic can be built in to the eCRF to show or hide additional fields based on the values provided in previous questions.
  • Streamlined discrepancy and query management infrastructure that allows issues around questionable data to be resolved more quickly.  A new interface for creating and responding to discrepancies, as well as new filters for query aging, to support faster resolution of data issues.  The number of clicks for filtering/sorting discrepancy notes, viewing the data responsible for the discrepancy note, and returned back to your filtered set of reports has been cut in half.
  • GUI-based creation, testing, and management of complex cross field/cross form multivariate edit checks.  A simple drag and drop interface has been implemented to facilitate the faster creation of complex edit checks.  This new interface interacts with authorized OpenClinica instances to speed up the study design process for OpenClinica Enterprise edition clients.
  • Plug-in architecture for exporting data collected in OpenClinica which supports the transformation of data into any output format.
  • OpenClinica Data Mart to easily report clinical trial results collected through OpenClinica.

These last two items have been covered extensively in previous blog posts.  Please see Plug-in Architecture for OpenClinica Data Extracts and Video Demo of New OpenClinica Data Mart.

We will be hosting an OpenClinica Community Virtual Forum shortly to demonstrate some of these new capabilities.  Also, keep this blog on your RSS feed or bookmarked in your browser, as future posts will dive into more details of the new features and functionality in OpenClinica 3.1.

– Paul Galvin

OpenClinica 3.1 Release Update

We are in the final development stretch of the OpenClinica 3.1 project.  Over the course of alphas and betas some items have been inevitably been added, removed, and changed, so I thought it would be useful to provide an up-to-date list of features and bugs that are being addressed in this release.

Those of you attending the OpenClinica Global Conference May 8-9 here in Boston will get to experience numerous demonstrations of 3.1 functionality, and of course get to interact directly with members of our rockstar development team 🙂

First, here’s a quick review of some of the more popular new features:

  • Dynamic items in a CRF
    • Supports showing and hiding of items based on values provided in a separate field
    • Supports insertion of data across fields and CRFs based on values provided in a separate field.
  • Re-factoring of the Extract Data module to support custom data transformations allowing you to extract data in essentially any conceivable format.
  • Improved capabilities for sharing data entry duties among a given site’s users
  • Discrepancy Note “Days Open” filter to better monitor discrepancy aging
  • Discrepancy Note “Days Since Updated” filter to ensure productive discrepancy resolution
  • Audit log and discrepancy note data included in ODM exports
  • Improved CRF page turn time (in many cases over 10x faster)
  • CRF Header updates to provide a cleaner data entry experience
  • Ability to assign Failed Validation Checks (in addition to Queries)
  • Relative Paths for Item OIDs in Rules to enable portability and reusability of Rules
  • Discrepancy Note flag colors now appear in the CRF
  • Additional study parameter configuration options to opt out of using certain fields such as Interviewer Name, Interview Date, and Location
  • OpenClinica Datamart for ad-hoc reporting (Enterprise only)
  • GUI Based, drag-and-drop Rule Designer (Enterprise only)

More detailed descriptions of the above features can be found in the previous blog posts “OpenClinica 3.1 (project “Amethyst”) Preview” and “New Capabilities Added to OpenClinica Version 3.1.”

For those sufficiently ambitious, yes, you can see a complete list of ALL the 457 separate enhancements and bug fixes in 3.1 as of April 6, on the OpenClinica Amethyst Project Roadmap.

And finally, here’s the current release timeline:

  • Beta 4 released week of April 11th
  • Release Candidate 1 released week of April 18th
  • Production Release of OpenClinica 3.1 early May.

Many thanks to the dedicated team of folks who, for the past 19 months, have worked tirelessly to make this the most significant OpenClinica release ever.

– Paul

New Capabilities Added to OpenClinica Version 3.1

For the past 12 months, the OpenClinica development team has been working diligently on the next major OpenClinica release. In a prior blog post (OpenClinica 3.1 (project “Amethyst”) Preview), I discussed some of the new functionality and key improvements this forthcoming release will include. Since then, the development team has added some more pieces of functionality, most notably:

  • Re-factoring of Extract Data to enable custom data transformations
  • Discrepancy Note “Days Open” filter
  • Discrepancy Note “Days Since Updated” filter
  • CRF Header updates
  • Additional study parameter configuration options
    • Interviewer Name – not used
    • Interview Date – not used
    • Location – not used
  • OpenClinica Data Mart for ad hoc reporting*
  • GUI-based Rules designer*

Custom Data Transformations

From a development perspective, perhaps the most significant piece of functionality in the above list is the complete re-factoring of the Extract Data module. In prior versions of OpenClinica, the Extract Data module would natively export CDISC ODM 1.2, CDISC ODM 1.3, both ODM 1.2 and 1.3 with OpenClinica extensions, tab-delimited text, and an SPSS file format. While these formats will continue to be available in 3.1, OpenClinica will have the ability to process (via XSL style sheets) any CDISC ODM 1.3 data set into any other data format.

