Skip to main content
We gratefully acknowledge support from the Simons Foundation, member institutions, and all contributors. Donate
arXiv logo
Cornell University Logo

Quantitative Biology > Quantitative Methods

arXiv:2411.12662 (q-bio)
[Submitted on 19 Nov 2024]

Title:bia-binder: A web-native cloud compute service for the bioimage analysis community

Authors:Craig T. Russell, Jean-Marie Burel, Awais Athar, Simon Li, Ugis Sarkans, Jason Swedlow, Alvis Brazma, Matthew Hartley, Virginie Uhlmann
View PDF HTML (experimental)
Abstract:We introduce bia-binder (BioImage Archive Binder), an open-source, cloud-architectured, and web-based coding environment tailored to bioimage analysis that is freely accessible to all researchers. The service generates easy-to-use Jupyter Notebook coding environments hosted on EMBL-EBI's Embassy Cloud, which provides significant computational resources. The bia-binder architecture is free, open-source and publicly available for deployment. It features fast and direct access to images in the BioImage Archive, the Image Data Resource, and the BioStudies databases. We believe that this service can play a role in mitigating the current inequalities in access to scientific resources across academia. As bia-binder produces permanent links to compiled coding environments, we foresee the service to become widely-used within the community and enable exploratory research. bia-binder is built and deployed using helmsman and helm and released under the MIT licence. It can be accessed at this http URL and runs on any standard web browser.
Subjects: Quantitative Methods (q-bio.QM)
Cite as: arXiv:2411.12662 [q-bio.QM]
  (or arXiv:2411.12662v1 [q-bio.QM] for this version)
  https://doi.org/10.48550/arXiv.2411.12662

Submission history

From: Virginie Uhlmann [view email]
[v1] Tue, 19 Nov 2024 17:12:17 UTC (3,694 KB)
Full-text links:

Access Paper:

view license
Current browse context:
q-bio.QM
< prev   |   next >
new | recent | 2024-11
Change to browse by:
q-bio

References & Citations

export BibTeX citation

Bookmark

BibSonomy logo Reddit logo

Bibliographic and Citation Tools

Bibliographic Explorer (What is the Explorer?)
Connected Papers (What is Connected Papers?)
Litmaps (What is Litmaps?)
scite Smart Citations (What are Smart Citations?)

Code, Data and Media Associated with this Article

alphaXiv (What is alphaXiv?)
CatalyzeX Code Finder for Papers (What is CatalyzeX?)
DagsHub (What is DagsHub?)
Gotit.pub (What is GotitPub?)
Hugging Face (What is Huggingface?)
Papers with Code (What is Papers with Code?)
ScienceCast (What is ScienceCast?)

Demos

Replicate (What is Replicate?)
Hugging Face Spaces (What is Spaces?)
TXYZ.AI (What is TXYZ.AI?)

Recommenders and Search Tools

Influence Flower (What are Influence Flowers?)
CORE Recommender (What is CORE?)

arXivLabs: experimental projects with community collaborators

arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website.

Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them.

Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.

Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)