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E-CELL2 User`s Manual

1. path ID Name GTY conc CELLACYTOPLASM SA Substance amp 1000000 Fix 0 0 CELL CYTOPLASM SB Substance B nn CELLACYTOPLASM SC Substance C E CELLACYTOPLASM SD Substance D D CELL CYTOPLASM SE Substance E i CELL CYTOPLASM E ab Isomerase of amp D 0 8 OF CELL CYTOPLASM Ebc Dehydratase of B I 0 0 CELL CYTOPLASM Ecd Isomerase of C C 0 0 CELL CYTOPLASM Ede Isomerase of D Eg 0 0 CELL CYTOPLASM C Ehc D Complex of E hc and D Figure 13 Substance Section QTY Section Qty defines the initial molecular amount of the substance in the user defined volume Qty cannot coexist with Conc displays a Warning message and adopts the Qty value If neither values are inputted Qty will start as 0 It is also possible to fix the Qty value at a certain amount refer to the later sections Wooo Name GITN ema c substance e 06 means 1 10 Fix SA is fixed oB substance B aL substance C aL substance D SE substance E E ah isomerase nf amp E hc Dehydratase of B Accumulator E cd Isamerase of C E de Isamerase nf Di C Ebc D Complex af E hc and O Figure 14 Substance Section Conc row For Conc define the concentration values in M mol I While converting er files to eri these values will be used for the init act of Reactor defined in the Volume part of the System section with the Avogadro s constant 6 022136 7e23 to be converted to molecular amount Conc cannot coexist with Qty Qty value w
2. Figure 7 ReactorWindow Normal Display Detailed Display Mode Switch Button S witches display to detailed display Detailed Display Mode on Reactor E ab U Figure 8 ReactorWindow Detailed Display Normal Display Mode Switch Button Switches display to normal display Reactant Display Area Displays a list of the parameters on the right and a list of the substrates products catalysts and effectors on the bottom from the left 3 7 PreferenceWindow mm 1 E i Preferences Figure 9 PreferenceWindow Step Interval Changes the interval of a computation step Window Update Interval Changes the interval of Tracer updating 4 E CELL2 Script Files 4 What are Script Files Script files are files for batch processing the startup and shutdown of the E CELL2 System the control of simulation such as the recording of its results and the control of its interfaces that display results Script files are text files and can therefore be created using normal text editors 4 2 Script File Syntax Script files are loaded one line at a time from the top In script files one command is described per line except for the NewInterface command The insertion of a new line in a single command is not allowed To declare a command inside a Newlnterface such as AddTrace please describe it directly under the NewInterface command that it belongs to inserting a space or a tab at the beginning of each line The text b
3. E Cett2 User s Manual Chapter 1 Setup Instructions 1 Introduction E CELL is a cell simulation software designed for Linux developed at the Tomita Laboratory of Keio University E CELL2 was designed to emulate every aspect of E CELL1 in multiple platforms MS Windows Solaris Linux This is an opensource project as of now MS Windows 2000 NT 98 XP version is under development The simulation environment of E CELL2 is a mixture of softwares including the following e Active Perl Perl Interpreter from ActiveState Required to create Rules and Reactors for E CELL2 26 Modeling tools included in the E CELL2 package require this software e Borland C t Compiler Free C C compiler from Borland Required to create Reactors for E CELL2 26 This is not required for running E CELL2 and performing simulations e J ava TM 2 Runtime Environment 1 3 Required to use the GUI environment and to run E CELL2 26 User are not required to install the software if RE 1 3 is already installed in their computer Advanced Users install J DK 1 3 or higher to customize the E CELL2 system 2 Quick Install CD ROM version Performing Quick Install installs the above mentioned third party software with the E CELL2 26 software and tools Since explanation here is aimed at the direction installed from CD those who downloaded the installer of E CELL2 26 need to refer to quick installation and custom installation of Section 4 or 5
4. In the MessageWindow messages from E CELL2 will be displayed To close this window please press the Close button If the Clear button is pressed the messages displayed in the window will be cleared EXISTE Figure 32 Version Information window Version Information can be selected from the Help menu in the Control Panel The version information for E CELL2 will be displayed here E Toy model Microsoft Internet Explorer Fie Edit view Favorites Tools Help Toy model sample sample Toy model that includes a simple feedback regulation mechanism as illustrated m the figure be To Toy Pathway Cytoplasm Five Substrates tour Enzymes and one Complex constitute the model Substrates are interconnected v reaction equations In this model there are tive Reactors A Reactor mdicates a chemical reaction equatic the Iichaelis IMenten scheme In the case of a cultured cell these reactions would exist inside a Cell surt called Environment A Membrane compartmentalizes the external world and the cell interior which is fille close Figure 33 Model Information Model Information of the Toy Model E Done Also if Model Information is selected from the Help menu in the Control Panel a description of the models will be displayed on a browser At the end of this section the methods for saving simulation states will be explained To save the progress of simulation please press the Stop butt
5. Let us now start with the installation procedures E E CELL Installer Inl x Select install type Quick install Recommended Automatically installs the following products E Cell Verz zb JZRE1 3 1 05 Active Perl 5 5 1 Borland C 5 5 1 Total disk space 188 MB Custom install selects the features to be installed Read Manual four Us type i amp WindowshT 2000 8F or later The name of the directory to install must contain only printable US ASCII characters The use of Spaces or non US ASCII characters e g Japanese characters is not allowed Figure 1 E CELL2 26 Installer Select Quick install Recommended fh oc Pu OB etup E CGELL2 26 License Agreement Please read the following important information before continuing Please read the following License Agreement Use the scroll bar or press the Fare D own key to wew the rest ofthe agreement Borland G Compiler 5 5 IMPRISE MO MOMSEMSE LICENSE STATEMENT AMD LIMITED WARRANTY IMPORTANT READ CAREFULLY This license statement and limited warranty constitutes 4 legal agreement License Agreement Jbetween you feither as an individual or a single entity and uus Sot ger sen ie re m UU a Tra 4k Fhin BITE S rami TN Rave IBI E idum r i d Do wou accept all the terms af the preceding License Agreement Ifyou choose Mo Setup will close To install E CELL2 25 you must accept this
