Andy’s, like, whatever  pages
ccGENIE.muffin EMIC
GENIE website (RIP)
got data?
Ocean observations [regridded, netCDF format]:
(1a) WOA2009 / worjh2 grid: NO3 O2 PO4 H4SiO4 temp sal
(1b) WOA2009 / worlg4 grid: NO3 O2 PO4 H4SiO4 temp sal
(2a) GLODAP / worjh2 grid: DIC ALK C14 CFC11 AnthCO2
(2b) GLODAP / worlg4 grid: DIC ALK C14 CFC11 AnthCO2
(3a) WOA2013 / worjh2 grid: NO3 O2 PO4 H4SiO4 temp sal
(3b) WOA2013 / worlg4 grid: NO3 O2 PO4 H4SiO4 temp sal
(4) OLD / worap2 grid: ALL
(5) Fe: worlg4 grid
(6) IO3-, I-: TBA
(7) Re-gridded PETM SST data from Dunkley Jones et al. [2013]: pre-PETM; peak-PETM
(8) Observations for ECOGEM
(9) Benthic d13C data for: late Holocene and LGM
got (the) runs?
got software?
linux netCDF 4.0 source code
Simple Windoz SSH client
Project cupcake
cgenie.cupcake on GitHub
cupcake GUI video
mailing lists
(TBA)
muffin resources: DOCUMENTATION
   * Current (cGENIE.)muffin documentation
   (cGENIE.)muffin combined user-manual and an introduction to Earth system modelling tutorials. (Also incorporating previous HOW-TO documentation.)
SEE: derpycode/muffindoc on GitHub for latex source.
WARNING: Documentation in varying degrees of not updated-ness ...
   Various model experiment EXAMPLES, including example model configurations, experimental designs, and associated namelist parameter descriptions.
   Namelist parameters in a separate and shocking incomplete/outdated Table.
GEO266 -- Introduction to Earth system modelling
   * GEO266 class guide (including syllabus and course overview) [CHECK BACK FOR UPDATES!].
   * GEO266 course text (the 'muffin manual'!) [CHECK BACK FOR UPDATES!].
   * GEO266 example (complete) class guide [old from 2019/20 and FYI only].
   * domino.ucr.edu cluster useage rules and account configuration instructions.
   * Lectures: ...
cGENIE resources: *legacy* (not current) documentation
   * (1) Previous cGENIE.muffin documentation
   The soon-to-be infamous Quick-start Guide (also see platform-specific variant -- box on left) plus the all important and vital READ-ME that you inevitably will not read ....
WARNING: Documentation in varying degrees of not updated-ness ... and there is no chance now of it ever being complete now either ...
   User manual, with details of the namelist parameters given in a separate and shocking incomplete/outdated Table.
   Various model experiment EXAMPLES, including example model configurations, experimental designs, and associated namelist parameter descriptions.
   The cGENIE HOW-TO - potted explanations of how to get useful stuff done, e.g., spinning up deep-sea sediment distributions.
   * (2) Original cGENIE branch documentation
   cGENIE (biogeochemistry focused) User manual.
Various model experiment EXAMPLES.
The cGENIE HOW-TO.
The soon-to-be infamous Quick-start Guide.
SYR 2020 muffin (Earth system) modelling workshop
   * 2020 SYR muffin workshop guide.
   * muffin model user manaul (and tutorials).
   * domino.ucr.edu cluster useage rules and account configuration instructions (for reference only).
LDEO 2020 muffin (Earth system) modelling workshop
   * 2020 LDEO muffin workshop guide.
   * muffin model user manaul (and tutorials).
   * domino.ucr.edu cluster useage rules and account configuration instructions (for reference only).
GE290: Introduction to Earth system modelling (2019/20)
   * GEO290 course guide *to-date* (including syllabus and course overview).
   * The GEO290 course text (the 'muffin manual'!) [in revision].
   * domino.ucr.edu cluster useage rules and account configuration instructions.
   * Lectures: 191002; 191004; 191016; 191023.
cGENIE resources: WORKSHOPS -- UoB 2018
   * Course Information:
   Workshop guide.
   Course book (muffin manual).
   * Additional resources and information:
   Basic use of the vi editor.
   Basic linux (MLP edition).
   Presentation
cGENIE resources: GEO290
   * Course Information
   Course guide.
   Course book.
   * Individual course tutorials
   Lesson #0 == cGENIE modelling basics
Lesson #1 == Snowball Earth + experiments in climate hysteresis.
