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COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Overview of attention for article published in BMC Bioinformatics, December 2014
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (88th percentile)
  • High Attention Score compared to outputs of the same age and source (85th percentile)

Mentioned by

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18 tweeters

Citations

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55 Dimensions

Readers on

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55 Mendeley
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4 CiteULike
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Title
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
Published in
BMC Bioinformatics, December 2014
DOI 10.1186/s12859-014-0369-z
Pubmed ID
Authors

Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez, Herbert M Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère

Abstract

BackgroundWith the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result.ResultsWe describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software.ConclusionsThe COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.

Twitter Demographics

The data shown below were collected from the profiles of 18 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 55 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 4 7%
United States 3 5%
India 1 2%
Spain 1 2%
Netherlands 1 2%
Unknown 45 82%

Demographic breakdown

Readers by professional status Count As %
Researcher 19 35%
Student > Ph. D. Student 14 25%
Professor > Associate Professor 5 9%
Student > Bachelor 4 7%
Other 3 5%
Other 9 16%
Unknown 1 2%
Readers by discipline Count As %
Computer Science 22 40%
Agricultural and Biological Sciences 10 18%
Biochemistry, Genetics and Molecular Biology 8 15%
Engineering 4 7%
Social Sciences 4 7%
Other 4 7%
Unknown 3 5%

Attention Score in Context

This research output has an Altmetric Attention Score of 12. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 14 September 2015.
All research outputs
#1,549,825
of 14,573,111 outputs
Outputs from BMC Bioinformatics
#582
of 5,420 outputs
Outputs of similar age
#33,735
of 301,154 outputs
Outputs of similar age from BMC Bioinformatics
#46
of 326 outputs
Altmetric has tracked 14,573,111 research outputs across all sources so far. Compared to these this one has done well and is in the 89th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 5,420 research outputs from this source. They receive a mean Attention Score of 4.9. This one has done well, scoring higher than 89% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 301,154 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 88% of its contemporaries.
We're also able to compare this research output to 326 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 85% of its contemporaries.