SpiralMaker User`s Manual v 1.0
Contents
1. 2 1 Software requirements Freeglut libraries http freeglut sourceforge net In Ubuntu this can be installed by running apt get install freeglut3 dev Mesa Openg libraries http www mesa3d org They are normally already installed in most linux distributions gfortran compiler https gcc gnu org wiki GFortran In Ubuntu this can be installed by running apt get install gfortran 2 2 Building Download the tar file from the website and save it in the place you want to install the software Uncompress the tar file You may do that by opening a terminal going to the directory where the tar file is stored and typing the following command tar xzvf lt SpiralMaker_directory gt tar gz where lt SpiralMaker_directory gt stands for the name the downloaded tar file has at that moment While in the terminal enter the lt SpiralMaker_directory gt and simply run the compile_SpiralMaker sh script You may need to grant execution permissions to the script first in that case type chmod x compile_SpiralMaker sh then to run the script type compile_SpiralMaker sh the following output should be printed in the terminal descending lt path_to_SpiralMaker_dir gt src core making object files linking cleaning executables installed in bin The executable is named SMaker and is placed in the bin directory 3 Command line execution options This section provides a brief description of how to run2. this means pressing the scrolling wheel not actually scrolling 4 2 2 5 Sphere options Submenu This submenu allows change sphere scale with left mouse button to set different options regarding the semitransparent select sphere max and min from terminal sphere display of nodes properties select sphere min with left mouse button select sphere max with left mouse button select sphere min with middle mouse button select sphere max with middle mouse button disable spheres 4 2 2 6 1 Change sphere scale with left mouse button Allows to change the maximum radius of spheres by dragging the mouse with the left button 4 2 2 6 2 Change sphere max and min from terminal This option will change the minimum and maximum values of the node property selected taken into account for setting semitransparent sphere radius for each node All values below the minimum value will have a sphere radius of 0 and all values above the maximal value will have a sphere radius equal to the sphere scale 1 by default The minimum and maximum values will be entered via terminal in the same line separated with a space in the respective order 4 2 2 6 3 Change sphere min with left mouse button This button allows to change the minimum value described above simply dragging the mouse with the left button 4 2 2 6 4 Change sphere max with left mouse button This button allows to change the maximum value described above simply dragging the mouse with the left but
3. a node has moved in Amount of regulatory molecule B the x axis will be displayed 4 2 2 5 As dy The distance a node has moved in the y axis will be displayed 4 2 2 6 As dz The distance a node has moved in the z axis will be displayed 4 2 2 7 As dtotal The total distance a node has moved will be displayed 4 2 2 8 As node index The index within the node matrix will be displayed 4 2 2 9 Amount of regulatory molecules The variable displayed will be the amount of a certain molecule expressed in each node There will be one of those options for each regulatory molecule A B or C described in the system to be simulated it may change in different developmental simulations 4 2 3 What to draw Menu Note that some drawing options will not have a visible effect if other things are drawn in front most notably one should chose to draw small balls only if one wishes to see the other options Note also that these options activate a specific drawing when chosen and deactivate it when chosen again 4 2 3 1 Smooth cells Draws the smoothed surface of the cells based on a 3D Delaunay triangulation 4 2 3 2 Box grid Draws a 3D grid around the embryo The distance between grid points is proportional to the maximal ADD of the nodes in the embryo 4 2 3 7 Connexions between cells Draws a lines between those nodes from different smooth cells box grid connexions between cells connexions between nodes draw cell contour draw inte
4. a submenu with a list of options to save the current state of the embryo into a file or to read previous states from a file See section 4 2 5 4 1 6 Selection menu This menu shows different options to select nodes or cells This is useful to simply track nodes or cells over time but also allows to use the editor options section 4 2 6 on them and to plot their gene expression over time using the gene plotting options menu section 4 1 9 4 1 7 Cursor menu This menu includes all options regarding the control of the cursor a tool mainly used to select nodes see Section 4 1 6 or to mark a reference point in space See section 4 2 8 4 1 8 7 iteration Runs the model for 1 iteration After this is chosen the window will lock while this number of iterations are running in the simulator When these are run the current state of the embryo will be shown in the window and the use will win control on the display again Notice that depending on the number of nodes and the running options this iteration may take more or less time 4 1 9 100 iterations As above but the model is run for 100 iterations 4 1 10 1000 iterations As above but the model is run for 1000 iterations gt show node mechanical properties vvv vv 4 1 11 x iterations When this option is chosen a prompt will arise in the deat terminal The user should enter the number of iterations he she wants to run 4 1 12 Quit Quits the simulator Section from minimal x
