https://sourceforge.net/p/dymmm/wiki/Home/Recent changes to HomeenTue, 15 May 2012 23:21:46 -0000https://sourceforge.net/p/dymmm/wiki/Home/<pre>--- v41 +++ v42 @@ -2,7 +2,7 @@ The Dynamic Multispecies Metabolic Modeling (DyMMM, pronounced /dĭm/) framework is a mathematical modeling tool that integrates multiple constraint-based metabolic models into a single dynamic community metabolic model. The DyMMM framework is designed to model competitive and syntrophic (cross-feeding) communities. It *should not be used* to model mutualistic communities. -The DyMMM framework is developed and maintained by Kai Zhuang. +The DyMMM framework is developed and maintained by [Kai Zhuang](https://sourceforge.net/users/kaizhuang). [[include ref=the_math]] </pre>Kai ZhuangTue, 15 May 2012 23:21:46 -0000https://sourceforge.net66bdc31494b1c608237d0d5a1625d635eaff0cb3https://sourceforge.net/p/dymmm/wiki/Home/<pre>--- v40 +++ v41 @@ -2,10 +2,7 @@ The Dynamic Multispecies Metabolic Modeling (DyMMM, pronounced /dĭm/) framework is a mathematical modeling tool that integrates multiple constraint-based metabolic models into a single dynamic community metabolic model. The DyMMM framework is designed to model competitive and syntrophic (cross-feeding) communities. It *should not be used* to model mutualistic communities. -DyMMM is formerly known as DMMM; the abbreviation was altered to make pronunciation easier. The DyMMM framework is developed and maintained by Kai Zhuang. - - [[include ref=the_math]] </pre>Kai ZhuangTue, 15 May 2012 23:18:18 -0000https://sourceforge.net85b2c5b0f46f0a139bd0be7dcceb260032f5dd87https://sourceforge.net/p/dymmm/wiki/Home/<pre>--- v39 +++ v40 @@ -1,4 +1,4 @@ -###OVERVIEW [[download_button]] +###OVERVIEW The Dynamic Multispecies Metabolic Modeling (DyMMM, pronounced /dĭm/) framework is a mathematical modeling tool that integrates multiple constraint-based metabolic models into a single dynamic community metabolic model. The DyMMM framework is designed to model competitive and syntrophic (cross-feeding) communities. It *should not be used* to model mutualistic communities. </pre>Kai ZhuangTue, 15 May 2012 22:24:16 -0000https://sourceforge.net9f05b252e2dcaa72d0b8f7b55aa197b6398c32e1https://sourceforge.net/p/dymmm/wiki/Home/<pre>--- v38 +++ v39 @@ -1,11 +1,11 @@ -###OVERVIEW - +###OVERVIEW [[download_button]] + The Dynamic Multispecies Metabolic Modeling (DyMMM, pronounced /dĭm/) framework is a mathematical modeling tool that integrates multiple constraint-based metabolic models into a single dynamic community metabolic model. The DyMMM framework is designed to model competitive and syntrophic (cross-feeding) communities. It *should not be used* to model mutualistic communities. DyMMM is formerly known as DMMM; the abbreviation was altered to make pronunciation easier. The DyMMM framework is developed and maintained by Kai Zhuang. -[[download_button]] + [[include ref=the_math]] </pre>Kai ZhuangTue, 15 May 2012 22:24:04 -0000https://sourceforge.netb8760e49f11423100d3dbde512e0969de6be7a5fhttps://sourceforge.net/p/dymmm/wiki/Home/<pre>--- v37 +++ v38 @@ -5,14 +5,15 @@ DyMMM is formerly known as DMMM; the abbreviation was altered to make pronunciation easier. The DyMMM framework is developed and maintained by Kai Zhuang. - - +[[download_button]] + + [[include ref=the_math]] [[include ref=the_code]] +[[include ref=howto]] + [[include ref=citations]] - -[[include ref=howto]] [[download_button]] </pre>Kai ZhuangTue, 15 May 2012 22:23:45 -0000https://sourceforge.net32e4bc6c6d5ff1ea0c2f096d2b47a401ea28dfe4https://sourceforge.net/p/dymmm/wiki/Home/<pre>--- v36 +++ v37 @@ -3,14 +3,16 @@ The Dynamic Multispecies Metabolic Modeling (DyMMM, pronounced /dĭm/) framework is a mathematical modeling tool that integrates multiple constraint-based metabolic models into a single dynamic community metabolic