Neighbour-Sensing version 3 - David Moore`s World of Fungi
Contents
1. 3 5 2 3 5 3 Whether growth is controlled by the number of neighbouring tips o click on the check box to bring this into effect when this is unchecked growth does not depend on the tip neighbourhood o also decide on the threshold number of tips that permits growth you will set the size of the neighbourhood in the next dialogue box The GROWTH RATE and Whether growth rate IS PROPORTIONAL TO HYPHAL LENGTH in this case you also need to specify the value of the proportionality coefficient or accept the suggested value of 0 1 AND the maximum value of the growth rate suggested value 5 effectively you are setting here the maximum specific growth rate otherwise the rate will go on increasing as hyphal length increases and could go through the roof The effect of this parameter is to make Page 9 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved hyphal tips more dispersed around the colony The way it works is that the set growth rate default value 1 but you can change that is compared with a calculated growth rate derived from hyphal length behind this tip x proportionality coefficient the higher value is used as the growth rate for the next branch providing it does not exceed the set maximum 3 6 The NEIGHBOURHOOD window is deceptively simple but its few controls allow you to establish the nature of the information that the hyp2. lt ITRICHOLOMA gt both autotropic growth response and branching are regulated by the hyphal density field and lt CONUS gt hyphal tips given a gravitropic reaction at 45 to the vertical so the simulation produces cup shaped tissues lt CORDS gt galvanotropism is turned on and results in aggregation of hyphae into linear structures similar to fungal cords and lt STANDARD gt which is a typical parameter set producing realistic fungal colonies and serves as a useful starting Page 6 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved 1 10 2 2 1 2 2 2 3 2 4 2 5 3 point for many experiments Any alteration made by the user to the parameter sets activates the lt MODIFIED gt entry in this menu The next major control button at the bottom of the main window is labelled DETAILS Pressing this button raises a set of dialogue boxes tabbed along the top of the window which group together the numerous parameters over which the user has control Also on the right of this window there are three additional tabs corresponding to three categories of hyphae this arrangement allows all parameters to be varied for all three hyphal types and a fourth tab labelled SUMMARY which displays a short summary of the coding equivalent to the complete parameter settings and is useful for documenting the experimental work Y
3. 3 2 along the bottom edge of the DETAILS window Pressing either one calls a Windows dialogue in which you can specify the path and file name for the SAVE or LOAD function you are carrying out The parameter sets are saved as XML files which are treated as text files by Microsoft Word so if you want to insert the control parameter settings into another document or print them for reference then use MS Word to access the XML file BUT NOTE that these XML files are working parts of the program so they are complete every parameter setting is recorded and every parameter is identified with its program tags If you only need a non redundant summary of your parameter settings then cut and paste from the SUMMARY tab screen see above Now let s return to the six tabs along the top of the DETAILS window The tab labelled TROPISMS gives access to the seven different tropisms that can be assigned to the hyphal tips 3 2 5 NEGATIVE AUTOTROPISM based on the hyphal density field intensity inversely proportional to distance with a persistence factor that controls the aversion vector and the opportunity to rotate the tropic sensor around the hyphal axis 3 2 6 SECONDARY LONG RANGE AUTOTROPISM and if it is activated the opportunity to set its impact the way it attenuates with distance either directly proportional to the square root of distance or inversely proportional to the square root of distance and the opportunity
4. other formats no GIF and don t bother begging The program is very simple and easy to understand The instructions are all in the README TXT file Here s a screenshot in case you re into those things fie MakeA I 5 i D Simage000 jpg Add Files D magell _Add Fes D image002 jpa 3 D image003 jpg Delete File D image004 jpg D image005 jpa i D image006 jpg Sort Files D image007 ipg i C D image008 jpg RE Move File D image003 jpg D image010 jpg D image011 jpg D Simage012 jpa D image01 3 jpg D image01 4 jpg D image015 jpg D image016 jpg Playback frame rate D image017 jpa s D image018 ipq fis fps I Crop to fi 76 x across by fi 44 Y down Exit x Introduction The core of the AVI generation is the Microsoft Windows AVI API Wrapped around that is a thin wrapper which I found at www codeguru com but it may be from a Microsoft sample app I don t know The image loading end is handled by the FreeImage library which is currently at http www 6ixsoft com It can handle many different image types but not GIF GIF is patent burdened and will not be supported so don t bother asking License MakeA VI is free software licensed under the GPL GNU General Public License Significant portions of MakeAVI specifically the FreeImage library are also licensed under the GPL For more information please read the LICENSE TXT file that should have come with this
5. 3 6 REPAINT MODEL MENU 4 4 1 RESTART 4 4 2 PAUSE or CONTINUE 4 4 3 SUBSTRATES opens the SUBSTRATE MANAGER to define SIZE POSITION and substrate tropisms 4 4 4 OPTIONS opens the model parameter panel to set the model parameters 4 4 5 ROBOT Activates the animation robot 4 4 6 HELP MENU APPENDIX 1 Using more than one processor Calling FUNGIMEDIA_3D JAR from the command line Page 4 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved 1 1 1 2 THE MAIN WINDOW When you first click on the Neighbour Sensing button on the World of Cyberfungi introductory page the Java environment is created using programs on the CD and as soon as this is completed you are presented with a button labelled START THE APPLICATION Click on this button to start the Neighbour Sensing program and the main window will appear This is largely made up of data space which is three dimensional of course in the centre of which is a red dot representing the first hyphal tip fungus spore The mycelium will grow from this point Around the data space are various controls in the form of buttons scroll bars and menus The control you might want to use first is the maximise button amongst the standard set of three Window controls at top right MINIMISE MA XIMISE CLOSE Press MAXIMISE for the full screen view At top left of the main Neighbour Sen
6. release If you do not have a copy of this file you can find it at http www gnu org licenses gpl txt Installation Page 22 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved Unzip all this stuff into one directory Run MAKEAVLEXE There it s installed If you want to get cute right click on MakeAVI hit Create shortcut and drag the shortcut onto your desktop Using MakeA VI You want to select all your images into the list on the left Use the Add Files button to choose your files Use the Add Files Delete File Sort Files and Move file Up Down buttons to get the images in the order you want them Any image that is selected on the left will be previewed in the middle If it isn t previewed properly then the program is unable to read the image can t access the file or the file is corrupt or something Cropping All the images have to be the same size to go into an AVI file If you have images of varying sizes or you have junk at the edge that you want to eliminate from the final AVI you can use the Cropping interface at the bottom Check the Crop to box and select the size you want the final images to be cropped to in the boxes to the right NOTE that the original images are NOT cropped on disk they are only cropped after they re loaded and before they re added to the AVI NOTE that currently images are cropped towards the cen