5. cursor 4 2 5 5 Undo selections All selected elements not only the latter one are unselected Cursor menu cursor ON OFF 4 2 8 1 Cursor ON OFF Toggle cursor function It is set set left mouse button for x y move OFF by default When activated the cursor appears in the set left mouse button for z move display window as a red solid ball which can be moved by set middle mouse button for z move the user across the system to select nodes and cells see section 4 2 5 2 Notice that since the cursor appears in a corner of the window it can be necessary to move it to make it visible By default the cursor is moved in the x y plane by dragging the mouse with the left button and is moved in the z axis by dragging with the middle mouse button pressing the scrolling wheel 4 2 8 2 Set left mouse button for x y move When selected the cursor can be displaced in the x y plane whith the left mouse button This is the cursor displacement mode by default 4 2 8 3 Set left mouse button for z move When selected the cursor can be displaced in the z plane whith the left mouse button The user can also alternatively switch between cursor displacements in the x y or z plane 4 2 6 2 or 4 2 6 3 options by pressing the DOWN key in the keyboard 4 2 8 4 Set middle mouse button for z move As in 4 2 6 3 but using the middle mouse button instead of the left mouse button
6. plane Section from maximal x plane left mouse button gt Section from minimal y plane reset to initial view Section from maximal y plane view from above Section from minimal z plane 4 2 Submenu options view from front Section from maximal z plane Undo sections 4 2 1 Basic View Modifier Menu Teggle Fixed sections when running iterations 4 2 1 1 Left mouse button Submenu By choosing one of the options the user decides what happens when dragging with the left mouse button 4 2 1 1 1 Rotate The camera rotates This is the default option 4 2 1 1 2 Zoom Zoom the camera in an out 4 2 1 1 3 Pan Moving the camera point of rotation 4 2 1 1 4 Section from the Minimal x plane The mouse will section the embryo as it is moved starting from the node with the minimal x position This is very useful to see the interior of the embryo By default all sections will be undone when the simulation resumes 1 e running some iterations Sections can be kept over time with the see section 4 2 1 6 to set it otherwise 4 2 1 1 5 Section from the Maximal x plane As above but starting from the node with the maximal x position 4 2 1 1 6 Section from the Minimal y plane As above but starting from the node with the minimal y position 4 2 1 1 7 Section from the Maximal y plane As above but starting from the node with the maximal y position 4 2 1 1 8 Section from the Minimal z plane As above but starting from the node with the minimal z positi
7. the program executable Open a terminal and go to the directory where the simulator has been installed Then type Smaker 4cellstage This runs the model with its full graphical interface and the default initial conditions 2500 nodes distributed in four equally sized blastomeres The parameter values of these initial conditions are one example of those generating a Trochus like blastula Rot 0 4 wsacus 0 5 Wsacus 1 16 0 and k 2 0 These parameters can be modified by opening the 4ce stage file in the bin directory and manually changing the parameter values in the lines 31 36 of the file 4 Running SpiralMaker with its graphic interface Linux After the program is executed a window will arise displaying the initial conditions in 3D This is the simulated blastula The user can run a number of iterations by choosing specific options in the menu and see how this blastula changes over developmental time The user can also modify how the blastula is viewed and how it is drawn When pressing the right button a menu will appear The following pages detail these options in detail 4 1 Principal Menu options 4 1 1 Basic View Modifier This option shows a submenu Basic View Modifier with options to modify the view of the model results By default pressing the left mouse button and moving the mouse A would rotate the embryo but other options in this menu allow Show other node properties the mouse to do different things on the view These o
8. SpiralMaker User s Manual v 1 0 Miquel Marin Riera Miguel Brun Usan Roland Zimm Tommi V likangas Isaac Salazar Ciudad Genomics Bioinformatics and Evolution Departament de Gen tica i Microbiologia Universitat Autonoma de Barcelona Barcelona Spain gt Evo devo Helsinki community Centre of excellence in computational and experimental developmental biology Institute of Biotechnology University of Helsinki PO Box 56 FIN 00014 Helsinki Finland Index Presentation 1 Download Software 2 Installation Linux 2 1 Software requirements 2 2 Building 3 Command line execution options 4 Running SpiralMaker with its visual interface Linux 4 1 Principal Menu options 4 2 Submenu options Presentation SpiralMaker is a modification of the EmbryoMaker a general model of animal embryonic development capable of simulating complex developmental processes in 3D Marin Riera et al 2015 SpiralMaker is only concerned with early cleavage and it only implements one kind of cells blastomeres and the limited repertoire of cell behaviors they display SpiralMaker does not consider gene regulatory networks GRNs as EmbryoMaker does Because of that many editing and plotting options that are available in the original EmbryoMaker have been disabled in the SpiralMaker 1 Download Software The SpiralMaker software can be downloaded from http www biocenter helsinki fi salazar software html 2 Installation Linux
