nyuuzyou/wikis huggingface dataset:
Labs Git

==Automated Version Control==
<BR>
Learning Objectives
*Understand the benefits of an automated version control system.<BR>
*Understand the basics of how Git works.
<BR>
We'll start by exploring how version control can be used to keep track of what one person did and when. We've all been in this situation before: it seems ridiculous to have multiple nearly-identical versions of the same document. Some word processors let us deal with this a little better, such as Microsoft Word's "Track Changes" or Google Docs' version history. Even if you aren't collaborating with other people, automated version control is much better than this situation:
PHD Comics: notFinal.doc
Version control systems start with a base version of the document and then save just the changes you made at each step of the way. You can think of it as a tape: if you rewind the tape and start at the base document, then you can play back each change and end up with your latest version.
 
 
 
 
Once you think of changes as separate from the document itself, you can then think about "playing back" different sets of changes onto the base document and getting different versions of the document. For example, two users can make independent sets of changes based on the same document. If there aren't conflicts, you can even try to play two sets of changes onto the same base document.
A version control system is a tool that keeps track of these changes for us and helps us version and merge our files. It allows you to decide which changes make up the next version, called a commit, and keeps useful metadata about them. The complete history of commits for a particular project and their metadata make up a repository. Repositories can be kept in sync across different computers facilitating collaboration among different people.
<BR><BR>
The long history of version control systems
Automated version control systems are nothing new. Tools like RCS, CVS, or Subversion have been around since the early 1980s and are used by many large companies. However, many of these are now becoming considered as legacy systems due to various limitations in their capabilities. In particular, the more modern systems, such as Git and Mercurial are distributed, meaning that they do not need a centralized server to host the repository. These modern systems also include powerful merging tools that make it possible for multiple authors to work within the same files concurrently.
<BR>
Labs Git 01

==Automated Version Control==
<- Back to Version Control Tutorial
<BR><BR>
Learning Objectives
*Understand the benefits of an automated version control system.<BR>
*Understand the basics of how Git works.
<BR>
We'll start by exploring how version control can be used to keep track of what one person did and when. We've all been in this situation before: it seems ridiculous to have multiple nearly-identical versions of the same document. Some word processors let us deal with this a little better, such as Microsoft Word's "Track Changes" or Google Docs' version history. Even if you aren't collaborating with other people, automated version control is much better than this situation:
PHD Comics: notFinal.doc
Version control systems start with a base version of the document and then save just the changes you made at each step of the way. You can think of it as a tape: if you rewind the tape and start at the base document, then you can play back each change and end up with your latest version.
 
 
 
 
Once you think of changes as separate from the document itself, you can then think about "playing back" different sets of changes onto the base document and getting different versions of the document. For example, two users can make independent sets of changes based on the same document. If there aren't conflicts, you can even try to play two sets of changes onto the same base document.
A version control system is a tool that keeps track of these changes for us and helps us version and merge our files. It allows you to decide which changes make up the next version, called a commit, and keeps useful metadata about them. The complete history of commits for a particular project and their metadata make up a repository. Repositories can be kept in sync across different computers facilitating collaboration among different people.
<BR><BR>
The long history of version control systems
Automated version control systems are nothing new. Tools like RCS, CVS, or Subversion have been around since the early 1980s and are used by many large companies. However, many of these are now becoming considered as legacy systems due to various limitations in their capabilities. In particular, the more modern systems, such as Git and Mercurial are distributed, meaning that they do not need a centralized server to host the repository. These modern systems also include powerful merging tools that make it possible for multiple authors to work within the same files concurrently.
<BR>
Labs WMT CEM

