Network Enumeration

Network Enumeration

For a detailed discussion of the networks and how they enumerated, please read our paper on arXiv.org:

Enumeration and Online Library of Mass-Action Reaction Networks

All data files available here are ZIP archives of text files containing encoded Network strings. We describe the format in detail here:

Network format description

The following table shows the number of networks for a given number of species and reactions. Click the number to download the file of networks. We will add more data in the table below as it becomes available.

1 Reaction 2 Reactions 3 Reactions 4
Reactions
5
Reactions
6
Reactions
7
Reactions
Total
2 Species 6 36 110 255 396 472 396 1,671
3 Species 5 218 4,082 52,679 527,339 4,306,169 running 4,890,492
4 Species 1 274 19,335 796,303 24,159,763 Estimate: 4 months Estimate: 2 years 24,975,676
5 Species 0 136 30,246 3,276,608 240,319,995 zip: 727 MB unzip: 17 GB Estimate: 10 months 243,626,985
6 Species 0 29 21,913 5,651,388 Estimate: 10 months Estimate: 47 Years 5,673,330
7 Species 0 3 8,526 5,0638,577 Estimate: 4-6 months Estimate: 900 Years 5,077,106
8 Species 0 0 1,865 2,666,292 Estimate: 6-9 years Estimate: 600 to 1000 years 2,668,157
9 Species 0 0 225 877,692 Insufficient Memory 877,917
10 Species 0 0 14 Insufficient Memory 14
Total 12 696 86,316 18,389,794 265,007,493 4,306,641 396 287,791,348

 

Source Code + Binaries

We developed the following software tools:

  • Viewer to visualize the encoded networks.

License

Copyright © 2009, Anastasia Deckard, Frank T Bergmann and Herbert M Sauro All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
  • Neither the name of University of Washington nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.