9. display box is useful to make sections of the system 4 2 3 16 Polarization vectors Draws a line for the polariztion vector of each cell 4 2 3 17 Centroids Shows the centroids this is average of the positions of the nodes in a cell of each cells by a white ball 4 2 3 18 Show displacement of nodes from origin Shows a line from the initial position of the node to its actual position For nodes that arise by growth this initial position is the position at which that node was created 4 2 3 19 Movement unitary vectors Shows a line for each node in the direction in which it moved in the last iteration 4 2 3 20 Force components repulsion and adhesion Shows a line for each node in the direction in of the repulsion and adhesion forces affecting the nodes in the last interation 4 2 4 Input Output Menu save present time save snaps periodically 4 2 4 1 Save present time change frequency of snapshots Save a present state of the read from file embryo This includes all add label to the name of the output file model parameters including save images automatically the window must be open and uncovered the genetic ones and also all save movie check terminal the window must be open and uncovered node and cell properties When this file is read either from the graphical interface or by calling the simulator with that file in the command line everything is recovered including the iteration number In that sense this file can be us
10. ed as the initial conditions for other simulator runs The file is saved in a directory within the output directory in the directory where the simulator has been executed The directory and the file have a random name that includes the date when it was run This name is the same than the name of the window The output file is a text file and it can be open by any plain text editor The meaning of the values saved in it are explained in the same file and can be directly used by the user as an alternative way to change the embryo s state 4 2 4 2 Save snaps periodically By choosing this option the state of the embryo is automatically saved into a different file every 1000 iterations 4 2 4 2 Change frequency of snapshots This options prompts a message in the terminal where the user should introduce the iterations intervals in which snaps are taken 4 2 4 5 Read from file A prompt would arise in the terminal asking the user to introduce the name and address of the file the user wants to read 4 2 4 6 Add label to the name of the output file Adds a label given trough the terminal at the end of the output files saved 4 2 4 5 Save images automatically Snapshots of the system will be taken during simulation time The amount and frequency of snapshots is set automatically 4 2 4 6 Save movie check terminal Same as previous option but you need to specify the amount and frequency of snapshots via terminal 4 2 5 4 2 6 Enjo
11. olor palettes 4 2 2 3 2 Change color max and min from terminal This option will change the minimum and maximum values of the node property selected taken into account for coloring each node All values below the minimum value will have the same minimum color depending on the palette and all values above the maximal value will have the same maximum color The minimum and maximum values will be entered via terminal in the same line separated with a space in the respective order 4 2 2 3 3 Change color min with left mouse button change color palette gt This button allows to change the minimum value described above simply dragging the mouse with the left button select color max and min from terminal select color min with left mouse button select color max with left mouse button select color min with middle mouse button 4 2 2 3 4 Change color max with left mouse button select color max with middle mouse button This button allows to change the maximum value described above simply dragging the mouse with the left button 4 2 2 3 5 Change color min with middle mouse button This button allows to change the minimum value described above simply dragging the mouse with the middle mouse button this means pressing the scrolling wheel not actually scrolling 4 2 2 3 6 Change color max with middle mouse button This button allows to change the maximum value described above simply dragging the mouse with the middle mouse button
12. on 4 2 1 1 9 Section from the Maximal z plane As above but starting from the node with the maximal z position These different directions of sectioning can be combined to section the embryo from different sides 4 2 1 2 Reset to initial view This shows the embryo from the same default view than when the program was started 4 2 1 3 View from above Adjusts the view to be from top from large z values 4 2 1 4 View from front As above but to see from the front 4 2 1 5 Undo sections All sections will be undone and the whole system will be visible 4 2 1 6 Toggle fixed sections when running iterations This allows to switch between keeping the sections during simulations time or being undone when some iterations are run By default this option is set to the second case x Y z 4 2 2 Show node mechanical properties Menu p EQD x p ADD 4 2 2 1 with colors Submenu This with colors gt YOU submenu allows you to select a with semitransparent spheres p ADH mechanical node property to be color options gt p REP displayed as node color sphere options b p REC 4 2 2 2 with semitransparent spheres Submenu This submenu allows you to select a mechanical node property to be displayed as semitransparent spheres of different radius over each node 4 2 2 3 Color options Submenu This submenu allows to set different options regarding the coloring of nodes 4 2 2 3 1 Change color palette Submenu Allows you to choose between 4 different c