==Coastal Evolution==
The Coastline Evolution Model (CEM) addresses predominately sandy, wave-dominated coastlines on time-scales ranging from years to millenia and on spatial scales ranging from kilometers to hundreds of kilometers. Shoreline evolution results from gradients in wave-driven alongshore sediment transport. The model has been used to represent varying geology underlying a sandy coastline and shoreface in a simplified manner and enables the simulation of coastline evolution when sediment supply from an eroding shoreface may be constrained. CEM also supports the simulation of human manipulations to coastline evolution through beach nourishment or hard structures. To learn more about the models in this lab, specifically the Coastal Evolution Model, CEM, you can download this presentation.
This lab includes experiments to couple the terrestrial and coastal domains. We will be looking at a river supplying sediment to a coastal zone, along which wave-driven longshore transport occurs. We will learn about the effect of incoming wave fields, the effect of sediment supply to the coast, and whether this supply happens through a single delta channel or multiple delta channels. Many deltas are classified as wave-dominated deltas, the Arno Delta in Italy is one example.
This lab will run CEM simulation with Python Modeling Tool (Pymt). If you have never used the Pymt, learn how to use it here. The Pymt allows you to set up simulations and run notebooks.
If you are a faculty at an academic institution, it is possible to work with us to get temporary teaching accounts. Work directly with us by emailing: csdms@colorado.edu 
Learning objectives
Skills:
*use Pymt to run CEM Model
*familiarize with a basic configuration of the CEM Model
*make changes to key input parameters
*hands-on experience with visualizing output in Python
Topical learning objectives:
*generate a wave-dominated delta
*explore the influence of wave conditions (e.g., wave height, wave angle) on delta formation
*explore the influence of river input on delta formation
Lab Notes
You can launch binder to directly run the Jupyter Notebook for this lab through a web browser. 
>> Open a new browser window and open the Pymt read the docs page here 
>> You will see that there are several example models. In this lab we will select the Coastline Evolution Model. 
>> Click on the 'Launch Binder' box and it will allow you to see this lab as a Jupyter Notebook.
>> You can execute the Jupyter notebook code cells using shift -enter.
References
* Ashton, A, A.B. Murray, and O. Arnoult. 2001. Formation of coastline features by large-scale instabilities induced by high-angle waves. Nature 414: 296-300., 10.1038/35104541
* Ashton, A.D. and Murray, A.B., 2006. High-angle wave instability and emergent shoreline shapes: 2. Wave climate analysis and comparisons to nature. Journal of Geophysical Research 111. F04012., 10.1029/2005JF000423
More on Model description and code
* CEM source code: Look at the files that have *deltas* in their name.
* CEM description on CSDMS: Detailed information on the CEM model.
Labs WMT Ganges Sediment Supply

==Modeling the Future Sediment Flux of the Ganges River with HydroTrend==
Introduction
The Ganges-Brahmaputra Delta is one of the largest deltas in the world. In Bangladesh alone, 160 million people live in the floodplains. The Ganges and Brahmaputra Rivers and their delta are strongly impacted by the Asian summer monsoon. Widespread hazards relate to the intense seasonal rainfall: flooding, river erosion and channel switches. The people of Bangladesh have adapted to this dynamic delta system, they have raised villages above the annual flood level and embanked agricultural land. 
Still, the lowlands of the Ganges-Brahmaputra Delta are considered one of the regions most at risk from climate change, and particularly from sea level rise. About 75 million people live in the GB coastal zone (defined as the region <10 m.a.s.l). It is thought that the impact of relative sea-level change will be profound in Bangladesh where 32% of the country is already affected by tides, salinization, and cyclones/storm surges. 
At the same time, the Ganges-Brahmaputra river system drains tremendous amounts of sediment (sand, silt and clay) from its steep Himalayan hinterland. We ask: how does this amount of sediment change with a changing monsoonal climate? Does this sediment aggrade fast enough to help counteract rapid sea-level rise? 
Classroom Organization
This lab investigates 1) the modeling of the incoming water and sediment load of the Ganges river, 2) the validity of model output compared to real-world observations, and 3) how future changes in the monsoon possibly affect this sedimentary system and 4) we try to assess the uncertainty of such predictions. 
This lab will run HydroTrend simulation with Python Modeling Tool (Pymt). If you have never used the Pymt, learn how to use it here. The Pymt allows you to set up simulations and run notebooks.
If you are a faculty at an academic institution, it is possible to work with us to get temporary teaching accounts. Work directly with us by emailing: csdms@colorado.edu 
Learning objectives
Skills
*use Pymt to run HydroTrend Model 
*familiarize with a basic configuration of the HydroTrend Model
*make small changes to key input parameters
*hands-on experience with visualizing output in Python
Key Concepts:
*Simulation of the river discharge for Ganges River
*Simulation of the suspended sediment discharge for Ganges River
*What is the mean annual flow for Ganges River
Lab Notes
You can launch binder to directly run the Jupyter Notebook for this lab through a web browser. 
>> Open a new browser window and open the Pymt read the docs page here 
>> You will see that there are several example models. In this lab we will select the HydroTrend model. 
>> Click on the 'Launch Binder' box and it will allow you to see this lab as a Jupyter Notebook.
>> You can execute the Jupyter notebook code cells using shift -enter.
Labs WMT VisualizeOutput