7. simulation includes SECONDARY HYPHAE these branches are displayed in grey and the rest of the mycelium will be displayed in black When you reset a colour choice after using the NO COLOURS option you should choose STANDARD FRONT VIEW to restore the mycelium to its default colours as well as default orientation 4 3 5 STANDARD FRONT VIEW Turns the mycelial view angle to the front view 4 3 6 REPAINT Repaints the mycelia Java sometimes fails to do this automatically 4 4 MODEL MENU The MODEL MENU controls the simulation process and model parameters 4 4 1 RESTART restarts the development from the single hyphal tip This is the menu equivalent of the START NEW button and it DISCARDS the current simulation 4 4 2 PAUSE or CONTINUE suspends or resumes the current simulation 4 4 3 SUBSTRATES opens the SUBSTRATE MANAGER panel referred to above section 3 11 and detailed below The SUBSTRATE MANAGER PANEL allows the user to add attractive or inhibitory substrates It contains the following controls Page 15 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved 4 4 3 1 RETURN TO MAIN WINDOW returns to the main simulation window 4 4 3 2 SIZE input field specifies the radius of the substrate The current version supports spherical substrates only The hyphae can enter inside the substrate subject to the parameters chosen 4 4 3 3 POSITION input fie
8. the third will fetch this Operating Manual pdf for you Our installation packages install our files in your lt C Program Files gt directory If you ever want to remove World of Cyberfungi from your hard disk you can do so using the Uninstall a program option on your system s Control Panel Page 2 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved Neighbour Sensing User manual CONTENTS 1 THE MAIN WINDOW 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 START button PAUSE check box SCALE magnification scroll bar SCALE BAR ORIENTATION scroll bars and FRONT VIEW BUTTON REPAINT BUTTON VIEWING WINDOW scroll bars STATUS REPORT LINE and CURRENT STRATEGY Built in parameter sets DETAILS control button 2 CATEGORIES OF HYPHAE 2 1 2 2 2 3 2 4 2 5 STANDARD hyphae LEADING hyphae SECONDARY hyphae Branching sensitivity Maximum branches 3 CONTROL PARAMETERS 3 1 3 2 3 3 3 4 3 5 SAVE and LOAD parameter sets TROPISMS tab 3 2 1 NEGATIVE AUTOTROPISM 3 2 2 SECONDARY LONG RANGE AUTOTROPISM 3 2 3 TERTIARY LONG RANGE AUTOTROPISM 3 2 4 PARALLEL CURRENT PARALLEL TROPISM 3 2 5 PARALLEL CURRENT POSITIVE NEGATIVE TROPISM 3 2 6 GRAVITROPISM 3 2 7 HORIZONTAL PLANE TROPISM GROWTH AND BRANCHING tab BRANCHING control 3 4 1 Control by the number of neighbouring tips 3 4 2 Probability of branching 3 4 3 DENSITY FIELD REGUL
9. value will replace the X in the above statements 3 8 The final regulatory window in this set is reached through the tab labelled DESTRUCTOR This implements the idea of removing some hyphae 3 8 1 If you select the check box HYPHAL REMOVING SUPPOSED then hyphae will be removed in accordance with the rules you specify in the rest of the window Removal proceeds in a basipetal direction from the hyphal tip that qualifies for removal to the closest branch point that does not qualify If this check box is unchecked hyphae are not removed When the check box is checked the rest of the options are made available You can select one of two conditions 3 8 1 1 Hypha is removed if the density at the tip exceeds a certain threshold value o Check the box to implement o Enter the threshold value in the data window 3 8 1 2 The second option is that a hyphal section is removed if the number of tips supported by the section is less than the given threshold value o Check the box to implement Page 10 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved o Enter the threshold value in the data window 3 8 2 Hyphal removal must be implemented after some delay otherwise the initial growth of the mycelium will be jeopardised so the next two controls establish those limitations o MINIMUM AND MAXIMUM AGE of a hyphal section o MINIMUM AND MAXIMUM LENGTH of a hyphal section
10. ATES BRANCHING 3 4 4 MAXIMAL BRANCH ANGLE 3 4 5 ENABLE SECONDARY INTERNAL BRANCHING 3 4 6 PROBABILITY FOR THE NEW BRANCH TO BECOME LEADING GROWTH control 3 5 1 Control by the number of neighbouring tips 3 5 2 GROWTH RATE 3 5 3 Growth PROPORTIONAL TO HYPHAL LENGTH Page 3 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved 3 6 3 7 3 8 3 9 3 10 3 11 The NEIGHBOURHOOD window 3 6 1 Specify the radius of the neighbourhood 3 6 2 Create the hyphal density field from HYPHAL TIPS and or BRANCH POINTS or ALL OF THE MYCELIUM AGE LENGTH LIMITS window DESTRUCTOR This implements the idea of removing some hyphae 3 8 1 HYPHAL REMOVING 3 8 2 AGE AND LENGTH of a hyphal section 3 8 3 KEEP REFERENCES TO THE DEAD BRANCHES COMMENTS to be saved with the parameter set DETAILS window buttons RETURN TO SIMULATION 3 10 1 LOAD PARAMETERS and SAVE PARAMETERS 3 10 2 MAKE THIS PAGE IDENTICAL and ALL IDENTICAL SUBSTRATE MANAGER dialogue to define SIZE POSITION and substrate tropisms 4 THE MENU BAR 4 1 4 2 4 3 4 4 FILE MENU 4 1 1 SAVE MYCELIA 4 1 2 SAVE IMAGE 4 1 3 OPEN MYCELIA FILE 4 1 4 WRITE CHECKPOINT TO 4 1 5 EXIT PROGRAM ANALYSE MENU 4 2 1 VIEW SLICE 4 2 2 MEASURE MYCELIA SHOW MENU 4 3 1 HYPHAL TIPS 4 3 2 FIELD VECTORS 4 3 3 ROOT DISTANCE BASED COLORS 4 3 4 NO COLOURS 4 3 5 STANDARD FRONT VIEW 4
11. Combining these two limitations enables young mycelia to develop and limits removal to hyphal sections that are not supporting the set minimum number of hyphal tips 3 8 3 Finally if the check box KEEP REFERENCES TO THE DEAD BRANCHES is checked then a hyphal branch which is deemed to be dead by the criteria set as above does not contribute to the hyphal density field but remains on display in the visualisation in a different colour green for the first ten iterations of the program then yellow However if the box is unchecked then the data is discarded and the dead branches are removed from the visualisation this option reduces the computational load and may be the option of choice if processor performance is an issue 3 9 The final tab COMMENTS allows the user to make notes about the parameter sets There is a separate COMMENTS window for each hyphal category STANDARD LEADING and SECONDARY What you write is up to you but it will be saved with the parameter set 3 10 At the bottom of the DETAILS window are a set of buttons If you just want to get back to see what your new parameter set does to the cybermycelium then simple press RETURN TO SIMULATION 3 10 1 The buttons LOAD PARAMETERS and SAVE PARAMETERS do just what their names imply Pressing them brings up a file management dialogue in which you can specify file name and path and were described above 3 10 2 The other two buttons save you the chore of copy
12. METERS the model parameters The parameters are also automatically stored when saving the whole mycelium in mycelia xml files 4 4 5 ROBOT Activates the animation robot Immediately on choosing this option you will be presented with a file management dialogue to choose the folder and filename of the AutoDoc robot file in which your manipulations will be recorded they will be saved as a TXT format file At the same time some new control options appear at the bottom of the main window When you ve made your choice of path and name of the file in which the manipulations will be logged you will have access to the new controls The new panel contains controls to alter some model parameters manually and interactively These alterations can be recorded in the AutoDoc robot file Later you can rerun the simulation and replay the automated parameter alterations so that parameters are automatically changed during the new simulation in the same way as they were modified by the operator during the original simulation when they were recorded At the start of the replay process you will be prompted for the file name where the original alterations were recorded The robot control panel consist of four parameters Each parameter has a checkbox that activates its scroll bar slider control on the robot control panel If this box is unchecked the value for the corresponding parameter will be taken from the model options panel in the usual way and N
