Replacing bar graphs of continuous data with more informative graphics: Are we making progress?

Barzooka is an automated screening tool designed to detect 9 graph types in scientific publications: 1) bar graphs of counts and proportions, 2) bar graphs of continuous data, 3) bar graphs combined with dot plots, 4) dot plots, 5) box plots, 6) violin plots, 7) histograms, 8) pie charts, and 9) study flow charts. This project contains data and code for two external datasets used to validate Barzooka, and one dataset used to examine changes in graph use from 2010 to 2020 in 23 fields

Blind spots on western blots: assessment of common problems in western blot figures with recommendations to improve them

This project contains protocols, data and code for a meta-research project examining the prevalence of image display, data presentation and methodological reporting practices in original research articles in cell biology and neurosciences that include western blots. Papers were identified from the top 25% of journals in each field

The future of scholarly communication

These different outputs were shared or generated as part of a virtual brainstorming event in January 2023 on "The future of scholarly communication". Early career researchers (ECRs) passionate about and/or actively involved in the improvement of scholarly communication met with scholarly publishers who understand the complexity of the publishing system. Participants shared experiences, discussed the strengths and weaknesses of the current system, and collaboratively explored ideas and solutions for improving scholarly communicatio

Western blot: From gel to publication.

Western blotting is a standard laboratory method that uses antibodies to detect target proteins in a sample. (1) The sample, typically a mixture of proteins, is loaded on the gel. A molecular weight (MW) marker, which contains prelabeled proteins of varied, known molecular weights, is loaded on the gel alongside the protein sample as a size reference. (2) Gel electrophoresis is used to separate proteins based on their molecular weight. (3) The proteins are transferred, or “blotted”, onto a membrane. (4) The membrane is blocked to reduce nonspecific binding and then sequentially probed with a primary antibody that specifically binds to the protein of interest and a secondary antibody. The latter binds the primary antibody and carries an enzyme or a fluorophore that allows subsequent detection. (5) The signal is detected through a chemiluminescent reaction or fluorescence, respectively. (6) An image of the western blot is prepared for publication: Annotations are added and often the blot is cropped. For the unprocessed image, see S1 Fig.</p

Western blot image minimal reporting standard.

Published western blots should show a minimum of 2 molecular weight marker bands of different weights if the protein of interest falls between the molecular weight marker bands, and 3 molecular weight marker bands of different weights if the protein of interest is directly at one of the marker bands. The molecular weight markers should be annotated with labels. An original, uncropped image of each blot should be published in the supplement or deposited on a public repository. The source data blot should be named in a way that links it to a specific figure, panel, and protein. The outline of the crop should be annotated on the original image. For the unprocessed image, see S1 Fig.</p

Number of articles examined by journal (cell biology).

Values are n, or n (% of all articles). Articles that were not full-length original research articles (reviews, editorials, perspectives, commentaries, letters to the editor, short communications, etc.) or did not include eligible images were excluded. (DOCX)</p