USER MANUAL
Contents
1. 918 Time 1 56 Radius 1 114 VolumeIncrease 1 9305 G 1 0 011854 k 1 9321 Time 1 6575 Radius 1 1163 Volumelncrease 1 9422 G 1 0 0098193 k 1 9438 Time 1 755 Radius 1 1181 Volumelncrease 1 9519 G 1 0 0081486 k 1 9535 Time 1 8525 Radius 1 1197 Volumelncrease 1 9599 G 1 0 0067734 k 1 9615 Time 1 95 Radius 1 1209 Volumelncrease 1 9665 G 1 0 0056382 k 1 9682 The first print is the content of the configuration file The part SPHERE CELL InitSphereVolume 3 0 EndSphereVolume 6 0 SphereGrowthTime 1 95 NumberOfTimePoints 20 InflowChangeDegree 3 0 MembInflowScaleFactor1 1 118 MembInflowScaleFactor2 1 0 TimeAxisScaleCoef 1 0 relates to computing of growth parameters of a sphere like cell You can configure the beginning volume the end growth volume time interval of growth number of points to compute on the time axis and a time axis s scale coefficient The last parameter is needed to adjust the location of theoretical growth curves to experimental data Three parameters InflowChangeDegree 3 0 MembInflowScaleFactor1 1 118 MembInflowScaleFactor2 1 0 define the dependence of the membrane s inflow on the size of the cell For the sphere it depends on radius as follows k F F R 2 Here D F F are the listed above configuration parameters This way the membrane s inflow can be changed in a wide range For instance the value D 0 makes the membrane s inflow constant while the value of D 1 provides linear dependence Valu2. This software application executable project files and supporting documentation can be freely used for any legitimate purpose except selling this application for profit without the author s prior consent The users can use change and distribute the code and executables under the terms of Free Software License which means that no additions can restrict the originally granted freedom of using this application in software textual hardware and other applicable forms 4 Modeling growth of cells using shesgr exe executable 4 1 Compatibility issues Although the author provides executable for Windows platforms the project can be rebuilt for other platforms supporting C STL standard template library The code is not platform specific 4 2 Getting help Application help Open command prompt You can type cmd exe in the Run window to do that Using command cd change directory to the project s Debug directory For instance cd CNDewCellGrowthNDebug Once in this directory type shesgr exe You will get the information on terms of using this application and following help message You should provide one valid argument from the list disk sphere frustum ecoli ecolicylinder Cell s parameters are configured in CellGrConfig txt file located in the config directory Calculation results will be shown on the screen and also written into the appropriate file located in Logs directory Project s source files Project s source files a
3. USER MANUAL SOFTWARE APPLICATION PHYSICAL GROWTH MECHANISM AND CELLS GROWTH Yuri K Shestopaloff Copyright 2008 2010 Yuri K Shestopaloff amp AKVY Press TABLE OF CONTENTS Ta TAOGE ONG oce aa a tese Da ROR OREO ary Re NG Lc E 3 2 PRO JEG descri Pti nui a nl aaa vate ie ca a Rau GG a M eh de 3 3 License terms AAK EN PEN AKK EN E EEN aaa aa BN BEN page Bi 4 4 Modeling growth of cells using shesgr exe executable sss 4 4 1 Compatibility 15S Saee AM ME M RL A EA MM dE Ee 4 BD Getting helped dena ERU Matt Rim 4 13 OI mp CLP DULL CATON acte a vies i d ea ete ud Mts Piu tee med ess 5 4 4 Computing growth parameters of a sphere like cell 5 4 5 Computing growth parameters of a disk like cell 8 4 6 Computing growth parameters of a cell formed by two joined frustum CONES MM 9 4 7 Computing growth parameters of E coli cell 10 5 Software implementation details seen 12 5 1 Programming language Application s portability sss 12 5 2 Application GESIT mania end deca RE as a iab bottes 306 a 12 5 8 Application s TRCOF TOOL ada Suta Seth te n Di a Sete tutes usd anulu 13 References aep REA war P av t tp OD SU RE aqu n e dotati 14 1 Introduction This software application computes growth dependences for cells that have different geometrical forms such as disk sphere two joined frustum cones cylinder cylinder with hemispheres at ends similar to E c