13. Neighbour Sensing User manual Operating details for version 3 7 of the Neighbour Sensing program STARTING THE PROGRAM The program is distributed as part of the 21st Century Guidebook to Fungi self start CD Insert the CD into your computer and the Autorun program will initiate your web browser and start the CD showing you the Contents page From that point just follow the links on screen to explore the CD and go to the World of Cyberfungi The Neighbour Sensing program on this CD will run under Windows from Windows 98 to Windows 7 If the CD does not self start click on your Windows START BUTTON then choose RUN and BROWSE to the CD folder CYBERFUNGI and choose to run AUTORUN EXE from within the CYBERFUNGI folder IMPORTANT Internet browsers have protective blocks against any Web page that tries to run active content on your computer Because we use your browser to navigate the Neighbour Sensing disk the Java program scripting that the Neighbour Sensing program depends on will trigger these blocks So when the program attempts to run you will receive a message prompting you to indicate whether you want to allow it to continue You may also see an information bar offering information about the block immediately beneath the browser s address bar This will happen each time you load the CD If you are happy to keep on clicking Yes to enable the program to continue then leave matters as they are You could change your browser s
14. OT FROM THE ROBOT PANEL To the right of the checkbox is a short label naming the parameter and its current value The value is changed by sliding the scroll bar located adjacent to this text The control parameters are 4 4 5 1 ANGLE The angle of the plagiogravitropic reaction This parameter only has effect if the gravitropic reaction is supposed in the current model 4 4 5 2 AUTOTROPISM b The long range positive autotropism used to force hypha to join together 4 4 5 3 GALVANOTROPISM The positive negative galvanotropism forcing hyphae to grow at a right angle 90 in relation to each other 4 4 5 4 GALVANOTROPISM The parallel galvanotropism which forces hyphae to grow in parallel forming stems and mycelial cords 4 4 5 5 The checkbox ROBOT at the extreme bottom right of the panel activates the automatic parameter alteration FOR THE REPLAY PROCESS After selecting this checkbox you will be prompted for the file where alterations were previously recorded IMPORTANT you must ensure that the parameter set s for the hyphal category ies you are attempting to manipulate DO have the appropriate parameters specified and activated Page 17 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved These check boxes on the ROBOT panel only activate manual manipulation You can twiddle the gravitropic reaction scroll bar as much as you like bu
15. VE and up will come a feedback box asking which video format you wish to save to The range of compression formats offered depends on the digital video codecs on YOUR computer At the moment we re recommending Full Frames Uncompressed even though it does generate HUGE files the hyphae in our images are so fine that they can be lost when the image is put through the compression codecs tried so far As experience accumulates we might change this recommendation Make your choice press OK and your video will be constructed Now you have your video you just have to double click on the file name and Windows will launch your multimedia software so you can enjoy it You could send it to your friends as a video greetings card Don t blame us if they think you re nerdy Page 21 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved APPENDIX 3 MakeA VI version 0 11 of June 18 2002 Developed by John Ridley Available from http makeavi sourceforge net This is a quick and dirty app that I wrote because I wanted to do some work with creating time lapse movies For that particular project I set up a digital camera to take a picture every 10 seconds for several hours then I wanted to string the JPGs together into an AVI and do any video work from there This program allows you to do that sort of thing It will read JPGs as well as PNG BMP and several
16. Y and Z in the bottom right hand corner change the orientation of the slice plane 4 2 2 Choose MEASURE MYCELIA from the ANALYSE MENU and the main panel will be replaced by the MYCELIA MEASUREMENT PANEL which allows you to collect data describing the statistical and macroscopic properties of the growing colony in your simulation The panel consists of three separate tabs 4 2 2 1 The DISTRIBUTIONS TAB allows selection of the property being measured and shows the statistical distribution of its value in the mycelium components This tab contains the following options 4 2 2 2 DISABLE MEASUREMENTS checkbox if selected this suspends all measurements but not the simulation 4 2 2 3 MEASURE ONLY TERMINAL SECTIONS checkbox when selected forces measurement of terminal sections only that is sections ending in a growing hyphal tip If this option is not selected all sections of mycelia are measured 4 2 2 4 RETURN button closes the measurement panel the measurement continues and can be viewed later by returning to this mode The statistical distribution histogram shows the statistical distribution of the measurements The graph is only active for individual properties like section length and not for global properties like colony diameter 4 2 2 5 The PROPERTY SELECTION LIST at the extreme left of the MYCELIA MEASUREMENT PANEL allows you to select the property to be measured This can be a local property like segment age or a global on
17. alisation the program will save the XML files into that folder These can be converted into animations later To stop saving the XML files it is best to pause the visualisation and then exit the program If you exit without pausing you may find that the final frame is not fully completed NOTE the default arrangement is for XML files to be saved after each 10 iterations that is at 10 program time unit intervals The timing can be adjusted by editing the value in the SAVE AT EACH box in the file management dialogue For real time videos save your XMLs every iteration Enter any value greater than in the SAVE AT EACH box and the video will run faster than the original simulation Saving XMLs every 50 iterations is useful for logging the progress of complex visualisations on an untended computer or supercomputer We have a separate program on the Neighbour Sensing program CD called Animator which will generate the JPG files from the XMLs you have just generated Double click on Animator bat to start Animator Animator has controls similar to the main program but you should also note that changing the size of the window regulates the size of the generated pictures At bottom left of the Animator window is a button labelled OPEN pressing this brings up a file management dialogue that enables Page 20 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserv
18. and your purpose you may need to run this file from a command line On most supercomputers this is the only way to run the program The program itself is called by the following command java jar FungiMedia_3D jar f taskFile mycelia xml c other keys The following keys are supported f file specifies the task file that is usually prepared to run the program under Windows or other graphic environment c Blocks the programs graphic user interface The key is mandatory in batch mode where the interaction with the user is not possible It can also be used to run a prepared task under Windows which results in faster execution save interval Specifies the interval in program time units for saving the current situation in a standard task file save 1 is used to create sets that can be later converted into animations If this is not planned it is better to use larger interval values as saving takes execution time The default value is 10 until time Specifies the time in program time units not the absolute time to terminate the program It is used when we wish to limit how long the simulation should continue r file Specifies if required the robot file containing changes of adjustable parameters output folder Specifies the folder where results must be written By default results are written to the folder from where the program was started p number_of_processors Specifies the expected number of processors on a multiproc