==Visualize and Analyze WMT Model Output==
CSDMS promotes standardized model output formats, i.e. NetCDF files. 
NetCDF, Network Common Data Form, is developed by Unidata. NetCDF files are specifically designed for array-based scientific data and the format is adopted in many domains of the computational geosciences. Good information on NetCDf can be found at Unidata
One option to visualize NetCDF files is to use the Panoply package. 
This free open-source software developed by NASA allows easily visualization of 1) vector data, especially time-series data, and 2) gridded model output. It is also relatively straightforward to makes movies of grid stacks.
In this short lab, we will learn how to do that with three example files created with WMT 
Download Panoply Software at NASA
Visualize a time series of data 
An example file is posted here. This file contains simulation output consisting of daily bedload flux data.
>> download this file, open it up with Panoply 
>> the name of the file reflects the CSDMS standard name of the parameter saved in it. In this case it is a file of the model hydrotrend (which we used in theWMT tutorial). 
>> The file lists sediment bedload, at the end of the river channel. And it has been recorded for 3650 days (or 10 years). 
>> Select the parameters to plot against each other from the header information 
>> Click on 'Create a Plot'
>> Using the menus under the Stroke, Grid and Labels Tabs you can manipulate what your plot looks like. 
Visualize grid data
>> download the example file 
 Plume netcdf file
. 
>> Import the example file into Panoply 
>> You will want to create a plot of the x and y variables 
>> Plot it and play around with the axis labels and colormaps to adapt it to how you want the plot to look like. 
>> Here is how mine came out 
Make a movie of a stack of gridded output
>> download the example file here
>> Just like a single grid, create a plot of the x and y variables 
>> Adapt the color table to an appropriate style 
>> Clean up the labels, and make the captions understandable 
>> Once the map view is to your liking, use export as animation under the Panoply File tab
Landlab

325 px | right 
Version 2.7.0
Landlab (http://landlab.github.io) is an open-source Python library of code that enables users to easily build unique earth surface processes models to address specific hypotheses. The Landlab library contains gridding engines for building regular and irregular grids, process components that act on grid variables, tools for storing and sharing data among the grid and components, and plotting and analysis tools. Process components represent individual processes occurring at the earth’s surface (e.g. growth and death of vegetation, surface water infiltration, linear diffusion of sediment), or drivers of these processes (e.g. rainfall, solar radiation). Users can build models by combining existing process components, or build new components if a required process component does not exist. Landlab was developed by members of the CSDMS community with support from CSDMS and the National Science Foundation (two ACI - SI2 grants).
==Why build another modeling tool?==
Landlab has the rare distinction of being built to make modeling accessible to a wide variety of earth scientists, including those who do not traditionally use computational models. In contrast, most other models are designed to answer a specific hypothesis posed by the developers. 
==What does this mean for new users?==
* Landlab is extensively documented. 
* Users can contact developers with issues. 
* There are tutorials to teach users how to use Landlab. 
* There are classroom tutorials to teach students about different surface processes.
* Many Landlab tutorials are accessible through Hydroshare, an online collaborative environment for sharing data and models, which allows users to test-out Landlab without installing it locally. 
* Landlab has integrated testing to ensure that new code contributions will not break existing code. 
* There is documentation to make contributing code a bit easier.
==Landlab Components and Models==
Numerous people have contributed components and models to landlab. Of these, are described in the CSDMS repository and are listed below. Would you like to add a Landlab component to the below list? Start here: 
</table>
Landlab is an element of the CSDMS Workbench, an integrated system of software tools, technologies, and standards for building and coupling models.
Landscapes into Rock 2010

