Calendar for DEB milestones
| year | milestones |
|---|---|
| 2024 |
"complete" taxa in AmP: branchiopods; distribution of parameter estimators |
| 2023 |
creation of GitHub repository SI with supporting information for a number of papers, e.g. to illustrate the use of AmPtool;
creation of simu_my_pet within AmPtool,
which shows trajectories of key variables in a variable environment over 4000 AmP entries; frequent revisions of entries/taxonomy Revision of a large number of entries |
| 2022 |
replacement of DEBwiki on IST-server by GitHub repository DEBportal; bi-variate and tri-variate data types in AmP with multiple visualisation options; creation of GitHub repository AmPtox with various examples of AmP supported tox applications; hax-model as typified model for some insects; compaction of AmPdata to speed-up AmP performance and improved graphics presentation and browsing; pages taxa, links and ecoCodes in the "COLLECTION" dropdown with hide-column and search-species option; |
| 2021 |
over 3200 AmP entries; frequent revisions of entries/taxonomy; get_id functions for 14 websites and update of all links "complete" taxa in AmP: cephalopods, turtles/crocodiles, carnivores/pangolins; over 1000 DEB library papers on Zotero (1.5 per wk); more DEB videos on many topics with search options; distance between species based on traits, linking to multi dimensional scaling; galleryAmP with links to species_tree; hosting of AmP at IUEM (Brest) (VU, Amsterdam continues), with automatized syncing; evolutionary algorithms as alternative for the simplex method for parameter estimation by Juan Robles; DEB Shiny App and DEBsea Shiny App in R by Mike Kearney; life-time cumulated neonate mass equals mass of female at death; |
| 2020 |
"complete" taxa in AmP: N-Am freshwater fish, rays/sharks; allEco integrated in allStat, ecoCodes & links in mydata; shstat with eco-codes; allStat and popStat in AmPdata on VU-server with version date; AmP entry prepare system with documentation; import info via structures; further improved presentation/ documentation/ archiving/ searching: e.g. report_my_pet, 6 results_output levels, get_links, select entries for char-strings; augmented loss functions for multi-species further developed; elasticities for bijection data- to parameter-space; pop growth at constant T, f; All entries have a population-traits page; macro-chemical reaction equation coefficients at population level; AmP code for CPM, EBT (Escalator Boxcar train), IBM (Ind-Based pop. Modelling in NetLogo); |
| 2019 |
1806 AmP entries; more cases with f(t), T(t): integration of estimation and environmental trajectory reconstruction; "complete" taxa in AmP: petrels/penguins; 790 DEB library papers on Zotero; better knowledge of pars and patterns: better context for par-evaluation (151 entries in archive); revisions of some basic functions: temperature correction for >1 parameters, maturity for large l_p; updates on evolutionary tree (detailed trees change more frequently); use of clade to identify AmP entries that are most related to one that is not in the collection (Taxonomicon, CoL); improved presentation/documentation/archiving/searching: bib's, citation, manual (DEBwiki, AmPtool); prt_results_my_pet for iteration results; prt_report_my_pet with searching, comparing species, color coding excentricity; application pages on AmP website: work in progress; |
| 2018 |
Searching in species_tree, links from entries to list & tree; self-made tree with distribution of statistics; pedigree with statistics; improved algorithms; confidence intervals based on loss-function profiles; multi-species parameter estimation, augmented loss functions; "complete" taxa in AmP: carnivores; |
| 2017 |
700 AmP entries; changes in the curator team; curation reports/procedure: modular setup; allStat & allEco on GitHub: eco-coding + selection/visualization functions; links to large websites/data-bases; general: Catalog of Life, Taxonomicon, EoL, ADW, Wiki, WoRMS; specialized: molluscabase, fishbase, amphibiaweb, reptile-database, avibase, msw3, AnAge; structure allStat.mat with data for all AmP species; |
| 2016 |
Start of DEBlib on Zotero; setup of DEBtheory.org portal, DEBwiki; |
| 2015 |
318 AmP entries, conversion from Excel-based old to web-based new system with code AmPtool and DEBtool on GitHub; set-up of BibTex-style reference list for each entry; use of Overleaf & Dropbox for organisation in the curator team; creation of debtheory.org; setup of standard in code-documentation and checking-procedures for new entries; Perl-based lists-of-lists for taxonomic structure of entries; creation of DEB mailing list; |
| 2014 |
NECs depend on specific somatic maintenance with Jan Baas; typical reproduction is much less than max with Dina Lika; formation of curator team with weekly Skype's and yearly workshops; set-up par-estimation procedure for multiple entries; use of .mat-files for continuation styling of DEB models, data, parameters; |
| 2013 |
