Evidence map›Paper›PMID 36648320›Full record

ArticleBioinformatics (Oxford, England)2023

JBrowse Jupyter: a Python interface to JBrowse 2.

Teresa De Jesus Martinez, Elliot A Hershberg, Emma Guo, Garrett J Stevens, Colin Diesh, Peter Xie, Caroline Bridge, Scott Cain, Robin Haw, Robert M Buels and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Teresa De Jesus MartinezDepartment of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-1947-9539
Elliot A HershbergDepartment of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA.ORCID 0000-0003-2068-3366
Emma GuoDepartment of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA.
Garrett J StevensDepartment of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-9781-5323
Colin DieshDepartment of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA.ORCID 0000-0003-2629-7570
Peter XieDepartment of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA.
Caroline BridgeAdaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada.
Scott CainAdaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada.
Robin HawAdaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada.
Robert M BuelsDepartment of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA.
Lincoln D SteinAdaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada.
Ian H HolmesDepartment of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA.

Funding

Web-based visualization of coronavirus genomes and proteinsR01HG004483 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI Ian H Holmes · 2007 to 2026
$9.3M
Novel Web-based Tools for Collaborative Community-Driven Genome Feature AnnotatioR01GM080203 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Ian H Holmes · 2007 to 2026
$8.5M
NHGRI NIH HHS R01 HG004483NIGMS NIH HHS R01 GM080203NIH HHS HG004483
6 · The paper itself

Abstract

motivationJBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis itself. However, emerging technologies such as Jupyter notebooks enable a more rapid iterative cycle of development, analysis and visualization.

resultsWe have developed a package that provides a Python interface to JBrowse 2's suite of embeddable components, including the primary Linear Genome View. The package enables users to quickly set up, launch and customize JBrowse views from Jupyter notebooks. In addition, users can share their data via Google's Colab notebooks, providing reproducible interactive views. AVAILABILITY AND IMPLEMENTATION: JBrowse Jupyter is released under the Apache License and is available for download on PyPI. Source code and demos are available on GitHub at https://github.com/GMOD/jbrowse-jupyter.

Indexed as

Computational BiologyGenomicsGenomeSoftwareWeb Browser

Identifiers

PMID36648320
PMCPMC9887080

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.