AimsAdd-my-Pet (AmP) aims to collect:
- referenced data on the energetics of animal species, such that the parameters of the standard Dynamic Energy Budget (DEB) model, and those of its different variants, can be estimated
- Matlab code for estimating DEB parameters from this data
- DEB parameter estimates
- properties of species that are implied by these parameters
Although this website offers a lot of information, an in-depth analysis cannot do without further computation and visualisation. Free Matlab packages DEBtool and AmPtool (see below) make this task a lot easier. Matlab itself is expensive, but the inexpensive student version will suffice in most cases. DEBtool or AmPtool do not use any of Matlab's toolboxes. Alternatively, the Matlab structures can be imported in R with some R-to-Matlab package. Free Octave and Scilab very much resemble Matlab.
AmP is an initiative in the context of much wider aims:
- Find the simplest organisation principles for metabolism upon which all life is based
- Understand taxon-specific patterns as variations on this common theme.
ResearchAmP is developed and maintained by a passionate community of scientists in the context of an ongoing 40 year research strategy to:
- Use general physical-chemical principles to develop an educated quantitative expectation for the eco-physiological behaviour of all species.
- Estimate parameters for any specific case and identify patterns of co-variation of parameter values among many animal species to study evolutionary and ecological adaptations.
- Use knowledge of the eco-physiological behaviour of species
- in combination with local environmental data to understand geographical ranges of species, e.g. in the context of climate change or bioconservation. More
- to use specimens for monitoring environmental quality parameters, such as temperature and food availability (e.g. in archaeological context)
- to use specimens for studying effects of toxicants, which reveal as deviations from natural eco-physiological behaviour, including environmental risk assessment. More
- as a basis to analyse population dynamics and ecosystem behaviour. More
- to optimise the production of biomass, or bioproducts and actions of organisms (e.g. in the context of aquaculture, sewage water treatment or setting fishing quota)
Organisation and navigationEach entry has 6 pages: "Predictions & Data", "Parameters", "Implied traits", "Population traits", "Bibliography" and "Citation". Dropdown "Results" in the entry-specific toolbar links these 6 pages. Dropdown "Code" gives access to 3 code files ("mydata", "pars_init" and "predict") and a zip file with these 3 files (and the run-file) for each entry, which has been used in combination with DEBtool to produce all information. For the role of the zip file, see the section on archiving. Dropdown "Links" lists some database sites, which give views on nomenclature, classification, general species properties and frequently also pictures. The scientific and common names on top of the entry-pages link to that entry on the Species List and Tree pages (see below), respectively, to navigate to related species. The buttons phylum, class, order and family on the top-right of the "Predictions & Data" pages link to the Species Tree. Hover above the eco-codes to see the corresponding labels.
Dropdown "COLLECTION" in the general toolbar provides access to the entry pages via several routes
- Species List page orders entries according to taxonomy; click on entry names to go to "Predictions & Data" pages.
- Species Tree page orders entries according to phylogeny; walk to the leaves of the tree and click on entry names to go to "Predictions & Data" pages. You can create your own tree with any root with AmPtool. Go from the tree to the list, by clicking on a leaf of the tree and then on the scientific name of the entry; from the list to the tree, by clicking on name of the entry and then on the common name of the entry.
- Species Names page orders entries according to scientific and common names; click on these names to go to "Predictions & Data" pages, while hovering shows the other name.
- Authors page orders entries according to authors; entries in dropdowns for each author are ordered according to submission date. Click on these names to go to "Predictions & Data" pages.
- Energy Budgets page orders entries according to taxonomy; click on pies to go to "Implied property" pages. The link is to energy budgets of fully-grown individuals; an extra dropdown "Energy Budgets" at this page gives access to 3 other energy budgets. The 4 Energy Budget pies on the "Implied poperty" pages link to 4 "Energy Budget" pages to compare species and to walk to related species via the "Energy Budget" pages.
- AmPdata links to a zip-file with all metadata, parameters and traits for all entries. Unpack and save the .mat files in a directory and make a path in Matlab to this directory. If loaded in Matlab, these files create corresponding structures. See AmPtool for its possible use and links for downloading.
Dropdown "CONTEXT" presents overview-pages and software for the analysis of the AmP database
- this page
- AmP Manual describes all of the more technical aspects of AmP's parameter estimation and the process of generating entries.
- AmP Tool guides through a powerful software package that allows you to make all sorts of comparisons between (functions of) parameters among all entries. The significance of this is that many physiological quantities, such as respiration and nitrogen-waste production, can be expressed as functions of parameters, since the set of parameters fully control the ontogeny of energy budgets from the start of development till death by aging.
