Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: One file to share them all: Using the COMBINE Archive and the OMEX
  format to share all information about a modeling project   Background: With 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.
  Results: We 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.
  Conclusions: The 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.

2
The categories of this paper are: math
37
The categories of this paper are: supr-con
35
The categories of this paper are: mtrl-th
20
The categories of this paper are: acc-phys
28
The categories of this paper are: alg-geom
22
The categories of this paper are: chao-dyn
15
The categories of this paper are: nucl-ex
7
The categories of this paper are: hep-th
11
The categories of this paper are: hep-lat
32
The categories of this paper are: atom-ph
34
The categories of this paper are: chem-ph
18
The categories of this paper are: econ
29
The categories of this paper are: funct-an
0
The categories of this paper are: hep-ph
33
The categories of this paper are: plasm-ph
3
The categories of this paper are: physics