4. Volume 1 0 EndDiskVolume 2 06 DiskHeightAsFractionOfDiameter 1 0 InflowChangeDegreeDisk 0 0 MembInflowScaleFactor1Disk 1 0 MembInflowScaleFactor2Disk 1 0 TimeAxisScaleCoefDisk 1 0 NumberOfRadiusPointsDisk 30 relates to configuration of a disk cell The growth equation is solved numerically in this computational implementation although there is analytical solution for the disk growth scenario with respect to the growth time same as for a sphere Membrane s inflow is configured in the same way 2 as for a sphere Unlike in the case of a sphere this time we define the computational points for discrete values of disk radius NumberOfRadiusPointsDisk parameter Default configuration parameters produce output shown in CellGrowth xls file tab Disk In this case the membrane s inflow is constant We used this model to compute amoeba s growth curves membrane s inflow of amoeba remains approximately constant during the growth 4 6 Computing growth parameters of a cell formed by two joined frustum cones Run a command shesgr exe frustum Once the application starts you will see the content of the configuration file The part FRUSTUM CELL ApexDiameterAsFractionOfBaseDiam 0 5 InitialLengthInBaseDiameters 1 5 EndLengthInBaseDiameters 3 0 TimeAxisScaleCoefFrustum 1 0 NumberOfLengthPointsFrustum 30 InflowChangeDegreeFrustum 2 0 MembInflowScaleFactor1Frustum 1 0 MembInflowScaleFactor2Frustum 1 0 relates to configurat
5. cenarios the membrane s inflow is constant when D 0 Cell s density is assumed constant in all considered growth scwenarios 4 7 Computing growth parameters of E coli cell Run a command shesgr exe ecoli Once the application starts you will see the content of the configuration file The part ECOLI CELL InitLengthInDiametersEcoli 3 0 EndLengthInDiametersEcoli 8 1 NumberOfLengthPointsEcoli 35 InflowChangeDegreeEcoli 2 0 MemblInflowScaleFactorlEcoli 1 0 MembInflowScaleFactor2Ecoli 1 0 TimeAxisScaleCoefEcoli 1 0 10 relates to configuration of a cell composed of a cylinder with two hemispheres at ends as it is shown in Fig 2 Fig 2 E coli cell modeled by hemispheres and a cylinder The configuration parameters are self explanatory Membrane s inflow is configured as for a frustum like cell equation 3 Note that this model does not provide proportionality between the length and volume because of the presence of hemispheres So if one needs to increase the grown volume twice he should increase the length more than that The actual number can be found from the basic geometrical considerations In units of diameter if the grown volume is M times larger then the length of a cylinder for the grown cell is defined as follows Lou M 213 Li 213 4 E coli can be modeled by a cylinder as well To compute this growth scenario run command shesgr exe ecolicylinder Configuration parameters produce output prese
6. e of D 3 makes the membrane s inflow proportional to volume Excel file CellGrowth xls in the Docs directory presents sample results of calculation and appropriate graphs for two growth scenarios with different end volumes 6 0 and 8 13 switch to the SphereGrowth tab in Excel spreadsheet These two scenarios present two evolutional types of growth described in the articles and books when the cell growth proceeds through the whole growth cycle defined by the physical growth mechanism value of 6 0 and when the growth stops once the growth rate provided by the physical growth mechanism begins to decelerate Note that we use a direct analytical solution of the growth equation as a computational algorithm Implementation details can be found in the project s source files The second print presents output data with parameters names G 1 denotes the value of the growth ratio minus one k is the membrane s inflow Similar output will be shown for all other growth scenarios The same data are written into output files in the Logs directory However there are no parameters names in order to make these outputs convenient to use in spreadsheets or storing in the databases If in doubt what column means what refer to the command window output 4 5 Computing growth parameters of a disk like cell Run a command shesgr exe disk Once the application starts you will see the content of the configuration file The part DISK CELL InitDisk
7. ical perspectives on living organisms development 2010 AKVY Press 174 p Yuri K Shestopaloff Growth and replication of cells and other living organisms Physical mechanisms that govern Nature s evolvement 2009 AKVY Press 84 p 14