Lesson #2 == Ocean circulation and overturning stability.
Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification.
Lesson #4 == Ocean biogeochemical cycles and the ‘biological pump’.
Lesson x  == Long-term regulation of atmospheric pCO2.
cGENIE resources: WORKSHOPS [OLD -- AWI.2017]
   * Course Introduction
   Boring presentation.
   * Earth system modelling course
   Course program details.
Lab instructions [basic course]:
Lesson #0 == cGENIE modelling basics
Lesson #1 == Snowball Earth + experiments in climate hysteresis.
Lesson #2 == Ocean circulation and overturning stability.
Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification.
Lesson #4 == Engineering the carbon cycle and the ‘biological pump’.
   Lab instructions [advanced]:
Lesson #5 (I) == Greenhouse climates of the past: the late Cretaceous.
Lesson #5 (II) == Greenhouse climates of the past: early Eocene.
cGENIE resources: WORKSHOPS [OLD -- UoB.2016]
   * Course Introduction
   Boring presentation
   * (1) Earth system modelling course
   Course details.
Lab instructions:
Lesson #0 == cGENIE modelling basics
Lesson #1 == Snowball Earth + experiments in climate hysteresis.
Lesson #2 == Ocean circulation and overturning stability.
Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification.
Lesson #4 == Engineering the carbon cycle and the ‘biological pump’.
   * (2) EcoGEnIE ecosystem modelling course
   Course details.
Lab instructions:
Lesson 0.a == cGENIE modelling basics
Lesson 0.b == Snowball Earth + experiments in climate hysteresis.
Lesson 0.c == Ocean circulation and overturning stability.
Lesson 0.d == The oceans biological pump.
Lesson 1.a == Running EcoGEnIE and visualising output.
Lesson 1.b == Ecosystem configuration.
Lesson 2.0 == Increasing ecological complexity.
Lesson 3.0 == Build it up, tear it down.
Lesson 4.0 == Ecology in a paleo-ocean.
cGENIE resources: WORKSHOPS [OLD -- Yale.2016]
   * INFO:
Course details.
   * Lab instructions:
Lesson #0 == cGENIE modelling basics
Lesson #1 == Snowball Earth + experiments in climate hysteresis [ + optional ideas for further investigation -- Lesson #1b].
Lesson #2 == Ocean circulation and overturning stability [ + optional ideas for further investigation -- Lesson #2b].
Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification [ + optional ideas for further investigation -- Lesson #3b].
Lesson x == Long-term regulation of atmospheric pCO2.
cGENIE resources: WORKSHOPS [OLD -- UoB.2015]
   * INFO:
Course details.
Presentation.
   * Lab instructions:
Lesson #0 == cGENIE modelling basics
Lesson #1 == Snowball Earth + experiments in climate hysteresis.
Lesson #2 == Ocean circulation and overturning stability.
Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification.
Lesson #4 == Engineering the carbon cycle and the ‘biological pump’.
cGENIE resources: WORKSHOPS [OLD -- AWI.2015]
   * INFO:
Workshop outline.
   * Lab instructions:
Lesson #0 == cGENIE modelling basics
Lesson #1 == Snowball Earth + experiments in climate hysteresis.
Lesson #2 == Ocean circulation and overturning stability.
Lesson #3 == Fossil fuel CO2 release and ‘ocean acidification.
Lesson #4 == Engineering the carbon cycle and the ‘biological pump’.
cGENIE resources: TEACHING LABS [OLD -- GEOGM1110 / GEOGM1404]
   * INFO: Course outline; non-intimidating linux 101 (MLP version).
Lab instructions: Session #0000 == cGENIE modelling basics + experiments in climate hysteresis // Session #0001 == Ocean circulation and overturning stability // Session #0100 == Fossil fuel CO2 release and ‘ocean acidification’ plus a supplement summerizing ocean acidification relevant results variables, and both together in a revised Session #0100 document // Session #0101: GEOGM1110 == Engineering the carbon cycle (GEOGM1110) // Session #0101: GEOGM1404 == Engineering the carbon cycle (GEOGM1404).
INFO: Simple introduction to ocean acidiciation // and a slightly more in-depth guide with fuller referencing.
Resources: potted references.
Software (PC): SSH client; Current Panoply netCDF viewer, OR ... (old) version of Panoply; SCIntilla based Text Editor ['full download' under: 'Windows Executables'].
cGENIE resources: WORKSHOPS [OLD -- Urbino.2013] Lab instructions: Session #0000 == cGENIE modelling basics + experiments in climate hysteresis // Session #0001 == Ocean circulation and overturning stability // Session #0100 == Fossil fuel CO2 release and ‘ocean acidification’.