===William Smith Meeting: Landscapes into Rock , September 21 - 23, 2010===
Date: September 21 to 23, 2010	
Location: London, UK 	
Host:	The Geological Society, London, UK	
 	
 	
 	
 	
 	
Conveners:
Philip Allen 	Imperial College London
Hugh Sinclair 	Edinburgh University
Paul Bishop 	Glasgow University
Robert Gawthorpe	Manchester University
Event Manager:
Alys Hilbourne	alys.hilbourne@beolsoc.org.uk
Call for Abstracts:
Abstract deadline is 31 May.
Website:
www.geolsoc.org.uk/williamsmith2010
Sponsors:
*Community Surface Dynamics Modeling System (CSDMS)
*Statoil 
Aim:
The aim of this meeting is to bring together geoscientists from different sub-disciplines to address the problem of the interactions between erosional and depositional landscapes, sediment routing systems and the building of stratigraphy. By studying these interactions we gain a better understanding of the dynamics of the coupling between exhumation, erosion, transport and deposition of sediment in source to sink systems, and an enhanced ability to invert stratigraphy for forcing mechanisms.
Conference themes:
* THE EROSIONAL ENGINE
** Convenors:
*** Alex Whittaker (Imperial College London)
*** Andy Carter (Birkbeck College, university of London)
** Keynote speakers:
*** Kelin Whipple (Arizona State University)
*** Niels Hovius (Cambridge University)
* THE DYNAMICS OF SEDIMENT ROUTING SYSTEMS
** Convenors:
*** Alex Densmore (Durham University)
*** Ruth Robinson (St. Andrew's University)
** Keynote speakers:
*** James Syvitski (University of Colorado, Boulder)
*** Chris Paola (University of Minnesota)
* LANDSCAPES INTO ROCK: THE MAKING OF STRATIGRAPHY
** Convenors:
*** Sebastien Castelltort (ETH-Zurich)
*** Emma Finch (Manchester University)
** Keynote speakers:
*** Mike Leeder (University of East Anglia) William Smith Lecture 2010
*** Rudy Slingerland (Pennsylvania State University)
* INTEGRATIVE STUDIES OF SEDIMENT ROUTING AND THE PETROLEUM SYSTEM
** Convenors:
*** Ian Lunt (Statoil)
*** Mike Blum (ExxonMobil)
** Keynote speakers:
*** Ole J. Mattinsen (Statoil)
*** Peter Burgess (Shell)
Lectures portal

Lectures are generously contributed by various people. Please make sure to credit the contributors when you are using these lectures.
Contribute lectures? Please email: csdms@colorado.edu
Lectures 	Lectures
200px | left | link=Deltas_short_course 	Deltas: Dynamics, Morphology and Observing of delta processes and human impacts
James Syvitski
Short course on defining the delta environment and its processes, how remote-sensing data is used in deltas, and how humans are impacting deltas
200px | left | link=Chapman_Source_to_Sink 	Source to Sink Systems around the World
Chapman Conference Keynote Lectures
Concepts of sediment dispersal from land origins to marine accumulation: source to sink.
Sediment production in uplands, transfer in rivers and coasts and deposition in the marine domain.
200px | left | link=Plug_and_Play_lectures 	Plug and Play Component Technology
CSDMS IF staff
An introduction in CSDMS models, components, and plug and play technology as a general concept, and a practical introduction into CMT in this context.
200px | left | link=Geological Modeling 	Surface Dynamics Modeling
Irina Overeem
These presentations are part of a graduate student short course on "Surface Dynamics Modeling".
200px | left | link=Source_to_Sink_Modeling_Lectures	Short Course on Source To Sink Modeling
Irina Overeem and Albert Kettner
These presentations focus on modeling of a drainage basin and its sediment supply to a marine basin over medium to long time-scales, intended for graduate level teaching. 
This short course consists of 4 presentations.
200px | left | link=Geological Modeling 	Geological Modeling
Irina Overeem
These presentations focus on Geological Modeling over medium to long time-scales, intended for graduate level teaching in geology and petroleum engineering. This course consists of 7 presentations.
200px | left | link= 1D Sediment Transport 	1D Sediment Transport
Gary Parker
These modules are developed as an online resource on sediment transport modeling intended for graduate level courses. Excel files serve as illustration and excercises with different topics. Part of the Excel files contain Visual Basic for Applications code.
200px | left | link=Morphodynamics of Rivers 	Morphodynamics of Rivers
Gary Parker
These modules are developed as an online resource on river morphodynamics intended for graduate level courses.
200px | left | link=Earth-Surface_Dynamics_Modeling 	Quantitative Earth-Surface Dynamics Modeling
James P.M. Syvitski
<BR><BR>
These presentations form a overview course on Earth-surface Dynamics Modeling & Model Coupling, intended for graduate level.
Logos