6. 4 will start by executing this script Using this script simulation would stop after 500 seconds WM GBP Fae N NW WeoaAsP W 13DPG W NAD fas E Cell Control Panel File Hew Interface Windows Help Rule Erythrocyte v236 er Script default ecs Elapsed Times 40 09999 Start Stop Step 0 661 666 0 283333 Figure 5 Simulation of the erythrocyte model To terminate E CELL2 before the script stops the simulation please press the Stop button in the Control Panel and then select Quit from the File menu In the next section the operating procedure for E CELL2 will be briefly explained After understanding the basic operation procedure please reload E CELL2 and experiment with it 3 Creating Rules for E CELL2 Before going into the details a simple simulation model will be introduced The figure below illustrates the so called Toy model which includes a simple feedback system c2 Toy Pathway Cytoplasm Figure 6 Toy model 5 S ubstrates 4 E nzymes and 1 C omplex constitute the model The Substrates are interconnected via 4 Reactors chemical reaction equations Reactors embody chemical reaction equations such as those based on the Michaelis Menten scheme In the case of a cultured cell these reactions would exist inside a Cell surrounded by culture medium called Environment A Membrane compartmentalizes the external world and the cell interior which is filled with C ytoplasm The
7. The process will terminate with a warning message if the target file do not exist If the filename is omitted all rd files under the target path will be converted e File menu The following can be performed 1 Select the target file Choose A file selection dialog will open and users are to select the target file to open The selected file will be displayed in the input field 2 Edit existing files Edit A file selection dialog will open and users are to select the target file to edit The selected file will be displayed in the input field 3 Create new file New This will create new spreadsheet files to be edited The selected file will be displayed in the input field 4 2 Process Scheme 4 2 1 Designating the rd files for input Designate the input rd file via its path A warning message will be displayed during the conversion process if non existing files are selected The RD directory under the Model directory designated under the Preference window will be chosen if the path information is not included in the input If a directory name is selected all rd files under that directory will be converted If no input the RD directory under the Model directory in the Preference window will be the target If Translate Immediately after editing rd file is checked in the Preference window Reactor file conversion process will start immediately after closing the editor window 4 2 2 Batch Process Conversion Pr
8. and do not contain any spaces Keywords begin with or 96 The contents of lines beginning with are directly read The contents of lines beginning with are delimited by and processed as arrays Lines beginning with are treated as comments To directly output the in the beginning of a line please type or place a space before However the Z other than those located in the beginning of a line are directly outputted Lines that do not include keywords at the beginning are interpreted as a continuation of the previous lines To start a new line when converting to Spec Sheets please place a XY where the new line should start Keywords may be omitted if they are not necessary An example RD file is shown below 1 This is the file for the MichaelisUniUniReactor This Reactor is based on the following rate reaction KcF E S y Kms 5 The file for the MichaelisUniUniReactor LASSNAME M chael i sUni Uni React or ASEAASS FI uxReactor UHR E CECLL Tutorial CGM L tutori al cel l org ATE 2000 12 12 WERSI CN ecs v1 0 1 BRI EF DESCRI PTI CN Uni reactor enzyne acti vi ty of whi ch ki netics can be descri bed by the Henr DESCRI PTI ON A reactor class for uni reactant enzyne acti vi ty where ki netics can be descri bec by the Henri M chael i s Menten equati on deri ved f romrapi d equi i bri umassunpt ons vspace 0 2cn This reactor is applicable to the follow
9. the required 4 sections with their lemmatizing lines will be described step by step by actually creating a rule file Note here that using the following in the columns are prohibited for these are used to separate the items in the spreadsheet program e tab e Quotation e double quotation Including these may cause an adverse effect to the eri converting process 2 1 Lemmatizing Words Lemmatizing words are required for starting a new section The columns with these lemmatizing words are called the Lemmatizing Columns where they must be included before starting a new section The blue columns in Figure 1 are the lemmatizing columns where the items are case order insensitive Users can add a memo item to write down comments which will not be included in the eri conversion process System oy Stern oy Stern oy Stern Substance Substance Substance Substance Substance Substance Substance Substance Substance Substance Reactor Reactor Reactor Reactor Reactor Reactor Reactor Include Cell CELL The cell ENVIRONMENT The culture medium The cytoplasm The membrane Substance 4 substance B substance C substance D substance E Isomerase of Denydratase of B Isomerase of C Isomerase of D Complex af E hc and O volume index for enviroanm Volume index for cytoplasr Isomerization of Dehydration of B Isomerization af C Isomerization of D Environment i Cytoplasm CELL CYTOPLA
10. CELL CYTOPLA MEMBRANE The menbrane Sh SENVIRCAMMENT Figure 7 System Section Inside row Outside row inside outside rows are used in defining Systems inside or outside of the membrane if the defined Class is Membrane Although current E CELL2 System cannot process these information it will be dealt with in further versions by limiting the accessibility for each System Figure 7 is an example of this a System of MEMBRANE framed by CYTOPLASM and ENVIRONMENT Inside Outside Memo m efinition af CellCampanent OLUME p of CellComponent fCELL CYTOPLASM ENVIRONMENT PCELLICYTOPLASMVOLUME Defitton of CellComponent Figure 8 System Section Volumelndex row In the E CELL2 System the System volumes are defined as Reactors When destinating FQEN of the Reactor as System s Volumelndex the activity value of the Reactor will be used as the volume of the System in Liters When destinating Volumelndex of the System the Reactor FQEN in correspondence must also be defined in the Reactor part Although System may or may not have a volume Membrane in the above example do not have a volume their volume and the Volumelndex is required in cases where Reactors use the substance concentrations for calculations or the Substance section uses Conc as the substance value to recalculate the molecular amount 2 3 Substance Section Substance Section in the rule file is used to define all of the Substances I
