Merge pull request #18 from DEMENT-Model/re-main

Fixing typos in READ.ME

Author: jgwalkup

README.md

@@ -23,19 +23,19 @@
 ![GitHub forks](https://img.shields.io/github/forks/bioatmosphere/DEMENTpy?style=social)
 <!--![Twitter Follow](https://img.shields.io/twitter/follow/bioatmo_sphere?style=social)-->
 
-This model is spatially and mechanistically explicit in simulating a microbial system comprising a large number of hypothetical microbial taxa in terrestial environments. As indicated by the 'py' in its name, DEMENTpy is developed and programmed in Python, based on its predecesor [DEMENT](https://github.com/stevenallison/DEMENT) developed by Steven Allison (promgrammed in R).
+DEMENT (Decomposition Model of Enzymatic Traits) is spatially and mechanistically explicit in simulating a microbial system comprising a large number of hypothetical microbial taxa in terrestial environments. As indicated by the 'py' in its name, DEMENTpy is developed and programmed in Python, based on its predecesor [DEMENT](https://github.com/stevenallison/DEMENT) developed by Steven Allison (originally programmed in R).
 
 <p align='center'> <img src="documentation/figures/DEMENTpy_conceptual_structure.jpg"> </p>
 
 ### Vision
 
-DEMENTpy, initiated with in mind practicing **Real Open Science**, is devoted to 100% OPEN SOURCE and longterm maintanence and development, which, however, will not be limited to ourselves but sincerely seek inputs from the communities that could be as broad as microbial ecology, systems biology, theoretical ecology, etc. Just because of community inputs, please read closely our statement on **policies and rules** of making contributions to DEMENTpy or applying it to your own research.
+DEMENTpy was developed with practicing **Real Open Science** in mind and is devoted to 100% OPEN SOURCE and longterm maintanence and development. We sincerely seek inputs from communities ranging from microbial ecology, systems biology, theoretical ecology, etc. Please read closely our statement on **policies and rules** of making contributions to DEMENTpy or applying it to your own research.
 
 <p align='center'> <img src="documentation/figures/DEMENTpy_programming_structure.png"> </p>
 
 ### Structure and Process
 
-This model is built upon its predecessor--DEMENT, an R-based framework initially developed by Steven Allison back in 2012. Except for the programming language change, a series of changes have been made with an overarching goal of making it more readily accessible to the research and teaching communities as broad as microbial ecology, theoretical ecology, and ecosystem ecology, as well as biology. This model simulates processes ranging from degradation of substrates through microbial processes encompassing uptake, metabolism, mortality, reproduction, and dispersal in a spatially explicit, mechanistically explicit fashion. For more detailed information about DEMENTpy, we refer readers/users temporarily to an [Appendix](https://github.com/bioatmosphere/microbiome-drought-legacy/tree/master/writing) of the 1st manuscript applying this model. An actual documentation is under conceiving.
+This model is built upon its predecessor--DEMENT, an R-based framework initially developed by Steven Allison back in 2012. In addition to the programming language, a series of changes have been made with an overarching goal of making it more readily accessible to the research and teaching communities. This model simulates plant litter decomposition from enzymatic degradation of substrates to microbial processes encompassing uptake, metabolism, mortality, reproduction, and dispersal in a spatially explicit, mechanistically explicit fashion. For more detailed information about DEMENTpy, we refer readers/users temporarily to an [Appendix](https://github.com/bioatmosphere/microbiome-drought-legacy/tree/master/writing) of the 1st manuscript applying this model. An actual documentation is under conceiving.
 
 
 ### Run DEMENTpy
@@ -81,11 +81,11 @@ Feel free to reach out, or directly fork, change, and create pull requests, or c
 
 ### References
 
-1. Wang, B., & Steven D. Allison. (2022) [Climate-driven legacies in simulated microbial communities alter litter decomposition rates](https://www.frontiersin.org/articles/10.3389/fevo.2022.841824). Frontiers in Ecology and Evolution 10,841824
+1. Wang, B., & Steven D. Allison. (2022) [Climate-driven legacies in simulated microbial communities alter litter decomposition rates](https://www.frontiersin.org/articles/10.3389/fevo.2022.841824). Frontiers in Ecology and Evolution 10,841824 [[GitHub Repo](https://github.com/bioatmosphere/microbiome-climate-gradient)]
 
-2. Wang, B., & Steven D. Allison. (2021) [Drought Legacies Mediated by Trait Tradeoffs in Soil Microbiomes]( https://doi.org/10.1002/ecs2.3562). Ecosphere 12, e03562
+2. Wang, B., & Steven D. Allison. (2021) [Drought Legacies Mediated by Trait Tradeoffs in Soil Microbiomes]( https://doi.org/10.1002/ecs2.3562). Ecosphere 12, e03562 [[GitHub Repo](https://github.com/bioatmosphere/microbiome-drought-legacy)]
 
-3. Wang, B., & Allison, S. D. (2019).[Emergent properties of organic matter decomposition by soil enzymes](https://doi.org/10.1016/j.soilbio.2019.107522). Soil Biology and Biochemistry, 136, 107522
+3. Wang, B., & Allison, S. D. (2019).[Emergent properties of organic matter decomposition by soil enzymes](https://doi.org/10.1016/j.soilbio.2019.107522). Soil Biology and Biochemistry, 136, 107522 [[GitHub Repo](https://github.com/bioatmosphere/An_emergent_soil_enzyme_decomposition_model)]
 
 4. Allison, S. D., & Goulden, M. L. (2017). [Consequences of drought tolerance traits for microbial decomposition in the DEMENT model](https://doi.org/10.1016/j.soilbio.2017.01.001). Soil Biology and Biochemistry, 107, 104-113.
 

src/dementpy.py

@@ -1,11 +1,7 @@
 """
 -------------------------------------------------------------------------------
-      DEMENTpy--Decomposition Model of Enzymatic Traits in Python,v1.0
-                                 Bin Wang
-              Department of Ecology and Evolutionary Biology
-                       University of California Irvine
-                  Emails: wbwenwu@gmail.com or bwang7@uci.edu
-                          Twitter: @bio_atmosphere
+      DEMENTpy--Decomposition Model of Enzymatic Traits in Python
+            by Bin Wang (wbwenwu@gmail.com|@bio_atmosphere)
 -------------------------------------------------------------------------------
 """
 import os
@@ -25,8 +21,6 @@ def main():
     ---------------------------------------------------------------------------
                                 DEMENTpy 
             (DEcomposition Model of Enzymatic Traits in Python)
-               Department of Ecology and Evolutionary Biology
-                     University of California Irvine
     ---------------------------------------------------------------------------       
     """)