13. ptions what to draw are described in section 4 2 1 input output 4 1 2 Show node mechanical properties This menu allows to selection menu display mechanical node properties in two ways through the cursor menu color of nodes or through drawing semitransparent spheres over nodes whose size reflect the value of the property There 1 iteration are also several options to tune the display of each of the two 100 iterations methods Node coloring and transparent spheres are 1000 iterations independent thus one can display a different node property 3 with each method but not more than one with the same x Iterations method at once See section 4 2 2 quit 4 1 3 Show other node properties This menu allows to display non mechanical node properties such as node type gene expression etc This can be displayed in two ways through the color of nodes and through drawing semitransparent spheres over nodes whose size reflect the value of the property There are also several options to tune the display of each of the two methods Node coloring and transparent spheres and independent thus one can display a different node property with each method but not more than one with the same method at once 4 2 3 4 1 4 What to draw This option shows a submenu with a list of options to choose which parts of the embryo are shown in the display and how are those shown These options are described in detail in section 4 2 4 4 1 5 Input Output This option shows
14. rcellular contour balls as radius EQD balls as radius ADD small balls no balls display box boundaries polarization vectors centroids cells that are in physical contact These lines ghow displacement of nodes from origin are red between nodes of different epithelial cells and green between apical nodes of the epithelium and mesenchymal nodes movement unitary vectors force component repulson adhesion 4 2 3 8 Connexion between nodes Draws red lines between the nodes of the same cell 4 2 3 9 Draw cell contour Draws cellular contours by rendering surfaces between neighboring nodes of the same cell using a 3D Delaunay triangulation 4 2 3 10 Draw intercellular contour Complements the previous option by also rendering surfaces between nodes belonging to different cells displaying thus the space occupied by a compact tissue 4 2 3 11 Balls as radius EQD Nodes are draw as balls of radius equal to the EQD node property of each node 4 2 3 12 Balls as radius ADD Nodes are draw as balls of radius equal to the ADD node property of each node 4 2 3 13 Small balls Draws the nodes with very small balls Very useful for the visualization of forces or connections between nodes 4 2 3 14 No balls Doesn t draw the balls Very useful for the visualization of forces or connections between nodes 4 2 3 15 Display box boundaries Shows the boundaries of the display box Only elements inside this box will be displayed The
15. ton 4 2 2 6 5 Change sphere min with middle mouse button This button allows to change the minimum value described above simply dragging the mouse with the middle mouse button this means pressing the scrolling wheel not actually scrolling 4 2 2 6 6 Change sphere max with middle mouse button This button allows to change the maximum value described above simply dragging the mouse with the middle mouse button this means pressing the scrolling wheel not actually scrolling 4 2 2 6 7 Disable sphere This option disables the display of semitransparent spheres 4 2 3 Show other node properties Menu It is exactly the same as the previous menu 4 2 2 except for the node properties you can set in each of the three submenus with colors and with semitransparent spheres The following descriptions doesn t refer to all the submenus and options since they are the same as in the previous menu Instead the node properties that available for display in this menu are described cells 4 2 2 1 Cell The cell index of the cell the node cell nucleus as blue belongs to is displayed as dx 4 2 2 2 Cell nucleus as blue Nodes specified as 99 dy nuclei will have a value of 0 the rest will have a as dz value of 1 as boxes 4 2 2 3 As cell cycle The value of the cell as node index property P 4 of the cell the node belongs to will Amount of regulatory molecule A be displayed Amount of regulatory molecule C 4 2 2 4 As dx The distance
16. y Selection menu select node by index 4 2 5 1 Select node by index When selected the user should enter in select node with cursor the command line the index es of the node s to be selected When select cell by index the last selected node has been introduced the user has to type 1 to select cell with cursor end selection When a node is selected it will be coloured in white or undo selections yellow and some of its basic properties such as position or energy will be shown in the terminal The last node selected will always be colored in yellow and will be the one set for using the editor options see section 4 2 5 and the moving options see section 4 2 10 The rest of the selected nodes if any will be colored in white 4 2 5 2 Select node with cursor This option allows the user to select nodes using the cursor By default the cursor is moved in the x y plane by dragging the mouse with the left button Pressing the DOWN key will toggle between x y movement and z movement by dragging the mouse with the left button In order to select node approach the cursor to the desired node and press the mouse middle button press the scroll wheel but don t scroll the wheel 4 2 5 3 Select cell by index As in 4 2 7 1 but in here what the user should enter in the command line are the index es of the cell s to be selected 4 2 5 4 Select cell with cursor As in 4 2 7 2 but in here what is selected is the cell that is closest to the
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