Facilitating Experiment Reproducibility Through Data Federation and Image Processing Tools Integration
Objectives: Recent studies have demonstrated the difficulties in replicating scientific findings and/or experiments published in past.
The effects seen in replicated experiments were smaller than previously reported. Some of the explanations
for these findings include the complexity of the experimental design and the pressure on researchers to report positive findings.
The International Committee of Medical Journal Editors (ICMJE) suggests that every study considered for publication must
submit a plan to share the de-identified patient data no later than 6 months after publication.
There is a growing demand to enhance the management of clinical data, facilitate data sharing across institutions and also to keep track
of the data from previous experiments. The ultimate goal in this project is to assure the reproducibility of experiments in the future.
Methods: Shiny-tooth, the tool presented here is focused on component reusability and a robust scalable application.
This application uses: Node.js, Hapi.js and Couchdb.
The front end of this application is based on Angular.js.
This framework facilitates the development and integration of plugins in order to generate new services
in a distributed environment. Reusable HTML components are also enabled in this framework.
Results: Figure 1, shows the architecture of the application. In green, the plugins that are currently used which include: login using JSON web tokens (JWT); shiny-tooth-static serves the static content (HTML) pages to the client; shiny-tooth-model handles storage and retrieval requests of clinical data and morphological to the database.
Figure 2, shows the procedure to create new data for a clinical study.
Figure 3, shows a 3-dimensional view of a condyle stored in the database for a given patient.
Conclusions: The application allows gathering clinical data and morphological data in a structured manner.
The tools and plugins described shown in Figure 1 have been published at https://www.npmjs.com/~juanprietob and are available for installation with the Node package manager (npm).
The current implementation of shiny-tooth has been deployed in the EC2 container and is available here https://ec2-52-42-49-63.us-west-2.compute.amazonaws.com:8180. The access to the data is restricted and will only be allowed after authorization from the project managers.