This new XSL method of extracting data from OpenClinica opens up a new world of formats in which data may be obtained from OpenClinica. To create a new extract format, all one has to do is configure a new XSL style sheet. Organizations can write their own XSL style sheets then configure a file called extract.properties that allows OpenClinica’s XSL transformation engine to convert the data in the ODM XML file into the organization’s desired format.

GUI-based Rules Designer*

The GUI-based Rules designer is a project currently underway that allows users to build cross-field/cross-form multivariate edit checks without having to interface directly with XML. Its intuitive, drag and drop interface hides much of the current complexity in creating and managing Rules, while retaining the system’s robust capabilities in this area. Users will be able to work directly with the Item Names as defined in a CRFs definition, eliminating the need to keep track of OIDs.

OpenClinica Data Mart*

The OpenClinica Data Mart presents clinical data from OpenClinica studies in a readily-accessible relational database for ad hoc reporting and analysis. The Data Mart enables data managers, project managers, and researchers to create reports and mine data using standard business intelligence software or SQL reporting tools

Beta Timeframe

We currently expect the first Beta of 3.1 to be available towards the end of November. This Beta will be feature complete, and blocking issues that prevent the testing of new features will have been resolved. Once the first Beta is released, we will begin the 3.1 Pilot Program. We currently have 10 organizations participating in the Pilot Program, but if your organization would like to volunteer as well please contact me.

Please be sure to check back the OpenClinica Blog often as I post future updates on the 3.1 timelines.

– Paul Galvin, OpenClinica Project Manager

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*Both the GUI-based Rules designer and Data Mart will be Enterprise only applications and will not be part of the publicly released 3.1 Beta.

OpenClinica 3.1 Release Timelines; Call for Pilot Program Participants

Last week I wrote about a few new features that will be part of the forthcoming OpenClinica 3.1 release and promised some information about when we expect to make different phases of the application available. Here is the release timetable we are currently targeting:

  • Alpha Release – June 21st, 2010
  • Beta I – July 9th, 2010
  • Beta II – August 2nd, 2010 (OpenClinica 3.1 Pilot Program)
  • Beta III – September 1st, 2010
  • Production Release – End of September/Beginning of October

The first Alpha release will contain, among other items, the following features mentioned in my previous blog post:

  • Dynamics (Show/Hide/Insert Actions)
  • Relative paths for OIDs
  • Multiple site level users accessing a CRF before it is marked complete
  • Modularization
  • Audit Log and Discrepancy Note Data with ODM Export
  • Discrepancy Note Flag Colors

We will try to also provide some concrete instructions on how to use each of these features before the Alpha is released. Updates to these instructions and additional documentation will be generated after the Alpha has been made available for downloading.

3.1 Pilot Program

As in prior releases, we will be conducting a Pilot Program with selected interested organizations. If you are interested in participating in the OpenClinica 3.1 Pilot Program (or just want more information about it), please send an email to contact@akazaresearch.com.  The Pilot Program is designed to give organizations an opportunity to test out new features of OpenClinica and provide valuable feedback on how the features are working. It was very successful prior to releasing 3.0 where 10 participating organizations received help and support from Akaza while experiencing and learning the new product features firsthand.

– Paul Galvin

OpenClinica 3.1 (project “Amethyst”) Preview

The next major milestone for OpenClinica (project code-named “Amethyst”) will be OpenClinica version 3.1. While this release contains roughly 85 tweaks, fixes, and enhancements, this post describes some of the more significant enhancements that will be included (check out the Amethyst project roadmap page for a full list—note: openclinica.org login required).

New features in OpenClinica 3.1 will include:

  • Dynamic Items in CRFs
  • Audit Log and Discrepancy Note Data with ODM Exports
  • Assignment of Failed Validation Check Discrepancy Notes
  • Relative Paths for Item OIDs in Rules
  • Discrepancy Note Flag Colors in the CRF
  • Modularization
  • Multiple Site Level Users Allowed Access to an Event CRF
  • Simple Conditions

Dynamic Items in CRFs

OpenClinica 3.1 will support Showing and Hiding of CRF Items using both the CRF template and a Rules file. When a user enters data and saves a CRF section, data fields may be shown or hidden based on value(s) that user provided in one or more other fields on that form. This capability is also commonly referred to as “skip patterns.” A simple example would be a CRF question asking if the patient is male or female. If the value provided is female, a pregnancy related question could then be displayed to the user entering data and all questions associated with males could be hidden from view.