19. at as a text file You will be prompted for the file name and path 4 2 2 14 SAVE IMAGE button saves the graph image as a JPG file 4 2 2 15 REFRESH repaints the graph 4 2 2 16 The HISTORY MONITOR TAB provides a comprehensive view of how the distribution of the measured property changes in time The vertical dimension of this image represents time one line per program time unit The horizontal dimension of the image represents the values of the measured parameter plotting a point for each measured value The ACTIVATE check box turns the history monitor on The SAVE IMAGE button saves the history image 4 3 SHOW MENU This menu allows you to customise your view of the mycelium 4 3 1 4 3 2 4 3 3 HYPHAL TIPS If this option is activated the hyphal tips are displayed as tiny coloured points Their colour indicates the state of the hyphal tip depending on its history surroundings and the parameter set of the current model simulation Growth Branching Colour possible possible Red Yes Green Yes Blue No Black No FIELD VECTORS If activated the field vectors which are currently sensed by each hyphal tip are displayed a short coloured lines emerging from the tip The number of lines depends on the number of fields currently included in the current model ROOT DISTANCE BASED COLORS If activated the colour of a hyphal segment depends on the distance from the point where growth originated i e
20. buttons at the ends of the sliders for more precise control over scroll bar movement Notice that as you change the magnification the SCALE BAR in the top left of the data space automatically adjusts It always shows 100 units and the length of the scale bar is determined by the magnification scroll bar These are program length units They are arbitrary in the sense that they are not standard physical length units but they are consistent in the sense that they are always the same each time the program runs Consequently the scale bar can be used to compare images of different simulations that you may have saved under different magnifications Alongside the PAUSE check box are two more scroll bars These are the ORIENTATION scroll bars and they enable you to select the viewing angle Z rotates the simulation around the vertical axis of your screen X rotates it around the horizontal axis Notice that as you rotate the simulation the angles of the current orientation are displayed to the left of the two scroll bars Again you can use the arrow buttons at the ends of the sliders for more precise control over scroll bar movement one degree rotation per click Note that you can also change the ORIENTATION by mouse dragging across the data space If you do this the X and Z angles will update to the final orientation when you release the mouse key Remember the simulation starts with both X and Z at zero degrees so you can always reinstate the initial
21. checked branching does not depend on the number of neighbouring tips o also decide on the threshold number of tips that permits branching you will set the size of the neighbourhood in the next dialogue window o Branching will take place at a randomly chosen position around the periphery of the hypha if OPTIMAL INITIAL BRANCH ORIENTATION is left unchecked If this box is checked then the position of branch emergence will be calculated to be optimal for the tropic vectors acting on the tip at the time of branching By default there is a 100 probability of branching subject to other rules you may set elsewhere but you can determine the probability of branching by o Checking the check box alongside the sentence IF THE TIP CAN BRANCH and o Entering your probability of branching in the adjacent window Checking the DENSITY FIELD REGULATES BRANCHING check box makes branching dependent on the mycelial mass rather than the number of tips in the neighbourhood you will define the meaning of hyphal mass in the next dialogue window MAXIMAL BRANCH ANGLE obviously allows you to determine the angle of branching by setting its maximum value the default is 180 which effectively means that any angle is acceptable user can set this to smaller angles of choice ENABLE SECONDARY INTERNAL BRANCHING and PROBABILITY FOR THE NEW BRANCH TO BECOME LEADING have both been described above 3 5 Under GROWTH you can determine 3 5 1
22. distance to the root This distance is computed as the total distance not just the shortest This is essentially colour coding on the basis of hyphal age In this case green represents hyphal segments close to the initial point and red those which are very far from the initial point This colouring is normalized Page 14 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved by the program first finding the longest distance in the mycelium and then assigning the colours for each point depending on the percentage distance to the root If this option is inactivated the colour of a hyphal segment depends on the number of branches it supports Colour Number of supported branches Black Over 64 Brown 32 64 Blue 16 31 Green 8 15 Magenta 4 7 Pink 1 3 Red None apical section Additionally in experiments that include dead leading or secondary branches the default colouring of normal branches is over ridden and the colour indicates the state of the hyphal segment Colour State Green Dead section 9 time units or less after death of the segment Yellow Dead section more than 9 time units after death of the segment Blue Leading branch Red Secondary branch 4 3 4 NO COLOURS Hyphae are displayed in black and white This is intended for illustrations planned for use in printed figures If the
23. e like hyphal growth unit 4 2 2 6 At the bottom of the panel you will see the INTERVALS input field which specifies how the data will be grouped into intervals for the distribution histogram 4 2 2 7 The MAX Y MAX x and MIN X fields specify the boundary values that can be displayed on the graph All fields can be left empty for the program to make automatic selections 4 2 2 8 The SAVE NUMERIC button saves the distribution histogram in numeric format as a text file You will be prompted for the file name and path if you press this button Page 13 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved 4 2 2 9 Press the SAVE IMAGE button to save the histogram image as a JPG file Again you will be prompted for the file name and path for the save operation 4 2 2 10 The MEASURE button updates the histogram view after you make a modification to the input fields 4 2 2 11 The TIME RELATED TAB brings up a graphic that shows how the measured property shown as the Y value and identified at the top of the graph changes in time X value For individual properties like the tip age it displays the averaged value 4 2 2 12 MIN yY MAX Y MIN X and MAX x input fields and the FIXED 0 checkbox specify boundary values that are displayed in the graph The input fields can be left empty for automated selection 4 2 2 13 SAVE NUMERIC stores the graph in numeric form
