MyLake

General Information
Acronym of the model	MyLake
Full name of the model	Multi-year simulation model for Lake thermo- and phytoplankton dynamics
Model components	Hydrodynamics, Chemistry, Biology
Supported platforms	Windows, Mac, Linux
Programming Language	MATLAB
Still maintained	Yes, by: Raoul-Marie Couture (et al.)
Most recent version	MyLake v1.2 (public); MyLake v2.0 & MyLake-C
Model structure
Needs compilation
1D
Other: Flexible grid
Model description
Model objective	Investigate, predict, or test hypotheses related to lake hydrodynamics and ice cover
Specific application	“The MyLake lake model is best suited for applications having the following characteristics: 1) the geometry of the lake basin lends itself to the 1D assumption, which neglects lateral heterogeneity, or if you can accept the limitation of working with a single 1D profile; 2) you favour short integration time over model complexity; 3) you do not need complex lake physics or ecological modelling (e.g., saline or groundwater intrusions, reservoir management, food-web, etc.); 4) you want access to the source code and would like to modify it yourself if necessary; 5) the lake experiences seasonal ice cover.” (Couture & Tominaga 2016)
Background knowledge needed to run model	Basic knowledge of MATLAB programming
Basic procedures

For one model time step*(24 h): 1) Calculate surface heat fluxes and wind stress, light attenuation, and phytoplankton growth and loss rates 2) Calculate profile of the diffusion coefficient K 3) Calculate the heat flux between water and sediment (taken as heat source/sink for each layer) 4) Solve new profile for each state variable taking into account advection, diffusion and local sources/sinks. Solving is done in following order: 1) temperature, 2) tracers, 3) chlorophyll-a, 4) particulate phosphorus, 5) dissolved phosphorus. 5) Update content of the sediment stores of chlorophyll a and particulate phosphorus A) *If no ice:* i) Check for (and possibly proceed) autumn/spring turnover B) If ice cover: a) If Ta(Table 1, from Saloranta & Andersen 2004) |
|\2. “MyLake (Multi-year simulation model for Lake thermo- and phytoplankton dynamics) is a one-dimensional process-based model code for simulation of daily 1) vertical distribution of lake water temperature and thus stratification, 2) evolution of seasonal lake ice and snow cover, and 3) phosphorus-phytoplankton dynamics. MyLake has a relatively simple and transparent model structure, it is easy to set up, and is suitable both for making predictions and scenarios, and to be used as an investigative tool. Short runtime allows application of comprehensive sensitivity and uncertainty analysis as well as simulation of a large number of lakes or over long periods (decades). MyLake aims to include only the most significant physical, chemical and biological processes in a well-balanced and robust way.”
(Saloranta & Andersen 2004) |
| Link to website/manual | Model Source Code
Manual
|
|_\2. Model characteristics |
| Input variables | Obligatory: – Lake morphometry and initial profiles
- Meteorological forcing (air temperature, air pressure, wind speed, relative humidity, precipitation, irradiance)
- Inflow loadings (water volume, particulates, total nutrients)

Optional:|
| Input file format | .xls
Other, namely: MyLake v2.0 requires .txt|
|Output variables | – Temperature profile
- Snow and ice cover (presence/absence, thickness, temperature)
- Nutrient profiles
- Chlorophyll-a profile
- Light attenuation profile
- Sediment heat flux|
| Output file format | Other, namely: .mat (can be exported from MATLAB as .csv or other file format) |
| Biogeochemical model components |- Nutrients: inorganic P, particulate P
- Phytoplankton: phytoplankton biomass C, measured as chlorophyll-a and dissolved inorganic phosphorus (phosphate) P; fixed C:P composition
- Zooplankton: not included in model|
|Model structure/mathematical framework | Partial differential equations|
| Temporal resolution | Daily|
| Minimal spatial resolution | 0.5 m|
| Variables needing calibration | – Primary: water temperature (dissolved oxygen in v2.0)
- Additional: nutrients, chlorophyll-a|
|\2. Has successfully been used in |
| Climate Change Scenario | Couture et al. 2015
Kiuru et al. 2018|
| Oligotrophic water| unpublished application |
| Mesotrophic water| Kiuru et al. 2018|
| Has coding for| Ice dynamics, sediment heat flux, sediment dynamics|
|\2. Accessibility |
|\2. Open-Source, Open-to-use, Test cases available|
| Available tools for pre- and post-processing | Some exemplary tools from individual applications available at https://github.com/biogeochemistry |
| Support | Support|
| How can someone get access to this model| To gain access to the Mylake private GitHub send your github username to: raoul.couture@chm.ulaval.ca|
|_\2. Miscellaneous|
| Comments | Development of new versions and revisions often occur in parallel due to the open source nature of the model. The MyLake GitHub keeps these rather up-to-date with relevant applications, publications, and manuals for new versions.|
| Useful tricks and hints | Publicly-available application of MyLake in R|
| Links | Manual
MyLake GitHub
Toolbox|
|\2. Form was updated: 2019-07-22 |

Reference list:

Saloranta & Andersen 2007 (https://doi.org/10.1016/j.ecolmodel.2007.03.018)
Gebre et al. 2014 (doi:10.5194/tc-8-1589-2014)
Couture et al. 2015 (https://doi.org/10.1002/2015JG003065)
Kiuru et al. 2018 (https://doi.org/10.1029/2018JG004585)
Couture et al. 2018 (https://doi.org/10.1016/j.scitotenv.2017.11.303)