Schedules and Project Page Redesign
This release introduces a new feature called Schedules along with a redesign to the Project Page.
Schedules and Events
Schedules are used to plan forms that a subject must fill out over a series of events. These events could be a baseline visit, a monthly call, or an initial meeting with the subject. The events are offset by a predetermined amount of days which can be set in the schedule. The first screenshot below displays a schedule which contains four events. The first and last event in the schedule, both of which are visits, require several forms to be completed at that event. Note that schedules now allow a single form to be collected at two distinct events (time points).
The second and third screenshots display two different subjects that are at different stages in each of their schedules. Selecting any of the entered or unentered designs from the subject page will allow the data to be entered or updated. We’re excited to see how our existing projects will leverage the new subject schedules and events, and we will also expand on this in upcoming releases.
Project Page Redesign
The project page has been redesigned into six key components each with a specific use for the project. The project is split into Collect, Explore, Setup, Share, About, and Activity.
The first screenshot reflects Slice’s strong focus on data collection. Our research staff spend most of their time entering various forms for subjects and participants, and will spend most of their time entering and reviewing sheets, and adding new subjects.
The second screenshot allows project managers and data managers the ability to export the data that has been collected in a variety of formats, as well as view preset reports, and create and save new reports.
While project setup is initially important, the emphasis on changing designs, events, and schedules becomes less important throughout the project. The third screenshot shows the setup tab that allows project editors to define exactly how they would like their data to be collected.
The fourth screenshot shows the share tab for the project where users can be added to the project as either an editor or a viewer. While editors can create, edit, and view everything on the project, viewers can only view sheets, subjects, and reports, and can make comments on existing sheets. The share page also displays site members. Site members are identical to project viewers with the small difference that site members can only view subjects and data collected for their site along with making comments on sheets.
The fifth screenshot displays the project documentation that includes includes project documents, news posts, contacts, and customized links. The tab provides additional project resources that a project manager may want the editors, viewers, and site members to view, i.e. MOPs, Study protocols, and other documentation. The links section also provides the project manager to set up links to commonly required reports, or links to other external sites and documentation.
The final screenshot display the activity tab for the project. Activity includes new sheets being created or updated, and comments being made on sheets. Activity provides a quick glance on what has happened on the project over the last week. Additionally, a short one day view of the activity that can be seen from any of the project tabs.
You can view a full list of changes here:
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Week View, Streamlined Filtering, and User Stats
We’ve released an update to Task Tracker that changes the default view that researchers see when they log in to Task Tracker, and also provides easier filtering across multiple views. We’ve also included a user stats page that breaks down a researchers tasks by tag and by project for a quick comparison.
The Week View
As researchers in our group are assigned more tasks, the default month view becomes unwieldy. To address this issue, we have changed the default view in Task Tracker to the Week view. The Week view combines information from a calendar view over the past couple of months along with a list view of tasks underneath the calendar visualization.
Days with a large amount of incomplete tasks are represented by a red background while days with a low number of incomplete tasks are shown with a yellow background. Days with all tasks completed are shown in green. In the screenshot below we can see that there is a large number of incomplete tasks on September 25th. Navigation is given by either clicking on the month name in order to go to the month view, or by clicking on a day to navigate to that particular week.
Advanced filtering has been often requested by researchers. This release combines various requests for filtering by allowing researchers to specify the filters for any view (month, week, day, or list) in Task Tracker. Filters can be set and cleared, and navigating between views will retain the specified filters. Additionally, researchers can copy the url to create bookmarks for their favorite filters and list views.
Task Tracker now provides quick statistics for researchers to provide a quick glimpse at task completion by tag and by project. Statistics are first broken down by tags, and are represented as a combination of completed and incomplete tasks.
Projects also display the breakdown of incomplete tasks, and are sorted by the project with the largest amount of incomplete tasks first to quickly identify projects that are falling behind.
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Okay, maybe the title is misleading; I’m not going to be teaching you how to work Slice. But that’s the exact beauty of it; you don’t need to be taught at all to use Slice. When I was first placed with the Bioinformatics group, I was seated in front of a computer and told to make an account on Slice. Within seconds, my account was activated and I was on my way to exploring this new, sleek, innovative data collecting tool. With no instructions and only data entry experience on REDCap (another data collecting tool), I was told to create a ‘Project,’ create a ‘Design’ (i.e. questionnaire, form), and the ‘Variables’ and ‘Domains’ that came alongside the ‘Design.’ During all this, Mike and Remo were standing behind me, watching me explore Slice and figure out everything on my own.