24. eath the START START NEw button Mouseclicking the PAUSE check box will halt the current simulation uncheck this box with another mouseclick to resume the same simulation IMPORTANT to resume a paused experiment click again on the PAUSE check box to remove the check mark If you press START NEW it will do just that discard any existing mycelium and start a new mycelium it will not resume growth of the existing one If you are running a simulation now let it grow to about 300 tips and mouseclick on the PAUSE check box so that you have a smallish mycelium within your data space We ll now introduce you to the rest of the controls and here and throughout this manual we will list controls starting from the top left of the screen proceeding to bottom right Page 5 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved 1 3 1 4 1 5 1 6 1 7 1 8 1 9 Alongside the START START NEW button is the magnification scroll bar labelled SCALE Mouse drag put the cursor on the scroll bar and hold down the left hand mouse key to take the scroll bar to the right and the magnification is increased With the scroll bar at the extreme right of the slider you can study the details of interactions of individual hyphal tips Mouse drag to the left and magnification decreases This provides you with a macroscopic view of your simulation Use the arrow
25. ed you to select the folder in which you saved the XML files previous paragraph When you Open the folder the number of files it contains is reported at bottom left of the Animator window The slider that occupies most of the bottom margin of the Animator window can be used to navigate through the XML file collection displaying the image they represent in the main dataspace window We recommend that you slide to the last of your images which we assume will be the largest and then size the window to frame that nicely Such a strategy will ensure that the window size of the animation is optimised Click on the button labelled PLAY and Animator will run through your images playing the animation it would produce so that you can check it and maybe modify the view using the controls along the top of the Animator window The rate of progress of this process is very dependent on the speed of your hard disk because the XML files are being read in succession and on the speed of your processor because the XML files are being rendered into images in succession A second click on PLAY will stop the run through When you are satisfied with the rehearsal you can press the small button numbered 1 alongside the OPEN button and this will open a file management dialogue which will show you your collection of XML files so you can choose which one will start the digital video Then check the check box labelled WRITE IMAGES at bottom ri
26. ed by a suitable graphics program to create an AVI format movie which can be viewed independently of the Neighbour Sensing program This approach is simply a digital video record of one particular visualisation but it can be incorporated into your presentations and displays just like any other digital video movie We will describe this approach now Making digital video records We think we should start this section with the warning that we can generate some VERY LARGE files using this approach We are talking GIGAbytes here even for a modest video We think they re really rather nice and well worth the disk space Just the thing to watch after dinner instead of the annual Christmas showing of The Great Escape but we must warn you that if you don t have a capacious hard disk then you need to think carefully about your tactics The basic process is as follows e Use the WRITE CHECKPOINT TO option on the FILE menu section 4 1 4 above to generate a regular series of XML files as a visualisation progresses e Use our independent conversion program to convert the XML files to JPG format e Use a third party graphics environment which we suggest and include on our CD to merge all the JPG files into an AVI file So let s go Choose the option WRITE CHECKPOINT TO on the FILE and you will be presented with a file management dialogue to choose the pre existing folder in which the XML files will be saved Then as soon as you resume the visu
27. elect the indicated file then right click and choose Create shortcut e one to the file AutoRun exe which will then run the World of Cyberfungi from your own machine exactly as it runs from the CD e and one to the file Run_standalone bat which will open the Java environment included within the Cyberfungi folder on your machine and then run the Neighbour Sensing program beyond your Internet browser s clutches If you want to save yourself the effort and sit back while we do it all for you then take the following steps to activate our Windows installer package e put your 2 st Century Guidebook to Fungi CD in the drive and let it autostart e from the 2 st Century Guidebook to Fungi Contents page choose to go directly to the World of Cyberfungi e onthe Welcome to the World of Cyberfungi page click the Neighbour Sensing blue button e atthe bottom of this page which is entitled PRESS THE BUTTON you will find our hyperlink to the installer so just click on lt CLICK HERE TO INSTALL NOW gt e this calls a standard MS Windows installer package if you are asked whether to RUN or SAVE choose RUN If you are asked if you want to allow this program to make changes to your computer answer YES The installer will add three shortcuts to your DESKTOP o one will run the Neighbour Sensing program independently of the Internet browser o the other will run the World of Cyberfungi from your own machine exactly as it runs from the CD o and
28. essor computer It must be equal to or a little larger than the actual number of processors available for use but too large a value slows the execution The program cannot use more processors than are specified with this key Page 19 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved APPENDIX 2 Animations There are two ways to generate animations with the Neighbour Sensing program One is to activate an ANIMATION ROBOT detailed in section 4 4 5 of the Neighbour Sensing Manual that records your use of the parameter controls as you modify the visualisation by manual interaction This saves a record of the parameter changes you make and allows you to re run a visualisation at a later date using the Neighbour Sensing program with exactly the same timing and sequence of parameter changes However each time you run the robot you are creating a new visualisation with a new population of hyphal tips so there will be some natural variation The combination of a pre saved file of parameter settings and an animation robot file of parameter settings is analogous to a living organism s combination of genome and developmental programme The ANIMATION ROBOT is described above and we will not explain it further here The second animation technique is to use the Neighbour Sensing program to generate a series of frames for a digital movie The frames can then be us
29. ettings look for Allow active content from CDs to run on My Computer but we don t recommend this as it means making a global change to your security settings and will permit active content from external Internet sources to run on your computer too Instead of this we suggest that you copy all the relevant content of the CD to your hard disk space required 160 Mb as described in the next few paragraphs Page 1 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved The Neighbour Sensing program will run very effectively from the CD BUT you will not be able to save any of your data This is due to the safety features within Internet browsers that bar browser access to your machine s resources Because we are using a website structure to navigate the CD we fall foul of this feature If you want to save your experiments you can avoid the browser security features by copying the program and other files from the CD to your own computer s hard disk There are two ways to do this you can do it with your own hands following the instructions below or you can use our INSTALL program and let us do it for you If you want to DIY you ll have to Explore the CD In the root folder you will find a folder called Cyberfungi Copy this intact to your choice of folder on your hard disk space required 160 Mb and then create two Desktop shortcuts s