Audit Log and Discrepancy Note Data with ODM Exports

Audit Log data and Discrepancy Note data for a subject will be available in the ODM data extract format with OpenClinica extensions. This will allow the user to have all of the clinical data, audit log data, and discrepancy note data in a single data file.

Assignment of Failed Validation Check Discrepancy Notes

Currently, OpenClinica supports assignment and workflows around only the Query type of Discrepancy Note. OpenClinica’s “assignment” capability will be expanded to also include the Failed Validation Check type of Discrepancy Note. For Failed Validation Checks, the first note in the Discrepancy Note thread will not be assigned, but Data Managers, Study Directors and Monitors will be allowed to assign the thread to a user for review/resolution. OpenClinica will also restrict the Clinical Research Coordinators and Investigators (both site-level users) from setting the status of Failed Validation Checks to Closed.

Relative Paths for Item OIDs in Rules

A new enhancement to Rules authoring will allow the Rule creator to write one Rule Assignment for a particular CRF Item, and have the Rule execute wherever that Item’s OID is used throughout all of the study events. This increases the “portability” of rules, allowing the user to write one Rule, and have it apply multiple times rather than having to author multiple Rules and multiple Rule Assignments.

As an example, a Rule Assignment would need to contain the following path in OpenClinica 3.0.x:

SE_OBSERVAT[ALL].F_GROU.IG_GROU_GROUP_1[ALL].I_GROU_TC_ADV_PRIMARY_05

If the CRF was used in multiple events, the creator of the Rule file would have to specify the path to the other event as well.

In 3.1, all the user has to do is write:

I_GROU_TC_ADV_PRIMARY_05

and the Rules will be executed wherever that Item shows up in the study.

Discrepancy Note Flag Colors in the CRF

OpenClinica 3.1 will include additional Discrepancy Note flag colors that correspond to the various statuses of a particular thread. Currently in OpenClinica, if a Discrepancy Note thread exists, the flag will always display in a red color regardless of the Discrepancy Note status. In 3.1, the color of the flag will be reflect the “most severe” status of any thread that is on a particular item (more than one thread may exist for any item). For example, if there is a Closed thread and an Updated thread on one item, the color of the flag will be yellow representing the Updated status. If there is just a Closed thread, the color of the flag will be black. To support people who are color blind or shade blind (like myself) there will be a roll over when you put your mouse on the flag, showing you the number of threads and each of their statuses when Viewing a CRF.

Modularization & New Web Services

Modularization is defined as a software design technique that increases the extent to which software is composed from separate parts, called modules. Conceptually, modules represent a separation of concerns, and improve maintainability by enforcing logical boundaries between components.

What this means for OpenClinica is we have started to separate the application into multiple pieces. In version 3.1, we have modularized the web application from the web services functionality. This will allow new web services to be developed on separate release timelines from the main web application, facilitating the system’s extensibility.

In addition, we are release some web services with 3.1, (these were contributed by Colton Smith of Geneuity and openXdata):

  • CRF Data Import
  • Retrieve a list of studies
  • Retrieve a list of events and their CRFs
  • Retrieve a list of subjects and their events

Multiple Site Level Users Accessing an Event CRF

OpenClinica 3.1 will allow different site level users access to an Event CRF, even if they are not the conceptual “owner” of that CRF. In prior versions of OpenClinica, once a user began data entry in a CRF, the system prevented other users from adding information or data to the CRF until it had been marked complete. The new feature will allow a second user to continue entering data before the CRF is marked complete.

This change to OpenClinica will also help facilitate the ease of recording adverse events in a separate CRF. A user will not have to mark it complete in order for another user to provide additional adverse events that have occurred for a particular subject. In addition, this new functionality will prevent users from accessing an Event CRF if another user already has the form open. In this case, the second user will receive a message saying that the form is currently being accessed by another user.

Simple Conditions

In addition to the Dynamics capabilities that will be part of 3.1, we have added a feature called Simple Conditions. This feature is similar to Dynamics in many ways, but can be implemented through the CRF Template directly rather than writing a separately Rules XML document.