Waste-to-hurry; DEBtool_Octave support is ceased; |
| 2012 |
Bijection between data- and parameter space; quantification of supply-demand spectra; |
| 2011 |
Type R-acceleration of maturation with Starrlight Augustine; interactions between photo-synthesis, -respiration & -inhibition; start of practical schools prior to DEB symposia with special issues; |
| 2010 |
Topology of allocation schemes with Dina Lika; start of comment-document on DEB3; embryo staging with Starrlight Augustine; |
| 2009 |
Reserve dynamics as consequence of weak homeostasis, partitionablility of reserve dynamics; evolution of central metabolism; start of AQUAdeb group on initiative of Marianne Alunno-Bruscia with regular meetings; first DEB symposium (Brest) with special issue; AmP entries as course exercise; |
| 2008 |
Start writing of DEB3; setting-up of add_my_pet; mergeability of reserve dynamics with Tània Sousa; |
| 2007 |
Type M-acceleration of metabolism with Laure Pecquerie; toxicity of mixtures of many compounds with Jan Baas and Tjalling Jager; |
| 2006 |
Isotope dynamics at individual level; |
| 2005 |
Stochastic mass-conserved formulations for DEB structured popopulations with Johan Grasman & Bob Kooi; entropy of living individuals with Tània Sousa; application of Adaptive Dynamics to DEB structured populations with Tineke Troost & Bob Kooi; |
| 2004 |
Handshaking protocols for Synthesizing Units; mitochondria-cytosol interactions with Lee Segel; |
| 2003 |
Generalisations of the κ-rule; tumour growth, consistency with Mayneord 1932; co-metabolism in microbial degradation, with Bernd Brandt; |
| 2002 |
Ageing acceleration; hazard model for lethal effects of toxicants; Gompertz stress coefficient with Ingeborg van Leeuwen; |
| 2001 |
First tele course, to be repeated each 2 years; stepwise merging of symbiontic partners into a new individual; |
| 2000 |
Conversion of private APL code to public DEBtool in Matlab/Octave; modules for mixotrophy; co-metabolism & inhibition with SUs; |
| 1999 |
Toxicity of mixtures of compounds; reconstruction of film models: explicit pde and boundary conditions co-var rules for parameters one-compartment and film models and for effects of toxicants; |
| 1998 |
Start writing of DEB2; symbiosis on the basis of mutual syntrophy; effect of ionization and lipid content on toxico-kinetics; diverse uptake and elimination routes for toxicants; interaction of toxico-kinetics with metabolism; |
| 1997 |
Excretion of reserves for multiple reserves; Canonical communities; |
| 1996 |
Synthesising Units (SUs) as alternative for enzyme kinetics; writing of analysis of toxicity data with Jacques Bedaux; presentation of this book in OECD workshop (Braunschweig); |
| 1994 |
Multiple substrates, reserves & structures: plants model; |
| 1993 |
First local DEB course based on DEB1; dynamic generalizations of the κ-rule; |
| 1992 |
Static generalisations of the κ-rule; |
| 1991 |
Multiple reserve & partition. of reserve kinetics; |
| 1990 |
Start writing of DEB1; type T-acceleration of metabolism; consistency with Nelder 1961 for bird growth; |
| 1989 |
Ageing as accumulation of damage in 2 steps; Weibull ageing rate; consistency with Gompertz 1825, Weibull 1951; microbial food chains with Bob Kooi; re-interpretation of Drent 1976 data; |
| 1988 |
Reconstruction of food uptake from growth; |
| 1987 |
Mass as conserved quantity in combination with energy; respiration as in indirect calorimetry; consistency with Lavoisier 1780; step from macro- to micro-chemical reaction equations; renovation of DEB notation; |
| 1986 |
The name DEB was chosen on instigation by Joos Joosse; microbial product formation & fermentation: consistency with Leudeking-Piret 1958; |
| 1985 |
Shape correction function; changes in shape; bacteria as static mixtures between V0- and V1-morphs, consistency with Marr-Pirt 1962; |
| 1984 |
Maturity maintenance as energy sink with Horst Thieme; |
| 1983 |
Physical co-variation rules of DEB parameters; consistency with Kleiber 1932; bacterial populations as juveniles; foetal development, consistency with Huggett-Widdas 1951; |
| 1982 |
Embryos are juveniles that don't eat; consistency with Rahn & Ar 1974 for respiration in bird embryos and Smith 1957 in fish embryos; costs of eggs & maternal effects; maturity as state variable; |
| 1981 |
Reserve dynamics reconstructed from cell quota of Droop 1973; effects of toxicants at population level; setup of DEB notation; |
| 1980 |
Sublethal effects of toxicants as changes in parameter-values; parameter values linear in internal concentrations; |
| 1979 |
Start of DEB work with Holling 1959, Pütter 1920, Arrhenius 1889 & κ-rule; start of work on physiologically structured pop. dynamics with Hans Metz & Odo Diekmann; |
| 1978 |
No Effect Concentration (NEC) as tox parameter; |
| 1977 |
Effects of toxicants on survival depend in internal concentration; one compartment model as basic transport model (first TKTD model) ; LC50 as function of exposure time; |