30. ght of the Animator window Now the images will be written to disk when you press and hold the PLAY button You can pause the writing process at any time by releasing the Play button While paused you can alter the image views scale rotation etc then press PLAY again and writing will resume from where it left off When the process is completed you will have a folder called images within the folder from which Animator was run which will contain a set of JPG files corresponding to your original set of XML files The next stage is to combine this collection of JPGs into an AVI digital video There are undoubtedly many ways of doing this What we re using at the moment is a freeware program called MakeAVI see Appendix 3 Run MakeAVL exe and then choose ADD FILES navigate to your images folder containing your JPGs and select all of them using Ctrl A The file names will then be loaded into MakeAVI s main window MakeAVI gives you some options to manipulate and arrange the files which will be the frames in your video but you ve probably done all you need to do in Animator The only remaining option on this screen to consider is the frame rate High values may create unnecessary difficulties for your hard in reading the frames so we suggest using 8 frames per second Press BEGIN to start the process You first get a file management dialogue in which you specify the filename and folder for your AVI file then press SA
31. hal tips sense and the range over which they sense it Well that s the effect but we re dealing with insensate cyberhyphae so in strict mathematical terms you are actually determining the nature of the information used to calculate the growth vector of and or branching capability of each hyphal tip in the visualisation and the range over which that information is collected 3 7 1 Enter a number in the first window to specify in standard length units the radius within which tips are considered to be neighbouring 3 7 2 Then choose by checking the check boxes whether to create the hyphal density field from o HYPHAL TIPS and or o BRANCH POINTS or o ALL OF THE MYCELIUM but note the warning that this last choice makes for slow calculation because it is very demanding of the processor o If you choose ALL OF THE MYCELIUM you get the opportunity to specify the CHARGE UNIT LENGTH which is the length of hyphal segment that generates the same field as a hyphal tip in the alternative hyphal tip driven mechanism 3 7 In the AGE LENGTH LIMITS window you can decide the conditions under which growth and or branching will be halted In each case you check the box to implement the control and then enter a numerical limiting value to Oo STOP GROWING AFTER THE TIP EXCEEDS X time units Oo STOP BRANCHING AFTER THE TIP EXCEEDS X time units Oo STOP GROWING AFTER THE HYPHAL SECTION LENGTH EXCEEDS X standard length units Your limiting
32. he file can be later reloaded using the OPEN MYCELIA FILE option for continuation or further manipulation The XML file will generally be much smaller than an image file but contains all the information the Neighbour Sensing program needs to recreate an image All these save operations can save data to a folder of your choice but we have provided an empty folder called Save_Data you might want to use for this purpose SAVE IMAGE Save the current view of the current mycelium as a graphic file in JPG format Choosing this option brings up a file save dialogue for you to specify the path and filename for the save operation but the dialogue box contains ADDITIONAL check boxes allowing you to save simultaneously and with matching file names the additional information about the parameter set as plain TXT and or XML AND an XML mycelia file OPEN MYCELIA FILE Open an XML mycelia file that was previously created by SAVE MYCELIA or SAVE IMAGE commands or as automated CHECKPOINT Choosing this option brings up a file open dialogue which you can direct to the appropriate path so that the program can find a MYCELIA FILE the filename of which will terminate in xxx mycelia xml WRITE CHECKPOINT TO This option activates inactivates automated mycelia saving after each model iteration The mycelia files which are stored as a consequence of activating this function can be used subsequently for animations or statistical analysis Activate the opti
33. ing over parameters between the different categories of hyphae If you make a change to one hyphal category say Standard hyphae and want it to apply to the other two then press MAKE THIS PAGE IDENTICAL and all your most recent changes will propagate to the other two hyphal categories In this case only your most recent changes will be copied over if you ve not changed parameters in which the categories differ then these differences will remain unchanged On the other hand if you want to make all three option sets identical to the current set then press ALL IDENTICAL and all parameter values for the currently active hyphal category will be copied into the other two categories In this case any parameter values that previously differed between the hyphal options will be over written to match the currently active category even if you ve not been working on them recently 3 11 Now press RETURN TO SIMULATION to get back to the main view screen so that we can mention the final button on that screen at the bottom right hand corner The control button labelled SUBSTRATES opens a SUBSTRATE MANAGER dialogue that allows the user to add substrates to which hyphae will have a positive tropism or inhibitors negative tropism User can select substrate size position and attractiveness It is important to remember to press the ADD NEW button after selecting the characteristics for a new substrate inhibitor A list of all currentl
34. lds specify the centre of the spherical substrate X Y and Z co ordinates in the same program conditional units in which the whole mycelium is measured 4 4 3 4 NEGATIVE TROPISMS INHIBITORY SUBSTRATE check box indicates that the hyphae will avoid this substrate rather than trying to get closer to it Inhibitory substrates are shown in red whilst attractive substrates that cause positive tropisms are shown in green 4 4 3 5 ATTRACTIVENESS specifies the attractive force of the substrate in relative units If the current model supposes that the autotropic field is generated by hyphal tips only this number indicates how much the field of the substrate is stronger than the field of the single hyphal tip If the autotropic field is generate by the whole mycelia this number indicates how much the field of the substrate is stronger than the field of the hyphal section with the length defined as charge unit length in the NEIGHBOURHOOD section of the model parameters 4 4 3 6 REMOVE ALL SUBSTRATES removes all substrates from the model 4 4 3 7 REMOVE SELECTED removes the substrate s you select by highlighting with your mouse 4 4 3 8 CHANGE SELECTED updates the properties of the selected substrate to the values of the input fields described above 4 4 3 9 ADD NEW Enables you to add a new substrate with the properties that you specify in the input fields The substrate list which takes up the majority of this panel shows all subs
35. nges that generated it Well remember that the AutoDoc robot file in which your manipulations are recorded is saved as a TXT format file The data in that file is actually formatted as a table the first column time in program time units when the alteration was made second column angle of gravitropic reaction third column level of long distance autotropic reaction fourth column level of parallel galvanotropic reaction fifth column galvanotropic reaction This text file is tab delimited and can be imported into graphical programs like Excel MathCad FigP etc as data for generating graphs and charts of the parameter variations to match with your illustrations of the developing visualisation AND FINALLY you can edit the robot file manually with a TEXT editor like Notepad So you could manually change the timings of the manipulations for example or cut and paste different manipulations together There s power in them ROBOT files 4 4 6 HELP MENU This currently provides a list of the program keys for running in console mode Page 18 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved APPENDIX 1 USING MORE THAN ONE PROCESSOR CALLING FUNGIMEDIA_3D JAR FROM THE COMMAND LINE FungiMedia_3D jar is a cross platform Java application able to run on any computer supporting Java 1 4 or compatible Depending on the platform
