Evidence map›Paper›PMID 24861624›Full record

ArticleNucleic acids research2014

Enhancing UCSF Chimera through web services.

Conrad C Huang, Elaine C Meng, John H Morris, Eric F Pettersen, Thomas E Ferrin

Abstract read
In one paragraph

Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.

0numbers the graph read from it
0cells of the map it votes in
101citing 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

101 citing papers in PubMed.

  1. Article
  2. Ribosome hibernation in zinc-starvedMicrobiology spectrum · 2026
    Article
  3. Article
  4. Article
  5. International journal of molecular sciences · 2026
    Article
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  13. Review
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41 more citing papers are in PubMed but not listed here.

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

5 authors.

Conrad C HuangResource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA.
Elaine C MengResource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA.
John H MorrisResource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA.
Eric F PettersenResource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA.
Thomas E FerrinResource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA tef@cgl.ucsf.edu.

Funding

Resource for Biocomputing Visualization and InformaticsP41GM103311 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERRIN, THOMAS E · 2012 to 2017
$8.2M
NIGMS NIH HHS P41-GM103311
6 · The paper itself

Abstract

Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive tasks and convenient searches of databases. We describe how we have enhanced UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/), a program for the interactive visualization and analysis of molecular structures and related data, through the addition of several web services (http://www.rbvi.ucsf.edu/chimera/docs/webservices.html). By streamlining access to web services, including the entire job submission, monitoring and retrieval process, Chimera makes it simpler for users to focus on their science projects rather than data manipulation. Chimera uses Opal, a toolkit for wrapping scientific applications as web services, to provide scalable and transparent access to several popular software packages. We illustrate Chimera's use of web services with an example workflow that interleaves use of these services with interactive manipulation of molecular sequences and structures, and we provide an example Python program to demonstrate how easily Opal-based web services can be accessed from within an application. Web server availability: http://webservices.rbvi.ucsf.edu/opal2/dashboard?command=serviceList.

Indexed as

Molecular StructureSoftwareInternetModels, Molecular

Identifiers

PMID24861624
PMCPMC4086125

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.