skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


This content will become publicly available on February 14, 2026

Title: GitHub enables collaborative and reproducible laboratory research
GitHub, a platform widely used in software development, offers a robust framework for documenting all activities of laboratory research projects. This Community Page highlights the benefits of, and provides guidance for, incorporating the GitHub ecosystem into “wet” lab workflows.  more » « less
Award ID(s):
1846521
PAR ID:
10652964
Author(s) / Creator(s):
; ;
Publisher / Repository:
PLOS Biology
Date Published:
Journal Name:
PLOS Biology
Volume:
23
Issue:
2
ISSN:
1545-7885
Page Range / eLocation ID:
e3003029
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Software projects frequently use automation tools to perform repetitive activities in the distributed software development process. Recently, GitHub introducedGitHub Actions, a feature providing automated workflows for software projects. Understanding and anticipating the effects of adopting such technology is important for planning and management. Our research investigates how projects useGitHub Actions, what the developers discuss about them, and how project activity indicators change after their adoption. Our results indicate that 1,489 out of 5,000 most popular repositories (almost 30% of our sample) adoptGitHub Actionsand that developers frequently ask for help implementing them. Our findings also suggest that the adoption ofGitHub Actionsleads to more rejections of pull requests (PRs), more communication in accepted PRs and less communication in rejected PRs, fewer commits in accepted PRs and more commits in rejected PRs, and more time to accept a PR. We found similar results when segmenting our results by categories ofGitHub Actions. We suggest practitioners consider these effects when adoptingGitHub Actionson their projects. 
    more » « less
  2. As modern social coding platforms such as GitHub and Stack Overflow become increasingly popular, their potential security risks increase as well (e.g., risky or malicious codes could be easily embedded and distributed). To enhance the social coding security, in this paper, we propose to automate cross-platform user identification between GitHub and Stack Overflow to combat the attackers who attempt to poison the modern software programming ecosystem. To solve this problem, an important insight brought by this work is to leverage social coding properties in addition to user attributes for cross-platform user identification. To depict users in GitHub and Stack Overflow (attached with attributed information), projects, questions and answers as well as the rich semantic relations among them, we first introduce an attributed heterogeneous information network (AHIN) for modeling. Then, we propose a novel AHIN representation learning model AHIN2Vec to efficiently learn node (i.e., user) representations in AHIN for cross-platform user identification. Comprehensive experiments on the data collections from GitHub and Stack Overflow are conducted to validate the effectiveness of our developed system iDev integrating our proposed method in cross-platform user identification by comparisons with other baselines. 
    more » « less
  3. Background and Context: GitHub has been recently used in Software Engineering (SE) classes to facilitate collaboration in student team projects as well as help teachers to evaluate the contributions of their students more objectively. Objective: We explore the benefits and drawbacks of using GitHub as a means for team collaboration and performance evaluation in large SE classes. Method: Our research method takes the form of a case study conducted in a senior level SE class with 91 students. Our study also includes entry and exit surveys, an exit interview, and a qualitative analysis of students’ commit behavior. Findings: Different teams adapt GitHub to their workflow differently. Furthermore, despite the steep learning curve, using GitHub should not affect the quality of students’ submissions. However, using GitHub metrics as a proxy for evaluating team performance can be risky. Implications: We provide several recommendations for integrating Web-based configuration management tools in SE classes. 
    more » « less
  4. Social coding platforms such as GitHub are increasingly becoming a digital workspace for the production of non-software digital artifacts. Since GitHub offers unique features that are different from traditional ways of collaborative writing, it is interesting to investigate how GitHub features are used for writing. In this paper, we present the preliminary findings of a mixed-methods, case study of collaboration practices in a GitHub book project. We found that the use of GitHub depended on task interdependence and audience participation. GitHub's direct push method was used to coordinate both loosely- and tightly-coupled work, with the latter requiring collaborators to follow socially-accepted conventions. The pull-based method was adopted once the project was released to the public. While face-to-face and online meetings were prominent in the early phases, GitHub's issues became instrumental for communication and project management in later phases. Our findings have implications for the design of collaborative writing tools. 
    more » « less
  5. Millions of software projects leverage automated workflows, like GitHub Actions, for performing common build and deploy tasks. While GitHub Actions have greatly improved the software build process for developers, they pose significant risks to the software supply chain by adding more dependencies and code complexity that may introduce security bugs. This paper presents ARGUS, the first static taint analysis system for identifying code injection vulnerabilities in GitHub Actions. We used ARGUS to perform a large-scale evaluation on 2,778,483 Workflows referencing 31,725 Actions and discovered critical code injection vulnerabilities in 4,307 Workflows and 80 Actions. We also directly compared ARGUS to two existing pattern-based GitHub Actions vulnerability scanners, demonstrating that our system exhibits a marked improvement in terms of vulnerability detection, with a discovery rate more than seven times (7x) higher than the state-of-the-art approaches. These results demonstrate that command injection vulnerabilities in the GitHub Actions ecosystem are pervasive and require taint analysis to be detected. 
    more » « less