36. on with a mouse click you will be prompted for the folder where to store the checkpoint files Completion of this operation will insert a check mark tick on this option on the FILE menu Subsequently you can deactivate the save option with a second mouseclick EXIT PROGRAM Quits the program and returns you to the Windows desktop 4 2 ANALYSE MENU The ANALYSE MENU turns on two additional modes slice view and mycelia measurement These two modes will be discussed separately immediately below The RETURN TO INITIAL VIEW option on this menu returns you to the main simulation mode 4 2 1 Choose VIEW SLICE from the ANALYSE MENU and the main panel will be replaced by the MYCELIA SLICE PANEL which offers the following options 4 2 1 1 SLICE THICKNESS scroll bar to set the thickness of the slice Page 12 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved 4 2 1 2 SAVE IMAGE button to save the slice not the whole mycelium as a graphic image 4 2 1 3 RETURN button to cancel the slice mode and return to the main mode The main part of this panel will show the mycelium slice including a scale bar as well as a scale bar indicating the slice thickness Mouse dragging in this view changes the viewing angle 4 3 1 4 At the bottom of the panel is the SLICE PLANE scroll bar which changes the position of the slice plane 4 3 1 5 The three buttons X
37. or some reason John Ridley 2002 Page 23 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved
38. ou can cut and paste from this window to make a summarised record of your parameters sets during your experiments Note that you can also access the text equivalent of your complete parameter sets by using the SAVE and LOAD parameter sets buttons which are described below CATEGORIES OF HYPHAE STANDARD hyphae are the hyphae that normally start developing when a simulation is started LEADING hyphae can emerge from the colony peripheral growth zone with a probability determined by the user in the parameter set under the tab labelled GROWTH AND BRANCHING to take on a leading role in the formation of mycelial cords for example and can have a completely different parameter set from other hyphae SECONDARY hyphae are branches that arise late far behind the peripheral growth zone when mature hyphal segments of either STANDARD or LEADING hyphae resume branching to in fill the older parts of the colony Again the user can enable secondary branching in the parameter set under the tab labelled GROWTH AND BRANCHING and the fresh secondary hyphal tips can have a completely different parameter set from the other hyphal tips in the mycelium Secondary branching is enabled by altering the sensitivity of the older segments to the regulatory factors that stopped their standard branching when the mycelium first formed Basically standard branching is suppressed in parts of the mycelium that are optimally dense according to the tropism rules set by the use
39. r To enable secondary branching the sensitivity threshold must be set higher using the SENSITIVITY ADJUSTMENT under the tab labelled GROWTH AND BRANCHING The default setting for this is unity i e no difference in sensitivity but the user can change this to say 2 or 4 to make branching 2 or 4 times less sensitive to the density field and secondary branching can then begin The related control MAX BRANCHES permits the user to decide the number of secondary branches that will be produced It is possible to enter any values for the sensitivity adjustment and max branches there are no limitations set in the program BUT BEWARE these are computationally intensive and high values are really only practicable with multi processor high performance computers With a desktop PC we recommend staying in the range 1 5 for sensitivity adjustment and not exceeding 20 max branches CONTROL PARAMETERS Along the top of the DETAILS window are a series of tabs identifying the control parameter groups These are detailed below 3 1 It is possible to SAVE and LOAD parameter sets so you can experiment towards parameter sets of interest to you without losing track of the parameter settings providing you save the parameters at regular intervals The SAVE PARAMETERS and LOAD PARAMETERS buttons are Page 7 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved
40. sing window is the START button mouseclick on this to press it and the program starts to grow a mycelium When a mycelium is growing the name of this button changes to START NEW Why don t you try that The program is able to grow mycelia as soon as it starts up So if you press START now you can grow a little mycelium that we can use to demonstrate the other controls Note the program will automatically save data about the mycelium it is simulating and if you want to do that now then read ahead to the WRITE CHECKPOINT TO option on the FILE menu section 4 1 4 below to direct the save operation to a folder of your choice we have provided an empty folder called SAVE_DATA you might want to use for this purpose As the mycelium grows you will see that some numerical data appear in a STATUS REPORT LINE on the bottom left of the window frame These data show you the elapsed time in the simulation the number of hyphal tips that have been created the total length of hyphae grown and the current value of the hyphal growth unit Note that the time displayed here is program time the number of iterations of the algorithm it is not standard time in seconds so the rate at which this time passes depends on the power of your computer and the amount of computation required to display the mycelium being simulated The second most important control for the beginner is the PAUSE check box immediately ben
41. t if you ve not activated gravitropism on THE DETAILS gt TROPISMS window for the appropriate hyphal category Standard Leading and or Secondary then nothing can happen If you just want to give the animation robot a try we suggest you use the lt CONUS gt sample parameter set This has a 45 gravitropic angle setting in its parameters and usually produces a conical fan of hyphae You can manipulate the gravitropic angle setting with the scroll bar and change the cone into well anything you like really When you want to repeat the manipulations you just check the check box labelled ROBOT and you will be presented with a file management dialogue to choose the folder and filename of the robot file containing your manipulations Once you ve loaded this file and resumed the visualisation all of your manipulations will be repeated for you on a timescale of program time units BUT THERE S MORE Remember that as the replay is proceeding you can pause the visualisation at any time in order to slice it re scale it rotate it and or save it So if you ve produced a structure of particular interest you can generate all sorts of illustrations of its development And you can always re run it again if you later think of something you should have examined at a different scale or from a different angle BUT THERE S EVEN MORE If you have produced a structure of particular interest you will really want a visual record of the parameter cha