11. Directories 1 2 1 Path settings Programs e Perl interpreter Set the path to Perl interpreter e Borland s Make Set the path to Borland s C Compiler 1 2 2 Path settings for the Model and Script files E CELL2 e Model Set the directory to create Rules and Reactors In default STANDARD under E CELL2 s installation directory is used e Conversion programs Set the directory where the conversion programs are located In default BIN TOOLS under E CELL2 s installation directory is used 2 Model wizard New Model tab Creates a new model directory ES EGELL2 Tool Launcher E m ra j ee Modelname sd Figure 3 New Model Wizard Input the name of the model to create in the input field and press Execute to copy the temporally stored data under Template directory to that directory The Model directory set at the Preference window will be changed with the execution of this process 3 Rule file wizard Rule file tab Creates an ERI file from a spreadsheet or an ER file EC E LL To al La F m her PELLI D E m ap T Ete il ne Spreadsheet file Cd le cute Figure 4 Rule File Wizard 3 1 Required Input 3 1 1 Spreadsheet file Select the spreadsheet file via its path by directly typing its location or by browsing for the target by the File button on the right If the path is omitted the Model directory set at the Preference window will be used The process will terminate with a warning message
12. Name Reactor X MichaelisUniUniReversibleReactor CELLYCYTOPLASK E ah Isomerization of amp L1 NENNEN CELL CYTOPLASM E bc 0 Dehydration of B A o l OPLASM E cd 0 Isomerization of C Oooo oo PLASM E de 0 Isomerization of D i IEG Ehc D Bonding of Ebc and D Type Reactor ConstantParameterReactor index for environ ConstantParameterReactor UME Reactor Volume index for cvtaplas CELL CYTOPLASM VOLUME Figure 20 Reactor Section path row Define the System Path for the reactions or the interactions in the Path row Similar to the paths for the Substance section it can be observed below that the Reaction occurs under CELL CYTOPLASM Note that the texts are case sensitive Class gath aD MichaelisUniUniReversibleReactor CELL CYTOPLASM E ab E SB MichaelisUniUniReversibleReactor CELL CYTOPLASM sc MichaelisUniUniReactar CELL CYTOPLASM E de SD RapidEquilibriumPReactor CELL CYTOPLASM E Ebe po SD Reactor ConstantParameterReactor ICELL CYTOPLASM Figure 21 Reactor Section ID row Name row Name rows are to define the names for the reactions or the interactions The ID will be the name for the eri file if this is left blank For Reactors with volume it is desired for that Reactor to have names that can be understood as volume related see chapter 3 for details However
13. O PRIVATE O CH PROTECTED O CH PUBLIC l O CH NCLUDE FILE C O INITIALIZE FUNC O C t O REACT FUNC O CH O OPTION FUNC O CH Figure Keywords target file format 1 will be treated as comments 2 Dependent on the Reactor dB range E CELL1 s gt stepper dad e o 9 9M B Isubstrate i coefficient ith Substrate stoichiometry substrate i concentration ith Substrate concentration in M substrate i gt quantity ith Substrate molecular amount substrate I gt substance supersystem gt volume System Volume of the ith Substrate product i gt coefficient ith Product stoichiometry product i gt concentration ith Product concentration in M product i quantity ith Product molecular amount product I substance supersystem gt volume System Volume of the ith Product catalyst i gt concentration ith Catalyst concentration in M catalyst i quantity ith Catalyst molecular amount catalyst i gt substance supersystem effector i gt concentration kh Effector Concentration in M effector i quantity ith Effector molecular amount effector i substance supersystem gt volume System Volume of the ith Effector Figure Method list 2 2 Reactor Description Example In order to create a Reactor file for the kinetic equation such as one below KcFKpl S KcRKs P E Y Ks P Kp S KsKp we shall n
14. TOPLASM Ems IPLA SM SE PLELLIL YTOPLASM E de CELLO YTOPLASM KmS IPLASM 1 CEbc D CELL CYTOPLASM IPLASM 1 ID Name VOLUME Volume index for environment VOLUME volume index for cytaplasm Figure 26 Reactor Section Arg tag row Arg coeff row In the arg tag row the constant name that the kinetic equation will use as a parameter must be defined This constant name is must exist for each Reactor in the example above the second last Reactor uses MichaelisUniUniReactor as the kinetic equation which make the arg tag KcF and KmS Refer to the spec sheet for specifications on general reactors If multiple parameters exist write them in the row under the another and no other data must be defined for that row see example Note that this section is also case sensitive For ConstantP arameterReactor For calculating the Volume of the Reactor insert Value in the Arg tag Also users are able to define any Effectors that exist in the reaction where the amount itself is not influenced by that reactor Define the Substance ID and its System location path under E ID and E Path Define the stoichiometric coefficient of the Effector in E Coeff Refer to the Reactor chapter for more information 2 5 Include Section Reactor RapidEquilibriumPReactar CELL CYTOPLASM IEG Ehc D Bonding of Ebe and D Figure 27 Include Section By including an Include Section in the rule it is possible to import other er files into the ERI conv
15. The E CELL2 System requires data files called rule files for running simulations Rule files will be explained in Chapter 4 Also to create new models new Reactors need to be constructed Reactors will be explained in detail in Chapter 5 After reading through these chapters one should be able conduct basic modeling using the E CELL2 System Please note that the guaranteed accuracy of calculation for GUI mode and batch mode is different it is 64 bits and 80 bits respectively 2 Basic Operation 2 1 Starting the E CELL2 System To start the E CELL2 System please click on the Standard shortcut in the desktop or select Start P rogram E CELL2 standard E CELL2 for the standard reactor model will start After the E CELL2 System starts the E CELL2 ControlP anel will first displayed first If a script file called default ecs is located under the E CELL2 startup directory The model directories under CX E CELL2 in a standard install the file will automatically be loaded However please note that if the LoadRule command does not exist in the script file while the Newlnterface command or the Run command does exist an error will occur and the file will be non executable The details regarding script files are explained in Section 4 of this chapter It is also possible to load settings with the file by adding options when directly starting ECELL2 BAT from the command line The options are shown below a Classn