8. ion of a cell composed of two frustum cones Fig 1 below shows the form of such a cell Default configuration parameters produce sample output and the appropriate growth curve presented in CellGrowth xls file tab Frustum Base diameter Apex diameter Cell s length 1 1 Fig 1 A cell composed of two joined frustum cones The cell s shape is characterized by diameters of the base and apex circles and the length All these values are measured as fractions of the base s diameter The convenience of this model is its universality When the apex diameter is zero then the frustum cone becomes a cone while when the apex s and base s diameters are the same the shape transforms to a cylinder For this form volume is proportional to frustum cone s length so that the differences in the beginning and end growth length present also the difference between the volumes of initial and fully grown cell Membrane inflow is defined by the following parameters InflowChangeDegreeFrustum 2 0 MembInflowScaleFactor1Frustum 1 0 MembInflowScaleFactor2Frustum 1 0 The functional dependence is as follows D L k L rfp E 3 Lui As a side note we computed numerically the form of the membrane s inflow dependence for known experimental data These are monotonically increasing convex functions Formulas 2 3 reflect on this specific although they can also provide concave and constant functions In all growth s
9. nner without changing the rest of the code 12 Configuration file functions tracing Configuration logging debugging module Auxiliary classes and Functions module ES Sphere Frustum E coli E coli Growth Growth Growth Growth cylinder Function Function Function Function Growth Output file Output file Output file Output file Output file Fog 3 Growth application s system design 5 3 Application s interface This is a command line application However if one wants to add a graphical interface the author would not recommend to embed the code into a graphical application but rather to build a GUI to manipulate the content of the configuration file Then from the same GUI application one should start the application s executable in order to compute the growth data The content of log files can be viewed from the same GUI application by opening them in some text editor For ergonomic reasons the author recommends to put the list of growth scenarios into combobox instead of adding tabs The author used this design for other applications and it worked well Divide and conquer this principle well complies with the suggested GUI design For the frustum cell the integration steps are chosen very small to make calculations more accurate However if one needs better performance increase the integration step 13 References Yuri K Shestopaloff Physics of growth and replication Physical and geometr
10. nted in the CellGrowth xls file open tab E coli cylinder The part of configuration file related to cylindrical e coli growth is this ECOLICYLINDER CELL TimeAxisScaleCoefEcoliFlat 1 0 The rest of model s parameters is defined in the ECOLI CELL section that we described above So the only new parameter is the time scaling coefficient For this model the volume is proportional to cylinder length So if the grown cell is twice as bigger than the initial cell then their lengths differ two times as well 11 5 Software implementation details 5 1 Programming language Application s portability Software application is written in C programming language with usage of STL Standard Template Library No platform specific code was used so that the application should be easily portable to any platform supporting C Executable was built for Windows platforms 5 2 Application design Application design is straightforward We intentionally isolated and made growth functions global in order to make them self sufficient This allows making changes easily while each function has a well defined interface Auxiliary functions support logging and debugging functionalities In memory configuration information is stored in the STL container map The configuration data are retrieved based on the name of key identical to one in the configuration file If one needs additional growth function he can continue adding them in the same ma