The greatest thing about this and the group is that while I was working my way through creating this new ‘Design,’ Mike and Remo were behind me discussing all the things they could change to make it more user-friendly, more self-explanatory, and essentially, better. Through detailed documentation, up-to-date archives, open source coding, and even a Twitter, Slice and all other tools made by Mike and Remo are in masterful hands. The group’s transparency and openness to feedback has only and will continue to help make Slice and other tools better (anyone can submit issues or suggestions via GitHub).
Just in case you didn’t think Slice was modern or innovative enough, Slice and the other tools employ Bootstrap, which has 4 viewing modes, Mobile (for your mobile devices), Small (for smaller tablets like iPad Mini), Medium (for large tablets like the iPad), and Large (for your regular computer/laptop). So now you can enter data using any platform, but be sure to follow the HIPAA guidelines!
Bootstrap 3 RC1
Our new release of Slice now runs on Bootstrap 3 RC1. Slice and our other applications have run on Bootstrap 2 for quite some time now, so the look and feel should remain very familiar.
Sleek, intuitive, and powerful mobile-first front-end framework for faster and easier web development.
You can also now favorite a project and in doing so, add up to three of your projects to the menu bar.
Once you have favorited the project, you will be able to access a quick project navigation menu that will provide some quick shortcuts.
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When too many variables is a problem
I have parried a number of data requests this week, which has led to more explanations about the nature of our polysomnography (PSG) datasets. Everyone’s eyes light up in disbelief when I mention that the dataset contains “around 1,200 variables” — the exact number is 1,235. For MESA Sleep, our actigraphy dataset was comprised of more than 1,300 variables. I cringe a little bit each time we share out our 2,500+ variable Excel workbook that describes the contents of our MESA datasets, which actually represents 226 printed pages of variable descriptions. Thankfully, we have started with only a subset of those variables for our “official” MESA Data Dictionary.
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Preceptor Form Updates
We’ve recently renamed our Training Grant application to Train Tracks. Along with the name change, we’ve also moved the open source repository to github.com/sleepepi/traintracks and are using GitHub to collect issues and provide better feedback to our users. » More »
We’ve released a new version of Slice that contains a few Quality of Life changes for Slice. Notably, public surveys can now have a unique survey slug that cleans up the URL for linking to that survey. For example, a survey may now be called:
task-tracker-survey is a slug that is based on the survey name.
Other changes have also been made to smooth out the design creation process, and also to reduce clutter when entering sheet data.
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Spout JSON Data Dictionaries
The 0.15.0 release has simplified the data dictionary specification process by integrating with Spout: Tested JSON Data Dictionaries.
Leveraging Spout for the SHHS Data Dictionary
Spout is a Ruby Gem that allows CSV data dictionaries to be converted into a corresponding JSON git repository. Spout provides a series of tests to assure variable and domain name uniqueness, variable type validation, and also tests to assure proper JSON formatting.
By breaking down a CSV into multiple JSON files (one for each variable and one for each domain), we are given the freedom to allow better collaboration on a data dictionary, while maintaining the integrity of the data dictionary itself.
For the Sleep Portal, our primary data dictionary is the SHHS Data Dictionary. Through the use of Spout and GitHub Issues, we were able to discover and address 46 issues across 124 commits for our v0.1.0 release of the SHHS Data Dictionary that is used in the current release of the Sleep Portal.
We were also able to discover data collection nuances in the SHHS
overall variable in Issue #40.
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I had this article pop up on my Google News alerts this week.
Results show that the mean number of nightmares per week fell significantly with CPAP use, and reduced nightmare frequency after starting CPAP was best predicted by CPAP compliance.
“Patients with PTSD get more motivated to use CPAP once they get restful sleep without frequent nightmares, and their compliance improves” said principal investigator Sadeka Tamanna, MD, MPH, medical director of the Sleep Disorders Laboratory at G.V. (Sonny) VA Medical Center in Jackson, Miss.
We worked with the VA Boston Healthcare System on our HeartBEAT clinical trial, and a quick gander back at the data gives an impression that the veterans in that study generally had higher CPAP compliance than participants from other sites. Nightmares and PTSD were not within the scope of HeartBEAT, but it would have been interesting to explore the factors that influenced CPAP compliance rates.
We have another VA collaboration in the works that is set to kickoff this year. Maybe the next discovery lies within!
Simpler Design Editing
While entering data on sheets for designs has been straightforward, creating and editing designs has been a tedious process. This release streamlines the design editing and creation process by:
- Removing the need to define variables and domains in advance
- Displaying changes on the design as they will appear on the final sheet
- Allowing every portion of the design to be clicked and edited
- Providing a clutter-free Preview Mode
Adding Sections and Variables to a Design
Sections and variables can be quickly added to a design. The screenshot below shows the variety of options of types of questions and data that can be collected on a design. To add a section, we will click on the “Section” option.
Next we want to provide a section name for our new section along with an optional description.
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