Welcome to the add-my-pet portal
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
- code for estimating DEB parameters from these data
- DEB parameter estimates
- properties of species that are implied by these parameters
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 a generalized species.
- Estimate parameters for any specific case and compare the values with expectations from scaling relationships: deviations reveal specific evolutionary adaptations!
- Study deviations from model expectations and learn about the distinction between general and specific aspects of energetics.
Organisation and nagivationEach entry has 4 pages: "Predictions & Data", "Parameters", "Implied properties" and "Bibliography". Dropdown "Results" in the entry-specific toolbar links these 4 pages. Dropdown "Code" gives access to 3 code files ("mydata", "pars_init" and "predict") and a zip file with these 3 files 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 entry name on top of the page links to that entry on the Species List page (see below) to navigate to related species.
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. An extra dropdown "ROOT" at this page gives access to shorter trees. You can create your own tree with any root with AmPtool
- 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.
Dropdown "CONTEXT" presents overview-pages and software for the analysis of the AmP database
- this page
- AmPtool is 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.
- Phyla page presents all animal phyla and indicates presence in the collection; it also shows the occurence of metabolic acceleration among phyla
- 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
- 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
- DEBtool describes a powerful software package, of which AmPtool makes frequent use
- DEBlab is a platform for material exchange, such as comments on DEB theory, notation, course material, software, such as DEBtool and AmPtool
- DEBwiki describes all of the more technical aspects of AmP
- DEBinfo provides general info about DEB theory, such as courses and bibliography; it will eventually be outphased by the DEB portal
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. If an entry is modified, the obsolete zip-file moves to directory entries_archive. A particular version of accepted entries can be referred to as "AmP my_pet_yyyymmdd", where my_pet stands for the scientific species name and yyyymmdd for the acceptance date.
VU Univ. A'dam
Instructions for submissionAdding your pet to the collection starts with editing the templates. Great care should be given to specify were all data come from. All references to the literature should be detailed and collected in the mydata-file, as specified by the templates. All data on rates and times should specify a temperature. If not known, it should be guessed and that should clearly be indicated. If all required files are functional and comply to the requirements and results are obtained, you send the files to one of the curators. If your mydata-file is complete, but you have problems with the rest, your can ask them for help.
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.