=CSDMS Logos=
Feel free to use one of the below CSDMS logos.
==Vertical Logo==
 
 
 Colored logo, vertical, transparent background with tag line: 'Community Surface Dynamics Modeling System'.
 Download high res. PNGDownload low res. PNG
 
 
 
 Colored logo, vertical, transparent background, no tag line.
 Download high res. PNGDownload low res. PNG
 
==Horizontal Logo==
 
 
 Colored logo, horizontal, transparent background with tag line: 'Community Surface Dynamics Modeling System'.
 Download high res. PNGDownload low res. PNG
 
 
 
 Colored logo, horizontal, transparent background, no tag line.
 Download high res. PNGDownload low res. PNG
Marine Discussion

===Discussion page Marine Working Group (WG)===
*A series of short-term (1-2 yr) objectives outlined in the CSDMS Strategic Plan, including:
** Developing a set of models that can be coupled via BMI. 
***A BMI version of SWAN was developed and provided in 2013 via GitHub (https://github.com/SiggyF/chenopis). There are currently no plans to integrate this version back into the main SWAN development line of Delft University, however.
***Deltares is actively working on the development of a new hydro-morphodynamic engine Delft3D-FLOW Flexible Mesh, which is to be released in open source later this year. That version will include a BMI compatible interface, and other components will likely follow over time. However, project context to raise priority at Deltares for the development of a BMI interface for the current structured grid Delft3D-FLOW engine is currently lacking.
***Marine working group called for an atmospheric / wind model. No update. 
***Patricia Wiberg (University of Virginia) has worked to add some tools to the CSDMS model repository to enable calculations of wave orbital velocity, surface wave characteristics, and bed shear stress. 
**Providing a hydrodynamic model to the CSDMS that is easier to use. An idealized continental shelf model has been provided that uses ROMS (the Regional Ocean Modeling System) to calculate hydrodynamics, salinity, and sediment transport fields for a planar-shaped continental shelf onto which a freshwater plume flows. A pre-compiled version of the model, with necessary input files, has been ported to the CSDMS computer, beach. We are calling this implementation “riverplume2”, or “ROMS-LITE”. Working with the EKT group, members of the Marine Working Group are developing lesson plans appropriate for a graduate level course. 
**Incorporating (wrapping in a BMI) a finite-element model (needs a champion). No update.
*The Marine Working Group has also discussed model intercomparison projects.
**Examples of large, funded, model intercomparisons have been seen where the studies yielded interesting results and took advantage of quantitative metrics for skill assessment, and tools such as being developed within IOOS (the Integrated Ocean Observing System).
**A true model intercomparison effort would require proposals, but other avenues for highlighting the potential of the various models exist including special journal volumes and special sessions at relevant conferences. 
*Summary of Marine Working Group Resources:
**The repository currently lists fifty-one marine models and 5 marine modeling tools.
**Models that have BMIs and are allied with Marine Working Group interests including [[Model:SWAN|SWAN], SedFlux, OceanWaves, CEM, ROMS-Lite.
===Discussion Page for the BP Oil Spill in the Gulf of Mexico===
Click here for a page devoted to sharing information about the BP oil spill.
Marine Reports

===Marine Working Group===
Reports
The Marine Working Group final summarizes the main discussions during our February 25 - 26, 2009, meeting in Charlottesville, VA.
The Marine Working Group met in March, 2013 during the CSDMS All Hands Meeting. Recommendations were made as to the overarching goals of the Working Group, as well as long-term and short-term steps toward those goals. Meeting input is summarized and available for comment.:File:Marine_Working_Group_Summary_March2013.docx