16. The file toy txt is an incomplete spreadsheet file for the Toy model These files are located in the tutorial related standard directory It has already been explained that Systems Substances and Reactors exist in the Substance Reactor model of E CELL The leftmost column in the spreadsheet is called Type Each field will include one of the above Types Systems are used to show the structures of a cell or the localization of substances Systems usually include Environment Cell Membrane and Cytoplasm Please refer to Section 4 2 2 for details regarding Systems Please keep in mind here that embedded structures such as cells can be described by distinguishing Inside from Outside A Substance implies a broad definition of a substance The spreadsheet includes a description similar to the table shown below In the Toy model Substances are the materials undergoing chemical reactions and the enzymes catalyzing the reactions Table 2 1 Example descriptions of Substances used as materials for chemical reactions mc LLL Susans CELLCTORLASN se susce 8 fo Suse ceru crrortasn sc susce cfo Path is the location of the Substance It is described in a fashion similar to the directory path in UNIX ID is the ID of the specified Substance and is an essential item Name is the name of the specified Substance Either the Qty or the Conc for a Substance has to described Qty is the initial Quantity value of the Subst
17. agreement Mo Figure 2 E CELL2 26 Installer License Agreement for the third party software will be displayed If you agree with the license please click Yes and select the installation directory to go on with the install fs EceSetBec l oj x E CELL install path C E CELL Your 08 type C Windows35 38 C Autoexec bat WindowsNT4 0 2000 XP HKEY CURRENT USER JE E CELL L i b bec55 Bin D E CELL Lib Fer Bin D XE DLELL SL ib IREXT 3 1 5xBin Create bcc32 cfg FIC XE CELL Y ib bech5 inelude L C E CELL ibxbecbbx ib C SE CELL 2X I i bY bech5 i il ink32 cfg PLC E CELL ib bec55 ibs D XE CELL2 1 ib bech5 Figure 3 E CELL 2 26 Installer Set the path information in the HKEY CURRENT USER registry for Borland C Compiler If the information is correct click OK to proceed ot aetup E GELLZ 28 Setup has finished installing E CELL 2 25 on your computer The application may be launched by selecting the installed icons Click Finish ta exit Setup Figure 4 E CELL2 26 Installer Click Finish ae x 2 Setup completed ET Please reboot after all the installations are campleted Do vau wish to reboot OK Cancel Figure 5 Restart Windows Please restart Windows to reflect the settings This is the end of the installation procedure For basic operations pleas
18. and Effector its naxi num anoeunt mini numanount and their conments separated by conmas The nax nhn anounts can be defined in deci nal integers but it is also possi bl e to set the naxinumas Inf for infinite Conments can be used as a secti on to descri be speci al Substances As of now the i nfornati on here wll only be reflected to the Spec Sheet Ex SUBSTANCE Substrate 1 10 neans that the anount of the substrate is between 1 and 10 NOIES line is to defi ne any coments that need to be noted Reactor Source Code Keywords e PARAMETER e ANCLUDE FILE H GPRIVATE PROTECTED PUBLIC e NCLUDE FILE C e INITIALIZE FUNC e REACT FUNC OPTION C YPARAMETER i ne is to defi ne the paraneters that becone the argunent for that Reactor in paraneter nane type unit conment fornat separated by conmas Input Int or Float as paraneter type accordi ng to the val ue wich are NJ i denti cal to the i nt s and float s used for CH Int s in E CELL2 Wndovs versi on are 32bit integers and Fl oat s are 80bit firm deci nal s but because of JN J ava Native Interface the accuracy is 64 bit in the GJ versi on and 80bi t i n the batch versi on 9 NCLUDE FI LE Hline is to define the h filename to be included in the reactor Do not embrace file names with or R VATE line is to define pri vate i tens used PROTECTED line is to define restricted items used P UBLIC line is to define the
19. creating eri files Deleted if not checked Translate immediately after editing spread sheet file If checked eri creation process will start immediately after the spreadsheet file is created Translate immediately after editing er file If checked eri creation process will start immediately after the er file is created e Translate immediately after editing rd file If checked Reactor source files and DLLs will be created immediately after rd files are created While er files are the RULE files of E CELL2 written in text format eri files are in E CELL2 executable format Details can be found in Chapter 4 of the user s manual Creating Rules section rd files are the Reactor files of E CELL2 Details can be found in Chapter 5 of the user s manual Creating Reactors section 1 1 2 Other settings e Select the Reactor source file extension from CPP or C In default use CPP in Windows 1 2 Directory Settings Directories Sets the paths to the programs and scripts and the directories for saving the files A warning message will be displayed if the target directory do not exist If left blank the directory of this launcher program will be used Directories rograms Perl interpreter C E CELL2ILibYP erhBin Borland s C Compiler CXE CELLALINBCCaSIBin Choose Model home ICAE CELLZistandard Choose Conversion programs IC E CELL Bin TOOLS Choose Figure 2 Preference
20. if the target file do not exist e File menu The following can be performed 1 Select the target file Choose A file selection dialog will open and users are to select the target file to open The selected file will be displayed in the input field 2 Edit existing files Edit A file selection dialog will open and users are to select the target file to edit The selected file will be displayed in the input field 3 Create new file New This will create new spreadsheet files to be edited The selected file will be displayed in the input field 3 12 er file ER file Select the er file via its path by directly typing its location or by browsing for the target by the File button on the right If the path is omitted the Model directory set at the Preference window will be used e f the spread sheet is selected Spreadsheet eer gt eri conversion will be performed er files do not need to be selected If blank the output files in spreadsheet filename er will be created under the Model directory set at the Preference window A warning message will be displayed on overwriting existing files If the spreadsheet is not selected er gt eri conversion will be performed er files need to be selected Conversion process will terminate with a warning message on assigning files or directories that do not exist e File menu The following can be performed 1 Select the target file Choose A fi