With Simple Conditions, a person creating an OpenClinica CRF will have the ability to designate Items as “hidden” from the data entry person’s view until a particular option is chosen for another CRF Item. The data entry person will not have to click “save” on the form–instead, as soon as the option is selected, this hidden field will be shown in real time.An example of the type of use case this feature targets, is a CRF question with two fields, one for “race” and the other for “comments” (which is hidden). If the data entry person selects the value of “other” for the race field, the hidden comments field will be display underneath.

Akaza Research is excited about bringing OpenClinica 3.1 to the community! Your comments and feedback are appreciated. Please check back in next week or so for an update on our timelines for Alphas, Betas and a Production release.

OpenClinica Community Virtual Forum

With over 8,000 members worldwide, OpenClinica is leading the charge on bringing professional quality open source software to the world of clinical trials. Many people within the OpenClinica community are interested in ways to influence the development of the electronic data capture and clinical data management system for their own purposes as well as for the greater benefit of the community. I want to briefly point out a little known, but powerful way to contribute by participating in the OpenClinica Community Virtual Forum.

The OpenClinica Community Virtual Forum is a bi-monthly web meeting of OpenClinica users who get together to provide input on new OpenClinica features and functionality and detail their experiences in working with the system. Meetings are kept small and intimate, and topics to the point. The Virtual Forum is oriented towards users of the system, not software programmers. Participants include data managers, study programmers, biostatisticians, and other users from a variety of organizations representing both the industry and academic worlds.

The exchange of ideas and feedback that has occurred in past Virtual Forums has significantly helped to refine the way functionality has been implemented and influence OpenClinica’s short and long term roadmap. In our most recent meeting last November, we discussed Dynamic Logic and received early feedback on the newly released OpenClinica 3.0.

The next Virtual Forum is scheduled for January 19th, 2010. If you would like to potentially participate in future Forum meetings, please send an email to community-forum@akazaresearch.com. For more information about the OpenClinica Virtual Forum, see https://www.openclinica.org/dokuwiki/doku.php?id=publicwiki:virtualforum:start.

OpenClinica 3.0.1 Features Improved CRF Save Times

Akaza Research will be releasing a maintenance update of OpenClinica 3.0, which by itself probably does not illicit much excitement.  Usually maintenance releases only fix small bugs and offer little noticeable improvements to a user’s overall experience.  However,  3.0.1 will offer a dramatic improvement for a user’s experience with regards to the amount of time it takes Rules to run on a CRF.

Users of previous versions of OpenClinica would reach pain points when trying to save data entered onto certain CRFs if the study build had applied very complex Rules on a particular CRF section. For example, if the system had to check more than 10 variables to ensure one particular field had accurate data, the user might experience a save time of 2 or even 3 minutes in some circumstances.  In a test environment, we were actually able to create a scenario where the CRF save time took 19 minutes!

As part of 3.0.1, among other things, we have dramatically improved the save time of a CRF with complex Rules.  For instance, in the extreme scenario utilized in our test environment, we were able to cut the save time from 19 minutes down to 10 seconds.  That is about a 11,400% improvement!  For more typical users who were experiencing 2 or 3 minute save times, this has been cut to 3-5 seconds.

We are committed to improving the performance of OpenClinica, and can even offer faster experiences to the users of the OpenClinica Enterprise Edition.  Please see our website for the differences between the Enterprise and Community versions of OpenClinica.

OpenClinica 3.0.1 will be out next week!

OpenClinica 3.0 Completes Functional Testing; Enters Deployment Testing

OpenClinica 3.0 is almost here! The quality team has successfully completed functional testing and has moved onto the phase of software quality assurance called deployment testing.  Deployment tests cover 8 different target “platforms” that range from a clean installation of OpenClinica 3.0 on a Windows server using Postgres, to upgrades of OpenClinica 2.5 to 3.0 on a Linux machine using an Oracle Database. Of course, we also test on all combinations in between.

Before the production version of the application can be released, it must successfully pass through our Quality System. For those of you familiar with such a thing, all of the testing and documentation that OpenClinica 3.0 is going through will end up generating thousands of pages of “paper” that include user requirements, traceability matrix, and a large set of screenshots which prove the expected results of the test cases did in fact happen.

In addition to the team at Akaza that has invested thousands of hours testing the application, this release has also undergone road testing in our first OpenClinica Pilot Program.  I would like to warmly thank the participants of the program for committing their time and effort in making sure OpenClinica 3.0 is our most well vetted release to date.

