Distributed collaboration: the case for the enhancement of Brainspell’s interface
AmanPreet Badhwar, David Kennedy, Jean‐Baptiste Poline, Roberto Toro · GigaScience · 2016
The past several decades have seen an explosive growth in the number of published neuroimaging studies. In concert, the demand for freely available and openly accessible ‘study data’, that would facilitate future reanalysis, meta-analysis, hypothesis testing and repurpos-ing has also soared. Here we report on developments made to Brainspell[1] one of several web-based initiatives (e.g. BrainMap[2], NeuroVault[3], Neurosynth[4]) that allow individuals to search through and organize massive numbers of neuroimaging studies and results in meaningful ways. Distinct from other databases, Brainspell [http://brainspell.org] is the first web-based initiative to allow users to manually annotate and curate machine-parsed data, as well as manually extend the database via its crowdsourcing user interface. The goal of our Brainhack project was to improve Brainspell’s interface. We worked to (a) provide supplementary manual data edit options (b) facilitate efficient manual database extension, and (c) aid meaningful organization of data. We used GitHub to manage the client and server code, and to coordinate its development. In the original version of Brainspell, users were able to edit experiment (table) title, caption and coordinates for each article. We added four supplementary options. In particular, users are now provided with enhanced ‘edit feedback’: Feedback indicating when a field is editable or has been successfully saved. Editable text fields now turn light grey, while a successfully stored field loses its coloring. Storage of fields can now be triggered by a tab key or by clicking elsewhere, in addition to hitting return. Users are also provided with additional edit options, specifically, the ability to: Add symbols to the title and caption fields. Remove empty tables. Add and remove rows from a table. While users were previously able to add new articles and their coordinate tables, the process was labor- and time-intensive, since each value had to be manually entered. We implemented a more efficient method to edit tables: Addition of an Import link to each table. When clicked it opens a popup window where comma-separated text can be entered and parsed. 3D volume and mesh showing the aggregated locations of a user/peer-defïned collection (Aman_Metaanalysis) containing 32 articles. This user nas a total of two collections (or 2 lists), as indicated on the header row. The second collection is named ‘test’, b Highlighted in yellow are the Split and Import links associated with each table in Brainspell. Note: With the exception of the Download link, peer-login is required to access all mentioned Brainspell enhancements Addition of a Split link to each table. Fine-tuning the Split link enhancement to allow more than ten splits. Option to add articles lacking PMID (or user-specific articles). Addition of a Download link to each article. When clicked it downloads article title, reference, abstract, and tables. Creation of ‘article collection’ functionality. Users can now store the results of their search into article collections. Clicking on an existing collection brings back the corresponding articles and re-computes the 3D volume and mesh of the aggregated locations. Users can create and edit multiple collections. We performed ten enhancements to Brainspell and provided instructions of use in Brainspell’s wiki. We tested these enhancements on Safari, Firefox and Chrome. Moreover, 25 articles were manually added to Brainspell as part of our extended beta testing phase. Our goal with these enhancements was to extend the functionality, and ease of use of Brainspell for curating machine-parsed neuroimaging data from a wide database of studies. During January 15 to February 5, 2016 alone, Brainspell was used in 282 sessions by 133 users who watched 1421 pages. Moreover, Brainspell was forked to “BIDS-collaborative/Brainspell” which itself was forked by approximately 10 data-science students to extend the platform. Availability of supporting data More information about this project can be found at: http://github.com/r03ert0/brainspell-brainhack. None. RT developed Brainspell. AB, DK, and JBP suggesled enhancements and performed bèta testing. AB and RT wrote the report. Report from 2015 OHBM Hackathon (HI). The authors would like to thank the organizers and attendees of Brainhack 2015 OHBM Hackathon.