21. in the reaction please click the ShowList button on the top left A new display area will then be added to the bottom Starting from the left the list of substrates products enzymes and effectors will be displayed 2 Saving Simulation Results To save the simulation results displayed in Tracers please click the Save button on the bottom left corner of the TracerWindow A directory called Data will be created under the directory that the E CELL2 System has been executed In addition subdirectories will be created according to the structure of the System Also data files in ecd format will be created for each Substance or Reactor A data file in ecd format is usually composed of a header more than 5 dashes lined up that represent the end of the header the data body and 3 slashes that represent the end of the file What has been improved compared to E CELL1 is that the time instantaneous quantity average quantity maximum quantity minimum quantity instantaneous concentration average concentration maximum concentration and minimum concentration can now be outputted in E CELL2 Header of an ecd file key word value DATA name of data number of columns and rows legend of each column NoE loptional comments Example of an ecd file for E CELL2 DATA CELL CYTOPLASM E ab 0 Quanti t y DATA CELL CYTCPLASM P Quant i t y sS 5 102 LABEL ti ne current quanti ty nean quantity nax quanti ty m
22. newly implemented for E CELL2 will also be introduced here Logger is a mechanism that continuously records the states of a cell It is more advanced than saving the cell states in a snapshot manner It can be used by adding the following descriptions to the script file New nterface Logger test l og AddTr ace AddTr ace AddTr ace AddTr ace AddTrace AddTr ace AddTr ace AddTr ace AddTr ace Subst ance CELL CYTCPLASM SA Subst ance CELL CYTCPLASM SB Subst ance CELL CYTCPLASM SC Subst ance CELL CYTCPLASM SD Subst ance CELL CYTCPLASM E bc Subst ance CELL CYTCPLASM C Ebc D React or CELL CYTCPLASM E ab O React or CELL CYTCPLASM E bc O React or CELL CYTOPLASM E cd 0 Please add the descriptions regarding the Logger after the 9th line in the ecs file that was first created and load it to E CELL2 Loggers have the following features 1 A directory called Logger will be created under the current directory Here the files for each Substance and Reactor will be recorded in a format similar to the one created when using the SaveAt function of Tracers 2 Because Loggers continuously record data throughout simulation execution the recorded data will remain regardless of crashes in the E CELL2 system 3 Because Loggers do not use virtual memory they record data faster than Tracers After simulation stops please try opening the ecd file located under the Logger directory using
23. of E CELL2 are written in J ava In E CELL2 there is a GUI mode that allows for interactive operation and a batch mode that supports command line execution This chapter provides explanations for only the former mode GUI mode Please refer to Chapter 3 Section 2 9 Batch mode and Logger for explanations on the latter mode batch mode Please note that the accuracy of the GUI mode and that of the batch mode is 64 bits and 80 bits respectively The inferior accuracy of the GUI mode is due to the limitations in numerical computation that exist in the J ava Native Interface NI 2 Demonstration of E CELL2 26 E CELL2 will be operated here using an actual model In this section a metabolic model of the Human erythrocyte will be simulated using E CELL2 Why is an erythrocyte suitable as a target of simulation The answers to this question are as follows e Mature erythrocyte cells do not undergo transcription translation or replication and are therefore simple e Because erythrocyte cells are relatively easy to handle as experimental materials there is a large accumulation of biochemical experimental data available The main metabolic pathways of an erythrocyte consist of glycolysis pentose phosphate cycle and nucleotide synthesis In addition large amounts of oxygen carrying hemoglobin exist in an erythrocyte An erythrocyte cell can therefore be likened to a bag full of hemoglobin that has self regulating functions based on t
24. speed in order to define the substance amount postern reactors do not consider the substance flux and handle all of the substance involved Thus while regular reactors use the velocity Float v method in performing calculations postern Reactors use the SetQuantity Float Q method in returning calculation results Postern reactors have PReactor on the end of their name ex ABCPReactor Each postern reactor must and can only handle a single substance where the substance cannot be defined more than once If so the simulation accuracy cannot be guaranteed If multiple reactions effect a single substance each reactions must be inside a singular postern reactor such as the GeneralRapid EquilibriumP Reactor 2 Reactor Description File Though several General Reactors for simulation is already included in the E CELL2 System Package refer to section 5 in order to create non standard reactions or to perform higher leveled simulations it is required for the user to create their own Reactor files 2 1 Creating a Reactor Description File RD files can be created by including the keyword value pair lines Note for the following while creating RD files e Keywords must be Alphabets uppercase only or underbars without spaces e Keywords must start with or While lines that start with will simply be included into the target the lines starting with will be treated as hash separated by dots Keywords that start with wil
25. warning CELLIMEMBRANE no volume index is specified arning CELL no volume index Is specified arning ICELL MEMBRAME na volume index is specified warning CELEMEMBRAME na volume index is specified ENVIRONMENT volume index is PEMVIROMMENT VOLUME Ichecking cell configuration Reactor initialization succeeded condition Good Figure 20 Messages during Rule Intermediate File loading Next please prepare for displaying the quantity of Substances as graphs If New Interface Tracer is selected a Tracer will be displayed a eum Tracer Figure 21 Tracer window Please press the Add button in the lower left corner of the Tracer to display an Entry Selector window Please click on the left panel and select a Substance that is located in the C ytoplasm E Entr y Selecto 5 E Figure 22 Entry Selector window 1 Please click on the Substance radio button to display the Substances on the right panel Reactors can be similarly displayed The method for choosing two or more Substances or Reactors will now be explained To select several entries please click on the left mouse button while pressing the Shift key After selection please press the OK button Simulation can now be started by pressing Start in the Control Panel Up to 8 Substances or Reactors can be displayed on a single Tracer mar Lc E