Please look for an announcement from me in the coming days of when OpenClinica 3.0 is available for download.

– Paul Galvin, Project Manager

OpenClinica 3.0 Features Preview: Part III

Welcome to the 3rd and final installment of the OpenClinica 3.0 features preview!  This post covers the new Web Services interface that is part of 3.0 and the job scheduler that can be used to automate Data Import and Data Export jobs.

OpenClinica 3.0 allows for programmatic interaction with external applications to reduce manual data entry and facilitate real-time data interchange with other systems.  The OpenClinica web services interface uses a SOAP-based API to allow the registering of a subject and scheduling of an event for a study subject.

OpenClinica provides a WSDL (Web Service Definition Language) that defines a structured format which allows OpenClinica to accept “messages” from an external system. For example, an EHR system could register subjects for a study in OpenClinica without direct human intervention. At the same time, the EHR could also be programmatically scheduling study events for these subjects. More information about the OpenClinica API can be found on the OpenClinica developer wiki.

An early reference implementation conducted by clinical lab Geneuity used the API to create a web service which inserts data programmatically into OpenClinica CRFs directly from laboratory devices. See the post by Geneuity’s Colton Smith below.

Another major productivity tool in 3.0 is the introduction of a Job Scheduler for automating bulk data import and export.  With this feature users can define a job that will generate an export at a specified time interval.  The Jobs Scheduler can also be configured to regularly scan a specific location for CDISC ODM files and run data imports when a new file is available. This feature can be particularly helpful in automating routing functions, such as the incorporation of lab data into OpenClinica from an external system.  The lab data does need to be in a valid CDISC ODM format (this can be accomplished via another great open source tool called Mirth), but it does save a person from entering data in two applications separately.

At time of this post, OpenClinica 3.0 is currently released as a beta3, but the production ready application is soon to follow. The application is passing through the highly rigorous strictures of our quality system (think Navy Seals training for software) and the output will be fully validated and ready of use in roughly a month. Needless to say, I, and everyone else here at Akaza is very excited to be so close to releasing 3.0. It is already quite clear that this release will have a momentous, positive impact on the community.

OpenClinica 3.0 Features Preview – Part II

Welcome to Part II of the OpenClinica 3.0 features! I previously wrote about three of the main features for 3.0, Source Data Verification, new User Interface for navigation in the system, and a new Home Page for each user.

This post is about three additional features: (i) the new Build Study module, (ii) setting the length and significant digits of items, and (iii) the improved performance of the Subject Matrix.

In 3.0,  all the study build tools will accessed from one main page following a task-based approach. There are five tasks available to the user at the outset. Once the user finishes these first five tasks, two more tasks will become available (see image). This allows the complete study from CRFs to event definitions to sites to assignment of users be done all from a single page. There is also a checklist to let the user easily see how many tasks have been completed so they know how much more configuration is needed before the study is ready to start enrolling subjects.

Build Study Page in OpenClinica

OpenClinica 3.0 also allows the creator of CRFs to set the allowable length of  text fields including the number of decimal places a REAL number should be rounded to. This parameter is set in the OpenClinica CRF Template in a new field called Width_Decimal. The user will specify the width and decimal for a particular field which will force the user to enter the most precise data as possible in a CRF. No longer will the system round to the 4th decimal place at all times and allow up to 255 characters in the field if the CRF creator does not want them to. For example, the creator could specify that a field should have no more than 5 digits total with a maximum of 1 decimal place by entering 5(1) in the Width_Decimal column of the OpenClinica template. If the data entry person tried to enter 3.4444 or 678913 they would told the value is invalid.

By providing this functionality, OpenClinica will help the users get their data into SAS and SPSS more easily.

One of the most important and information-rich pages in OpenClinica is Subject Matrix page, and OpenClinica 3.0 provides significant performance enhancements on this page for studies with large numbers of of subjects.  From the Subject Matrix page users can see a snapshot of where the subjects are in the study, schedule a new event, view a subject record, view a subject event, enter data in a CRF and sign a subject’s record without having to navigate to different pages in this system. A number of users were reporting sluggish performance with the Subject Matrix when they had 5000 or more subjects enrolled in a study.

OpenClinica 3.0 utilizes a new table structure that allows users to load the Subject Matrix containing over 10,000 subjects and 15 event definitions in fewer than 5 seconds (this process could take upwards of a minute in previous releases of OpenClinica).

Please feel free to download the Beta version of OpenClinica 3.0 at http://svn.akazaresearch.com/OpenClinica-3.0-distros/.