Software (PC): SSH client; Panoply netCDF viewer; SCIntilla based Text Editor ['full download' under: 'Windows Executables'].
   * INFO: Workshop outline.
cGENIE resources: WORKSHOPS [OLD -- UoB.2013]
Lab instructions: Session #0000 == cGENIE modelling basics + experiments in climate hysteresis // Session #0001 == Ocean circulation and overturning stability // Session #0100 == Fossil fuel CO2 release and ‘ocean acidification’ // Session #0101 == Engineering the carbon cycle.
   * INFO: Workshop outline.
cGENIE resources: WORKSHOPS [OLD -- LifeAndThePlanet.2013]
Lab instructions: Session #0000 == cGENIE modelling basics + experiments in climate hysteresis // Session #0001 == Ocean circulation and overturning stability // Session #0100 == Fossil fuel CO2 release and ‘ocean acidification’ // Session #0101 == Engineering the carbon cycle.
   * INFO: Workshop outline [REVISED].
cGENIE resources: WORKSHOPS [OLD -- AWI.2013]
   * INFO: Workshop outline [REVISED] (also: Basic course flier, Advanced course flier).
Lab instructions: Session #0000: cGENIE modelling basics + experiments in climate hysteresis; Session #0001: Ocean circulation and overturning stability; Session #0010: Greenhouse climates of the past: the late Cretaceous; Session #0100: Fossil fuel CO2 release and ‘ocean acidification’; Session #0101: Engineering the carbon cycle; Session #1000: How long is ‘forever’? -- The long tail of CO2 and other tales from the sediments.
cGENIE resources: WORKSHOPS [OLD -- Caltech.2013]
   * INFO: Workshop outline.
Lab instructions: Session I+II: cGENIE modelling basics + experiments in climate hysteresis; Session III+IV README; Session III: Ocean circulation and overturning stability; Session IV: Consequences of fossil fuel CO2 release and ‘ocean acidification’, Session V: How long is ‘forever’? (role of deep-sea sediments in long-term carbon cycling), Session XX: 'Preformed nutrient' tracers of ocean biogeochemical cycling.
cGENIE resources: WORKSHOPS [OLD -- UCSC2012]
   * INFO: Workshop outline.
Lab instructions: Session I+II: cGENIE modelling basics + experiments in climate hysteresis; Session III+IV README; Session III: Ocean circulation and overturning stability; Session IV: Consequences of fossil fuel CO2 release and ‘ocean acidification’; Session V: How long is ‘forever’?.
Software (PC): SSH client; Panoply netCDF viewer (requires Java -- unzipping is only installation required); Freeware 'SciTE' text editor [direct link].
cGENIE resources: WORKSHOPS & TEACHING LABS [OLD -- MISC]
   * *UoB2012* Presentations: Course introduction.
   * *USSP2012* Handouts (main): Session I; Session II; Session IIIa; Session IIIb; Session IIIc. Software (PC): SSH client; Panoply netCDF viewer OR ... old Panoply (works better); SCIntilla based Text Editor.
   * *Cardiff2012* Handouts (main): Session I; Session II; Session III; Session IV; Session Va; Session Vb; Session VI.
   * *AWI2011* Handouts (main): Session I; Session II; Session III; Session IV; Session V; Handouts (additional): Session VI; Session VII; Re-starts: Basic re-start package (Labs I - V); 'glacial' re-start (VI + VII).
   * *USSP2011* Handouts: Session I; Session II; Session III; (Session IV); Session V; (Session VI). Software (PC): SSH client; Panoply netCDF viewer; SCIntilla based Text Editor.
Miscellaneous
   * Project home page for the Grid Enabled Integrated Earth system model - GEnIE (a Grid-based, modular, distributed and scaleable Earth System Model for long-term and paleo-climate studies). Sounds good? Hell; that's because it is ;)
   * Graphics resources (various project logos and GEnIE model schematics).
   * Original marine carbon cycle 'tutorial' (including cb/s-goldstein user-manual), in html and PDF formats.This is actually something of a standard project joke, as it is well known that I rarely get around to finishing anything useful. Maybe I should get my finger out? You, the jury decide. Vote here.
   * Miscellaneous model documentation such as descriptions of previous model versions and stuff.