26. B iBiReactor RandomUniB iReactor RandomBiUniReactor RandomBiB iReactor RapidEquilibriumR eactor IsoUniUniReactor CatalyzedMassA ctionReactor DecayReactor zero order reaction lst order reaction follow MichaelisMenten follow MichaelisMenten rapid equilibrium Constant D 2 202 20 D D 2 D D WD I JI GeneralRapidEquilibriumP Reactor RapidEquilibriumP Reactor Figure Standard Reactor e Standard Reactor Specifications Adobe Portable Document Format PDF Acrobat Reactor is required to view a pdf file Chapter 6 Modeling Launcher 1 Initial Settings Preference 1 1 Options Tab Options 1 1 1 Behavior settings zr Preference it Ful a a la L Latter pO LI a LEE Lee HIT J Lad a j quil a r E 4 A Fr s meten aeu ME a yo eT I TRE x ee re J petes iT wee BETS a Baa Ar Of Tl EF Bd TIN a I ou AT i E iit EL LE L i P i 4 Lr IE ey een ule dci ri c 2 Uu RR A yi bz a v a a CX dl PU a D Tw Dn PALS DAI xt pee get men e ga re ete Lr gt e ll a T Sent ie e E i Se Le Ea aa a a mem rn z z en Other options vie quud vice rote oes ne eon eee nena tta 8 figs b lactate ee LL EM Output source extension CPP v Figure 1 Preference Options S ave spread sheet files If checked spreadsheet files will be saved when creating er files Deleted if not checked e Save er files If checked er files will be saved when
27. CR MyMichael isUniUniReactor cpp 2 Borland C 6 5 1 far Wind Copyright fc 1333 2000 Borland srcr amp mvmichaelisuniunireactar cpp ilink32 Ted c x L BIM WIM BCC c d32 obj Michael isUniUniReactor ob MyM i cha Turba Incremental Link 5 00 Copyright fc 1997 2000 Borland Return value I lt lt finished Completed F igure 12 Messages during compilation After the compilation process has finished MyMichaelisMentenUniUniReactor will actually be used Please open toy txt using the modeling launcher Please replace MichaelisMentenUniUniReactor with MyMichaelisMentenUniUniReactor then save the file and press the Execute button O E CELL2 standard toy txt Spreadsheet path ID Substance CELL DYT E bc Dehydrata jSubstance CELLZBYT IE ed Isomerase jsubst ance os Isomerase jsubst ance ils Complex o Type Class Name IReactor Mi ichaelisllnillniReversibleReactor VEELL ENT E ab ll Isomeriza S 1l Michael isUniUniReversibleReactor MCELL CYT E be 0 Dehydrati pod Dc et hte mim 13 Rule File editing Please start E CELL2 then load toy eri by selecting Load Rule from the File menu and begin simulation If the behavior is the same as that of sample eri the Reactor has been successfully created Please continue working on Reactors so that in the future you will be able to design and create n
28. OPLASM The cytoplasm MEMBRANE The menbrane Figure 3 the System Section Type Class Input System in the Type row and the destination of the system and class in the Class row Cell Environment C ytoplasm and Membrane can be defined as Class in this row While these Classes are able to handle Substance Reactor and Volume inside itself Environment and Membrane cannot create a System under itself Each Class is able to hold the following items Class Substance Reactor Volume J9tem under itself C ell O O O O Environment O O O X Cytoplasm O O O O Membrane O O O X Figure 4 Classes and their types Syston Cell Ur system Cell TELL The cell E System Environment ENVIRONMENT The culture medium System Cytoplasm CELL CWTOPLASM The cytoplasm oy stem Membrane CELL MEMBRANE The menbrane Figure 5 Systems Section path row The path row defines the destination of the System created acting as an address Paths start with a RootSystem the uppermost directory of the E CELL2 System and continue with user defined directories Paths
29. S Path Substrate Path System Path S Coeff Substrate Stoichiometric Coefficient 1 P ID Product ID required P Path Product Path System Path P Coeff Product Stoichiometric Coefficient 1 C ID Catalyst ID required C Path Catalyst Path System Path arg tag Constant name for Reactor use required for certain reactions arg coeff Reactor value of the constant required for arg tag reactions E ID Effector ID required unless specified E Path Effector Path system P ath E Coeff Effector Coefficient 1 Figure 18 Reactor Section Specifications path IL Mame CELL CYTOPLASM E ah n Isomerization of amp sibleReactor CELL CYTOPLASM E bc 0 Dehydration CELL CYTOPLASM E cd 0 isomerization of C ECELLICYTOPLASM E de 0 Isomerization of D fCELLYCYTOPLASM EG Ehc D Bonding of Ebe and Do path ID Mame ENVIRONMENT VOLUME Volume index far environ CELL CYTOPLASM VOLUME Volume index far cytoplas Figure 19 Reactor Section T ype row Class row Reactor Types Class Kinetic Equations are defined in the class row In the row the Reactors must be written as Reactor name format The Example below describes the MichaelisMenten related equations and thus are written as Michaelis Reactor each defining Reactor items with Volume Please refer the spec sheet for other predefined Reactors Define the ID for the reaction or the interrelations Note that the items must be written case sensitive Type Class ID
30. SM Membrane CELL MEMBRANE MLELLICYTORPLASM FLELLYCYTOPLASM SB CELL CYTOPLASM 5C CELL CYTOPLASM SD CELL CYTOPLASM SE FLELLICYTOPLASM E ab FLELLICYTOPLASM E hc FLELLICYTOPLASM E cd FLCELLICYTOPL amp ASM E de CELL CYTOPLASM C EBc D ConstantP arameterReactor ENVIROMNNERNT VOLUME ConstantP arameterReactor CELL CYTOPLASM VOLUME MichaelsU niUniReversibleReactor CELLYCYTOPLASM E ab U MichaelisunilniReversibleReactor CELLYCYTOPLASM E bc U MichaelisUnilnifeversibleReactor CELL CYTOPLASM E cd O MichaelisunilniReactor FOELLICYTOPLASM E de O RapidEquilibriumPReactar CELL CYTOPLASM EG Ebc D Bonding af Ebc and D simple er Figure 1 Lemmatizing columns 2 2 System Section The System Section sets the simulation system architecture and the environment which are required to perform a simulation the destination and the volume of the simulation target System Below are the descriptions Names Definition Type System Class Type of the simulation for Path ID ID of the Default if left blank required required required required Name Name of the ID inside Define inner space In required Systems with membranes Define outer space In required Systems with PUEDE membranes j Designate required for Systems with Volumeindex Weine Figure 2 System Section ID Name CELL The cell ENVIRONMENT The culture medium CYT
