Andy’s, like, whatever  pages
cGENIE 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: TBA
(6) IO3-, I-: TBA
(7) Re-gridded PETM SST data from Dunkley Jones et al. [2013]: pre-PETM; peak-PETM
(8) Observations for ECOGEM
got muffin?
Quick-start Guides:
(1) Bristol cluster
(2) generic linux
(3) Mac
(4) Windows
general:
READ-ME
got software?
linux netCDF 4.0 source code
Simple Windoz SSH client
mailing lists
CGENIE-DISCUSS @GENIE_ESM
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   Namelist parameters in a separate and shocking incomplete/outdated Table.
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: Legacy 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   User manual, with details of the namelist parameters given in a separate and shocking incomplete/outdated Table.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.
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: TEACHING LABS [OLD -- GEOGM1110(EC4)/M1404]
   * INFO: Course overview; GENIE overview/review; Snowball Earth (Week 2 LECTURE); Ocean Acidification (Week 6 LECTURE); The long tail of fossil fuel CO2, glacial carbon cycling, and other tall tales (Week 7 LECTURE); Assessment #1 instructions; Ocean acidification animation [WARNING: LARGE FILE!] -- surface aragonite; Ocean acidification animation [WARNING: LARGE FILE!] -- benthic calcite; Assessment #2 instructions.
Lab handouts: Session I lab; Session II lab; Session III lab; Session IV lab; Session V lab.
Resources: potted references.
Software (PC): SSH client; Panoply netCDF viewer OR ... old Panoply is old (but works with current netCDF!); SCIntilla based Text Editor ['full download' under: 'Windows Executables'].
Re-starts: Modern (standard 16-level ocean); pre-snowball state(8-level ocean).
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.