scholarly journals Peer Review #2 of "WHONDRS-GUI: a web application for global survey of surface water metabolites (v0.1)"

2020 ◽  
Keyword(s):  
Surface Water ◽  
Peer Review ◽  
Web Application ◽  
Global Survey

scholarly journals WHONDRS-GUI: a web application for global survey of surface water metabolites

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9277
Author(s):  
Xinming Lin ◽  
Huiying Ren ◽  
Amy E. Goldman ◽  
James C. Stegen ◽  
Timothy D. Scheibe
Keyword(s):  
User Interface ◽  
Surface Water ◽  
Web Application ◽  
Data Types ◽  
Global Survey ◽  
Link Type ◽  
Sampling Campaign ◽  
Domain Integration ◽  
River Corridors ◽  
The Web

Background The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created. Results The web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811, which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server (https://xmlin.shinyapps.io/whondrs/).

scholarly journals search.bioPreprint: a discovery tool for cutting edge, preprint biomedical research articles

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1396 ◽  
Author(s):  
Carrie L. Iwema ◽  
John LaDue ◽  
Angela Zack ◽  
Ansuman Chattopadhyay
Keyword(s):  
Peer Review ◽  
Biomedical Research ◽  
Web Application ◽  
Research Articles ◽  
Journal Publication ◽  
Publication Delay ◽  
New Information ◽  
One Stop ◽  
To Receive ◽  
Timely Dissemination

The time it takes for a completed manuscript to be published traditionally can be extremely lengthy. Article publication delay, which occurs in part due to constraints associated with peer review, can prevent the timely dissemination of critical and actionable data associated with new information on rare diseases or developing health concerns such as Zika virus. Preprint servers are open access online repositories housing preprint research articles that enable authors (1) to make their research immediately and freely available and (2) to receive commentary and peer review prior to journal submission. There is a growing movement of preprint advocates aiming to change the current journal publication and peer review system, proposing that preprints catalyze biomedical discovery, support career advancement, and improve scientific communication. While the number of articles submitted to and hosted by preprint servers are gradually increasing, there has been no simple way to identify biomedical research published in a preprint format, as they are not typically indexed and are only discoverable by directly searching the specific preprint server websites. To address this issue, we created a search engine that quickly compiles preprints from disparate host repositories and provides a one-stop search solution. Additionally, we developed a web application that bolsters the discovery of preprints by enabling each and every word or phrase appearing to with articles from preprint servers. This tool, search.bioPreprint, is publicly available at http://www.hsls.pitt.edu/resources/preprint.

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