model. The DyMMM framework is designed to model competitive and syntrophic (cross-feeding) communities. It *should not be used* to model mutualistic communities. DyMMM is formerly known as DMMM; the abbreviation was altered to make pronunciation easier. -The DyMMM framework is developed and maintained by Kai Zhuang. - - - +The DyMMM framework is developed and maintained by Kai Zhuang. + + + [[include ref=the_math]] [[include ref=the_code]] [[include ref=citations]] + +[[include ref=howto]] [[download_button]] </pre>Kai ZhuangTue, 15 May 2012 22:22:41 -0000https://sourceforge.net103eebb689f39856356c71c573c30d5f9ff7f874https://sourceforge.net/p/dymmm/wiki/Home/<pre>--- v35 +++ v36 @@ -7,8 +7,7 @@ -**Mathematics** -The base mathematics of DyMMM was first published by Zhuang *et al.* (2011). The system of equations can be solved either numerically, or through an analytical approximation method. Since the initial publication, the mathematics of DyMMM has expanded to include additional capabilities. See [here](https://sourceforge.net/p/dymmm/wiki/Mathematics/) for the DyMMM [mathematics](https://sourceforge.net/p/dymmm/wiki/Mathematics/). +[[include ref=the_math]] [[include ref=the_code]] </pre>Kai ZhuangTue, 15 May 2012 19:52:23 -0000https://sourceforge.neta1ce7e22faa5620413aa1514af38431eb0d3b0achttps://sourceforge.net/p/dymmm/wiki/Home/<pre>--- v34 +++ v35 @@ -10,7 +10,8 @@ **Mathematics** The base mathematics of DyMMM was first published by Zhuang *et al.* (2011). The system of equations can be solved either numerically, or through an analytical approximation method. Since the initial publication, the mathematics of DyMMM has expanded to include additional capabilities. See [here](https://sourceforge.net/p/dymmm/wiki/Mathematics/) for the DyMMM [mathematics](https://sourceforge.net/p/dymmm/wiki/Mathematics/). +[[include ref=the_code]] -[[include ref=Citations]] +[[include ref=citations]] [[download_button]] </pre>Kai ZhuangTue, 15 May 2012 19:44:31 -0000https://sourceforge.net6ef218f47808ea7f4f20e1580b8ed29094facaf3https://sourceforge.net/p/dymmm/wiki/Home/<pre>--- v33 +++ v34 @@ -11,6 +11,6 @@ The base mathematics of DyMMM was first published by Zhuang *et al.* (2011). The system of equations can be solved either numerically, or through an analytical approximation method. Since the initial publication, the mathematics of DyMMM has expanded to include additional capabilities. See [here](https://sourceforge.net/p/dymmm/wiki/Mathematics/) for the DyMMM [mathematics](https://sourceforge.net/p/dymmm/wiki/Mathematics/). -[[[include ref=Citations]]] +[[include ref=Citations]] [[download_button]] </pre>Kai ZhuangTue, 15 May 2012 19:24:37 -0000https://sourceforge.netef8395cfe9dd01ad44ba8aa5df8e137f968455b2https://sourceforge.net/p/dymmm/wiki/Home/<pre>--- v32 +++ v33 @@ -11,11 +11,6 @@ The base mathematics of DyMMM was first published by Zhuang *et al.* (2011). The system of equations can be solved either numerically, or through an analytical approximation method. Since the initial publication, the mathematics of DyMMM has expanded to include additional capabilities. See [here](https://sourceforge.net/p/dymmm/wiki/Mathematics/) for the DyMMM [mathematics](https://sourceforge.net/p/dymmm/wiki/Mathematics/). - -**Citations** -Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., & Lovley, D. R. (2011). Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. The ISME journal, 5(2), 305–316. doi:10.1038/ismej.2010.117 - -Zhuang, K., Ma, E., Lovley, D. R., & Mahadevan, R. (2012). The design of long-term effective uranium bioremediation strategy using a community metabolic model. Biotechnology and Bioengineering. doi:10.1002/bit.24528 - +[[[include ref=Citations]]] [[download_button]] </pre>Kai ZhuangTue, 15 May 2012 19:24:20 -0000https://sourceforge.net66d556b393e1e12eba965a7dfc5d9e59d37feb34