31. Trace FQPN Chapter 4 Creating Rule Files 1 Introduction Rule files are data files used to define the models to simulate in E CELL2 In this file enzymatic and substance related data are included with their inner relations reactions network and environment settings such as the cell volume Users can also edit Reactor files to define the kinetic equation of the reaction Details in Chapter 5 and define the necessary substance and parameters in that Reactor inside the Rule file There are three types of Rule files e SS file e er file e eri file Rule files can be written in spreadsheet format ss or directly as text er While writing rules as ss files under general spreadsheet programs or the model launcher are visually and simplicity Wise advantageous er files can easily be batch manipulated under script programs and macros In any case they will eventually be converted to eri files where ss files must first be converted to er files before eri Rules files are divided into 4 sections the System section define the model environment for simulation the Substance section define substance name and value the Reactor section define reactions and inner relation networks and the Include section to import other er files These sections are not required to be in a single file or in this order This chapter describes the methods in creating rule files in spreadsheet format 2 Editing spreadsheet files ss In this section
32. Trace FQPN SaveAt seconds directory e SubstanceWindow Command Contents Is declared only within the SubstanceWindow Displays the Substance in the argument in the SubstanceWindow The argument needs to not only include the Substance ID but also the System that it belongs to and uses FQEN Substance FQEN e ReactorWindow Command Contents Is declared only within the ReactorWindow Displays the Reactor designated in the argument in the ReactorWindow Similar to the Reactor FQEN Substance command the argument has to not only include the Reactor ID but also the System that it belongs to and uses FQEN e Logger Command Contents Records the time series data of the Substance or Reactor written in the argument The argument has to include not only the ID but also the System and Type that it belongs to and uses FQPN A directory called Logger is created under the model directory that E CELL2 has been executed Files for each S ubstance or Reactor will be recorded under the Logger directory in a format similar to the one created using the SaveAt function of Tracers Because file recording is done continuously during execution records will remain even if E CELL2 happens to crash In this file information on the time instantaneous quantity average quantity maximum quantity minimum quantity instantaneous concentration average concentration maximum concentration and minimum concentration is listed Add
33. X em Tracer Reactor Activities Sinn n Figure 23 Example of a simulation using E CELL2 Based on the rules the quantity of Substances or the activity of Reactors will be displayed in the Tracer The simulation results displayed in the Tracer can be saved by pressing the Save button in the Tracer Please refer to Section 3 2 7 for details The quantity of Substances can be changed manually to observe how the whole system is affected by such changes Please select Substance Window from the New Interface menu E Entr y Selecto 7 RE aba E Er o os P CR zx zr Figure 24 Entry Selector window for SubstanceWindow Because this Entry Selector is only for Substances Reactors cannot be selected If a Substance Is selected and then the Ok button is pressed a window displaying the individual details of the selected Substance will appear Substance CELL CYTOPLASMSB Figure 25 SubstanceWindow The quantity of the designated Substance can be forced to increase or decrease by pressing the and buttons respectively or by inputting a value in the Quantity or Concentration text field If the Fix check button is checked the quantity of the Substance can be made to ignore the computation results and maintain at a constant value To terminate operation of the SubstanceWindow
34. Y Description of a mathematical expression gt o SUBSTANCE The definition of Substance Can either be Substrate Product Catalyst or Effector o NOTES Notes regarding the implementation of this Reactor 4 Reactor Source Code related keywords o PARAMETER The parameter name parameter type unit and descriptions regarding the parameter are written delimited by o PRIVATE The private members of this object Member variables should be defined as private members o PROTECTED The protected members of this object Can be referred from derived classes o PUBLIC The public members of this object o INITIALIZE FUNC Executes the initial settings Includes range check of parameters and calculation of values that are constant throughout the simulation o REACT FUNC Specifies the processes executed in every simulation step The following two step process is described 1 Calculation of the rate 2 Increase or decrease in the quantity of substances based on the rate The argument for the Process method is the number of reacted molecules per second and is a Float type Reactors have been briefly explained in this section Please refer to Chapter 5 for details regarding Reactors 4 2 Creating Reactors A simple example will be given to explain how to create Reactors Please start the modeling launcher and then click on the Reactor tab Please click on the File button in the RD file column then select Edit and open the
35. Z BIN TOOLS ergzeriv exe 09 37 27 Input sample er inc qty 9 37 z27 Output sample eri 08 37 27 gt gt Executing command C E CELL2Z BIN TOOLS erzeriw exe sample er inc qty gt sal 09 37 27 Return value O 09 37 27 lt lt finished 09 37 27 Deleted sample er inc qty 09 37 27 Completed Figure 10 Message Viewer 8 Other Settings 8 1 Current Version Displays the version of this launcher E CELL 2 C Tool Launcher 1993 2003 KEIO University Mitsui Knowledge Industry Co Ltd and JST Version 1 1 Date 2003 03 25 22 12 15 This is free software without amy warranty licensed under GPL For detail please see http bioinformatics org project group id 49 Figure 11 Version Information E CELL2 User s Manual Last Update Date 2003 3 25 V 7 Copyright Keio University and Mitsui Knowledge Industry Co Ltd 2000 2003
36. Z Tool Launcher Execute Figure 28 Modeling Launcher After selecting the input file from the file window eri file will be created from pressing the Execute button In the GUI version By selecting Load Rule from the File menu loads up the file for input Refer to chapter 3 on loading E CELL2 Chapter 5 Creating User Defined Reactor Files 1 Introduction In the E CELL2 System cellular models can be created with the combination of three object types Substance to describe substance amount Reactor describe the reaction and the reactor system path and System to describe certain functions Reactor describes the time change of the Substance amount which plays an essential role under an E CELL2 model Reactor objects can be freely manipulated by the user Reactor objects must be compiled in separate with the E CELL2 System and therefore must be converted to a format that E CELL2 can read if correctly written the E CELL2 System loads up the defined Reactor For Reactor objects are written in C users can create almost any kind of a kinetic model Spread Sheet Reactor Descrpton s xb SSZEY rch rd te x Eule File 22 Reactor Source Godet bi Reactor spec Sheet tex erre ri eam pile Intermediate oder ri Reactor shared Object idi Figure The scheme of files used in E CELL2 System The graph above describes the files used in E CELL2 System As it can be seen Reactors are created and compiled in separat