11. oli s shape Frustum model can be changed from two cones joined by bases to a cylinder by changing the apex radius in the application s configuration file CellGrConfig txt that is located in the application s config directory The theory and some results can be found in the book by Yuri K Shestopaloff Physics of growth and replication Physical and geometrical perspectives on living organisms development ISBN 13 9780980966756 ISBN 10 0980966752 Library of Congress Control Number 2009943094 The book was published by AKVY Press 2010 174 p 1 2 However for the most up to date information refer to the latest author s articles that can be found on the author s web site 2 Project description The project includes 1 User manual 2 Four sample data files in the Logs directory 3 Sample configuration file in the config directory Note that the supplied sample configuration file contains parameters that were used to generate sample data and sample Excel graphs 4 Excel file with sample data for the sphere disk frustum cylinder E coli cells models and graphs for these data in the Docs directory 5 VC project with source files 6 Executable shesgr exe in the Debug directory that can be used on Windows platforms to compute growth dependencies for different cells The user has a great deal of flexibility to define the cells parameters changing the appropriate values in the configuration file 3 License terms
12. re commented Studying these comments and the code will help to understand the application and its logic as well Help documentation Refer to User Manual and sample text and spreadsheet Excel files in the Docs directory 4 3 Starting application Once in the project s Debug directory type the following and press Enter shesgr exe sphere 1 This way you compute the growth parameters for a sphere like cell Substituting instead of a command argument sphere another one such as disk frustum ecoli ecolicylinder you will accordingly compute growth parameters for the cells that have a disk form a form composed of two frustums joined by bases cylinder with hemispheres at ends and a cylinder like cell 4 4 Computing growth parameters of a sphere like cell Run command 1 Once the application starts you will see the following output SPHERE CELL InitSphereVolume 3 0 EndSphereVolume 6 0 SphereGrowthTime 1 95 NumberOfTimePoints 20 InflowChangeDegree 3 0 MembInflowScaleFactor1 1 118 MembInflowScaleFactor2 1 0 TimeAxisScaleCoef 1 0 DISK CELL InitDiskVolume 1 0 EndDiskVolume 2 06 DiskHeightAsFractionOfDiameter 1 0 InflowChangeDegreeDisk 0 0 MembInflowScaleFactor1Disk 1 0 MembInflowScaleFactor2Disk 1 0 TimeAxisScaleCoefDisk 1 0 NumberOfRadiusPointsDisk 30 FRUSTUM CELL ApexDiameterAsFractionOfBaseDiam 0 5 InitialLengthInBaseDiameters 1 5 EndLengthInBaseDiameters 3 0 TimeAxisScaleCoefFrustum 1 0 NumberOfLengthPointsF
13. rustum 30 InflowChangeDegreeFrustum 2 0 MembInflowScaleFactor1Frustum 1 0 MembInflowScaleFactor2Frustum 1 0 ECOLI CELL InitLengthInDiametersEcoli 3 0 EndLengthInDiametersEcoli 8 1 NumberOfLengthPointsEcoli 35 InflowChangeDegreeEcoli 2 0 MemblInflowScaleFactorlEcoli 1 0 MembInflowScaleFactor2Ecoli 1 0 TimeAxisScaleCoefEcoli 1 0 ECOLICYLINDER CELL TimeAxisScaleCoefEcoliFlat 1 0 Time 0 Radius 0 8947 Volumelncrease 1 G 1 0 25992 k 1 0008 Time 0 0975 Radius 0 92038 VolumeIncrease 1 0886 G 1 0 22477 k 1 0895 Time 0 195 Radius 0 94623 Volumelncrease 1 1829 G 1 0 1913 k 1 1839 Time 0 2925 Radius 0 97145 VolumeIncrease 1 28 G 1 0 16039 k 1 2811 Time 0 39 Radius 0 99516 Volumelncrease 1 3761 G 1 0 13274 k 1 3772 Time 0 4875 Radius 1 0167 Volumelncrease 1 4672 G 1 0 10878 k 1 4684 Time 0 585 Radius 1 0355 Volumelncrease 1 5504 G 1 0 088592 k 1 5516 Time 0 6825 Radius 1 0516 Volumelncrease 1 6238 G 1 0 071926 k 1 6251 Time 0 78 Radius 1 0651 Volumelncrease 1 6871 G 1 0 058356 k 1 6885 Time 0 8775 Radius 1 0762 Volumelncrease 1 7406 G 1 0 047395 k 1 742 Time 0 975 Radius 1 0854 Volumelncrease 1 7853 G 1 0 038573 k 1 7868 Time 1 0725 Radius 1 0929 VolumeIncrease 1 8224 G 1 0 031474 k 1 8239 Time 1 17 Radius 1 0989 VolumeIncrease 1 8531 G 1 0 025754 k 1 8546 Time 1 2675 Radius 1 1039 VolumeIncrease 1 8784 G 1 0 021132 k 1 8799 Time 1 365 Radius 1 108 Volumelncrease 1 8992 G 1 0 017386 k 1 9008 Time 1 4625 Radius 1 1113 Volumelncrease 1 9164 G 1 0 01434 k 1
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