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I'm looking for datasets for biological systems that have been modeled by systems of ODEs (or more generally biological time series data). I can't even find a simple predator-prey dataset (from a legit source). Where can I find biological data (ecological, protein concentrations, etc vs. time)? Thanks.

  • Do you have enough answers to validate one of them? – Laurent Duval Aug 16 '16 at 20:28
  • I discussed it with my advisor and I ended up using your dataset Laurent Duval. – Robopoto Dec 7 '16 at 19:56
  • Very glad! Good luck with your research – Laurent Duval Dec 7 '16 at 20:33
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You can find data related to the Canadian lynx and snowshoe hare pelt-trading records of the Hudson Bay Company, starting in 1845. It seems to be a standard dataset, described for instance in Predator-Prey Models.

Canadian lynx and snowshoe hare evolution

The base repository is Lynx and Hare Data, and you can find for instance the csv file lynxhare.csv.

The Lotka-Volterra Models for predactor/prey pairs have apparently been used here and here, for instance. Run, hare, run.

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  • Thanks, yeah, if you go up a few folders there are other datasets. My concern now is are this lynx-hare datasets usable in a paper (i.e. legit). – Robopoto Jan 12 '16 at 18:27
  • I pointed this one as an example, on purpose (took some time to find it). You can trace a lot of papers using this data. As long as you cite them, I can foresee a little chance that Hudson bay fur trader, hare or lynx descendants sue you. – Laurent Duval Jan 12 '16 at 18:44
  • Lol, that's not the problem. If you look at the other suggested website LTER Network. It is a well-managed data repo, associated with the NSF. So I could comfortable cite one of its datasets in a paper. I don't know where B. Blais got his hands on the dataset he is using (or if I could comfortable cite it in a paper). – Robopoto Jan 12 '16 at 19:16
  • Sure. I am not from the domain, just tried to help with an example I though was "visible". – Laurent Duval Jan 12 '16 at 19:35
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I didn't get it: are you looking for synthtic datasets only, or are you looking for real time series data for validating your own ODE models?

In any case, try perhaps The Long Term Ecological Research Repository

" The Long Term Ecological Research (LTER) program concentrates on studies of ecological processes that play out at time scales spanning decades to centuries. Long-term data sets from the LTER program provide a context to evaluate the nature and pace of ecological change, to interpret its effects, and to forecast the range of future biological responses to change."

  • Thanks. I'm looking to do parameter estimations, so real data that already has an ODE model associated with it. – Robopoto Jan 12 '16 at 18:43
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I don't know what exactly you would qualify as 'biological' data, but I would classify predator/prey relationships as 'ecological' ... and therefore I'd look in one of two places:

  1. DataONE (Data Observation Network for Earth). Searches about 30 archives of environmental & ecological data.

  2. Dryad, a repository for evolutionary & environmental data. Some journals in the field require data be deposited here if you publish papers through them.

DataONE searches Dryad, but Dryad also allows browsing, or searching by the journal in which the data was used, which might help you to find data of interest.

I'm personally not aware of any search engines in the ecological & environmental sciences that allow for searching by the dimensionality of the data. You tend to see that sort of restriction when there are many different types of instruments observing the same regions ... like in astronomy and solar physics.

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