- AmP Ecology is a coding system that is used in AmPtool to specify climate, ecozone, habitat, migration/torpor and food for each entry. It can be used in AmPtool to link energetic properties to ecological ones.
- Phyla page presents all animal phyla and indicates presence in the collection; it also shows the occurence of metabolic acceleration among phyla, which is key to the interrelationships between the various DEB models.
- Parameters page presents frequency distributions of general parameters to ease comparison with other species; hovering over parameter names explains the functionality of each parameter.
- Patterns page presents plots of some functions of parameters to expose co-variations in values, just for illustrative purposes.
- Entry prepare page presents guidance for preparing an AmP entry.
- About page presents general info about the collection.
Dropdown "DEB" provides access to pages relating to Dynamic Energy Budget theory, of which AmP is an application, and software
- DEB Portal provides general info about DEB theory.
- DEB Wikipedia presents a summary of DEB concepts that concern the standard DEB model.
- DEB Tool describes a powerful software package, of which AmPtool makes frequent use.
- DEB Laboratory is a platform for resource exchange of code, data bases, supporting material for DEB research and courses.
- DEB Notation gives notation rules and descriptions of DEB symbols as used in DEB theory.
- DEB Library presents papers in which DEB theory plays a substantial role. Please report missing items to Starrlight Augustine
- DEB Videos lists videos on varying topics, ranging from lectures to technical explanations.
- DEB Calendar lists milestones over the years; knowlegde of from where we came helps to identify future directions
- DEB Events presents the upcomming and past courses/workshops/meetings/symposia on DEB theory.
- DEB Net gives an overview of the working groups/departments that presently do research on DEB theory. Please contact us, if you want to join.
We also have a topic-sorted short-list of selected items.
- Population Dynamics explains how AmP entries can be used to specify population dynamics. It also gives background for the population traits pages
- Physical Biology explains how AmP entries can be used as input for software package NicheMapR which specifies the behaviour of individuals, given models for micro-climate.
- Ecotoxicity discusses software for the analysis of data on effects of toxicants.
VU Univ. A'dam
Archiving and referencingA curator will review any submitted entry and has the freedom to edit entries. At the moment of addition the entry gets an identifier for the curator, who did the addition, and a date of acceptance. The 4 source files (mydata, pars_init, predict, run) are zipped into my_pet_yyyymmdd.zip, where yyyymmdd stands for the acceptance date as specified in the mydata-file, and parked in directory entries_zip. Existing entries can change in several ways, such as more data that become available, other ideas about parameter values that fit best, or the species changes name. The author and date of the modification are specified and the author name is appended to the list of authors for that entry. If an entry is modified, the obsolete zip-file moves to directory entries_archive. The obsolete zip-files can also be downloaded from the code-dropdown. How to refer to a particular entry is indicated on the "Predictions & Data" pages. Refer to the AmP collection as: AmP, online database of DEB parameters, implied properties and referenced underlying data, bio.vu.nl/thb/deb/deblab/add_my_pet/. Last accessed: yyyy/mm/dd.
Instructions for submissionAdding your pet to the collection starts with the preparation of an entry. If your mydata-file is complete, but you have problems with the rest, you can ask the curators for help. If your submission is a modification of an existing entry, please insert a discussion point that explains what changed and why. If no arguments exist for why previous data is not included in the update, it should be included.
Please realize that, when you submit an entry to the AmP collection, you agree that your entry will be posted on the AmP website (after curation). If it contains data outside the public domain, please ensure that all involved parties agree. It is generally a good idea to include people who contributed to the data in the author-list of the entry; the bibitem of the corresponding bibkey of data-sets should make clear where the data came from.
Why submit an entry to the collection?
- Knowledge base: Contributes to building a large comprehensive data base on species data and DEB model parameters the allows comparison of species, see AmPtool
- Transparency/quality control: data and references and code used for estimation are freely available for anyone to download and inspect, the files and methods are already documented. A good fit shows that the data is consistent
- Its possible to refer to the entries in papers and treat the published entry as supporting material, saving detailed technical explanations.
- Facilitate application of your experimental results to real world problems.
- Security: If you move, change jobs, break your computer you only need to download your entry and DEBtool and voila.
You can (un)subscribe to the DEB mailing list at email@example.com. Once you are subscribed you can post and receive announcements (new research, jobs, etc) to and from the mailing list here: firstname.lastname@example.org. You can follow AmP on ResearchGate, Facebook and Twitter.
By contributing you can partake in DEBnet, an active platform for research on aspects of DEB theory.