42. to rotate the tropic sensor around the hyphal axis 3 2 7 TERTIARY LONG RANGE AUTOTROPISM which attenuates as rapidly as the negative autotropism but can be given a large impact so the user has the opportunity to set its impact and to rotate the tropic sensor around the hyphal axis 3 2 8 PARALLEL CURRENT PARALLEL TROPISM which is a galvanotropism based on an electric field being produced by the hypha which is parallel to the hyphal long axis which can orient hyphae in parallel arrays the field is directional it corresponds with the growth direction of the hypha any other hyphal tip which responds to this field will turn to grow in the same direction 3 2 5 PARALLEL CURRENT POSITIVE NEGATIVE TROPISM which is a galvanotropism which can bring hyphae together positive or keep them apart negative on the basis of their response to the intensity of the galvanotropic field this works very similarly to long range autotropism but of course depends on an assumed electrical field rather than density of hyphae 3 2 8 GRAVITROPISM which orients hyphae relative to the vertical axis of the user s screen and can be adjusted for angle of response 0 90 positive and negative sensitivity range 0 to 1 rotation of the gravitropic sensor around the hyphal axis and implementation of a root distance dependent gravitropic angle turn Root distance is the distance from the hyphal tip to the initial point from which mycelial de
43. trates currently present in the model simulation Substrates in this list can be selected with your mouse for modifying and removing Substrates can be modified at any time during simulations The substrate information is stored in mycelia xml files together with other mycelial data 4 4 4 OPTIONS opens the model parameter panel explained in detail in section 3 above 4 4 4 1 The PARAMETER PANEL sets the model parameters The model supports three hyphal types STANDARD LEADING and SECONDARY Each group has its separate independent parameter set In the top right corner it is possible to choose the current parameter group The last tab in this group SUMMARY displays a short non redundant summary of the complete model parameter set It is used for documenting the work 4 4 4 2 The model parameters for each hyphal type are also classified into categories TROPISMS GROWTH AND BRANCHING NEIGHBOURHOOD AGE LENGTH LIMITS DESTRUCTOR and COMMENTS Page 16 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved 4 4 4 3 The button MAKE THIS PAGE IDENTICAL makes the currently visible parameter setting valid for all hyphal types 4 4 4 4 The button ALL IDENTICAL overrides all settings for other hyphal types with settings for the currently selected hyphal type 4 4 4 5 At the bottom of the panel there are buttons for loading LOAD PARAMETERS and storing SAVE PARA
44. tre you can t select where the cropping occurs As an aid to filling in these values if you add new images to the list the size of the last image added is put into those edit boxes Also you can double click on any image in the list at any time and the size of that image will be copied in to the boxes Ready to go When you ve gotten the images all in order input your frame rate in the box provided when you play the final AVI file that many images will be played per second Then press the Begin button The feedback box will be displayed and you will be asked which video format you wish to save to I won t try to talk about video formats here except for a few observations If you will be continuing to work with the video perhaps encoding it to other formats then you may want to use Uncompressed though that generates HUGE files In general time lapse stuff is not that big so your file will probably only be a few gigabytes so this is not a bad choice but it should NOT be used for the final product the data rate is so high that most computers will not be able to play the video smoothly If you are going for a final AVI product Indeo 4 5 or higher is a good choice since everyone either has it or can get the codec automatically when they start to play the video under Windows media player Possible future enhancements Cropping other than from the center Resizing images Fixing support for a few codecs that don t work f
45. velopment started the root it s effectively hyphal age but expressed in a way that the program can more easily measure Consequently this feature allows you to set an age dependent change in gravitropism So when the root distance reaches the value you set in START AT the angle of the gravitropic reaction starts changing gradually towards the value you set in TILL VALUE as the root distance increases towards the value you set in END AT If growth continues and the root distance increases further the angle of the gravitropic reaction remains equal to the final TILL VALUE setting Page 8 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved 3 2 9 HORIZONTAL PLANE TROPISM provides a way of producing colonies growing in on a substratum like agar or soil the user can set the impact determining how strongly the hyphal tips are limited to the horizontal plane and the permissible Layer thickness in standard distance units 3 3 The tab labelled GROWTH AND BRANCHING allows the regulation of these two features to be determined Remember the two are independent growth can be regulated separately AND DIFFERENTLY from branching 3 4 Under BRANCHING you can control 3 4 1 3 4 2 3 4 3 3 4 4 3 4 5 3 4 6 Whether branching is controlled by the number of neighbouring tips o click on the check box to bring this into effect when this is un
46. viewing orientation by adjusting the X and Z scroll bars to 0 You can do this by hand if you want to but the button labelled 0 at top right is the FRONT VIEW BUTTON Pressing this instantly restores X and Z to Zero The button labelled R alongside the front view button is the REPAINT BUTTON which will redraw the simulation screen at the conclusion of a manipulation this is a fail safe facility because Java sometimes fails to do this automatically The data space is always much larger than the field of view shown on your screen so you will notice the usual Windows scroll bars at the right hand and bottom edges of the window These move your VIEWING WINDOW around the available data space We ve already mentioned the STATUS REPORT LINE on the bottom left of the window frame and to the right of that yov ll notice a drop down menu box called CURRENT STRATEGY for fast setting one of the built in parameter sets At first start up the menu contains several simple ready prepared parameter sets any of which can be selected if the user wants to begin with a known model parameter set The ready made parameter sets are lt RANDOM gt random growth and random branching lt BOLETUS gt branching but not growth regulated by the number of neighbouring tips lt AMANITA gt growth regulated by negative autotropism to the density of neighbouring hyphae and branching regulated by the number of neighbouring tips not by the density field
47. y placed substrates inhibitors is maintained in the lower part of this window Any one of the list can be selected at any time and modified modifications are put into effect by pressing the CHANGE SELECTED button The button labelled REMOVE ALL SUBSTRATES will clear all settings Single items can be used by selecting with the cursor and pressing CHANGE SELECTED Any number and any combination of substrates or inhibitors can be added or Page 11 Neighbour Sensing program v 3 7 operating details as of 08 10 2010 Audrius Me kauskas amp David Moore 2011 All rights reserved removed at any time during a simulation Just PAUSE your simulation click on the PAUSE CHECKBOX and make the changes then un PAUSE click again on the PAUSE CHECKBOX to resume the simulation More information on the SUBSTRATES MANAGER is in section 4 4 3 4 THE MENU BAR The menu bar along the top of the main view screen has the following menus and submenus 4 1 FILE MENU 4 1 1 4 1 2 4 1 3 4 1 4 4 1 5 SAVE MYCELIA Store information about all model parameters the state of the current mycelium and any currently existing substrates into an XML file Choosing this option brings up a file save dialogue for you to specify the path and filename for the save operation The string mycelia will be added to your chosen filename to enable the program to identify this as a MYCELIA FILE This is a highly effective way to store simulations T
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