37. ZE FUNC Ksp Ks Kp In the G EACT FUNC i ne vari abl e S nust be decl ared to descri be Substrate concentrati on Thus GEACT FUNC Fl oat S Substrate 0 2ceoncent rati on P and E must identically be declared 3 Conversion to Reactor Source Code C h file and DLL To create Reactor source and executable DLL modules for E CELL2 system first press the Reactor tab of the ModelingLauncher By selecting the rd for input and pressing the Execute button the launcher will automatically create the source code and DLL files by compiling Refer to the ModelingLauncher tutorial in Chapter 6 for more details EGELL2 Tool Launcher Figure Modeling Launcher 4 Load the E CELL2 System In order for E CELL2 to be executed the following precautions must be noted The Reactor dll files defined in the Rule must be placed under the Reactor Directory As default DLLR and DLLRB are set in ECELL2 BAT and ECELL2BB BAT Normally the created reactor dlls will be placed in these directories E CELL2 will terminate with an error message if the designated Reactor itself or the path do not exist 5 General Reactors from the E CELL2 Project Reactor Classname Reversible Irreversible Reaction ZeroReactor MassActionReactor MichaelisUniUniReactor MichaelisUniUniReversibleReactor RapidEquilibriumR eactor ConstantP arameterR eactor OrderedUniB iReactor OrderedBiUniReactor OrderedB iB iReactor PingP ongBiReactor PingP ong
38. ally be loaded at the time of startup Please note that if an error occurs during the loading process there is a possibility that E CELL2 will abnormally shut down Script ecs files are files for controlling and automating simulation and interfaces Script ecs files need not be loaded To load a Script file please select Load Script from the File menu in the ControlP anel and then select the appropriate Script ecs file from the newly displayed FileSelector window Please refer to the startup option c 2 4 Executing Simulations If the Start button in the ControlP anel is clicked after loading a rule file the time progress within the simulation system will be displayed in the time counter To stop simulation please press the Stop button Also if the Step button next to the Stop button is clicked a single time step worth of simulation will be executed 2 5 Changing Step Sizes A step refers to a single cycle that first calculates the rates of reactions and then updates the quantities of the affected Substances At default the size of an integration time step is 1 1000 seconds To change the size of this time step please select PreferenceWindow from the Windows menu in the ControlP anel and then input a numerical value in the text box that will be displayed This can also be designated using ecs files If the step size is increased the time necessary for simulation will be shorter but will result in an increase i
39. ame Designates the default Accumulator class Refer to Chapter 4 If this option is designated and if a cell state file is loaded when the simulation elapsed time is 0 the simulation elapsed time recorded in the cell state file will be set to the present simulation progress time In all other i cases the simulation progress time will not change even if a cell state file is loaded For details regarding cell state files please refer to Section 2 7 in this chapter d Starts in debug mode f filename ecs Loads the designated scriptfile h Displays a list of options t directory name Designates the target directory for writing the temporary files Designates the number of times Postern Reactors are called at the time of u integer value initialization For details please refer to the explanation of Postern Reactors in Chapter 5 2 2 Loading Rule Files Rule eri files which are data files describing information that is necessary for the E CELL2 System to run simulations must be loaded prior to executing simulation To load Rule eri files please select Load Rule from the File menu in the ControlP anel and then select the appropriate Rule eri file from the newly displayed FileSelector window Please note that if Rule files are loaded more than 2 times E CELL2 will display an error message 2 3 Loading Script Files If a file called default ecs is located under the E CELL2 startup directory the file will automatic
40. ame the Reaction MichaelisUniUniReversibleReactor and the keyword definition will be such as the following OLASSNAME M chael i sUni Uni Reversi bl eReact or GBASECLASS Fl uxReact or UTHR Kouichi Takahashi MN L shafi fc kel o ac j p ATE 1999 2 22 WERSI CN ecs v08 0 1 BRI EF DESCRI PT CN Si npl e Henri M chael i s Menten Uni Uni Reversi bl e ki netics DESCRI PTI ON Si npl e Henri M chael i s Menten Uni Uni Reversi bl e ki netics GQATI ON v2f rac K cF K_p S K cR K s PI EE HK s P HK pL SI 4KS Kpj 9OUBSTANCE Substrate 1 1 9OUBSTANCE Product 1 1 SUBSTANCE Catal yst 1 1 SUBSTANCE Effector O O YPARAMETER Ks Float nol l Mchaelis Constant of Substrate YPARAMETER Kp Float nol I Mchaelis Constant of Product PARAMETER KcF Float nol l Catal yti c Constant Forvard 9PARAMETER KcR Float nol l Catalytic Constant Reverse R VATE Float Ksp N TI ALI FUNC Ksp Ks Kp REACT FUNG Fl oat S substrate 0 gt concentrati on Fl oat P product 0 eoncent rati on Fl oat E catal yst 0 guanti t y Float velocity KcF Kp S KcR Ks P E KS P Kp S Ksp pr ocess vel oci ty For Ks and Kp are both paraneters in the equation The product Ks Kp will always be constant Thus the product of this function need only be calculated once at the initialization point Declaring Ksp as a R VATE functi on N TI ALI
41. ance whereas Conc is the initial Concentration value of the Substance The unit of Conc is mol l If the Quantity and Conc should not change during simulation the values may be fixed by adding a Fix tag to the row right beneath Please refer to Section 4 2 3 for details regarding Substances The following are descriptions regarding enzymes Table 2 2 Example descriptions of Substances that catalyze reactions as enzymes NE Substance CELL CYTOPLASM 01 Substance CELL CYTOPLASM C E bc SD Complex of E bc and SD P roblems 1 In toy txt a few descriptions for Substance D and Substance E are missing Please fill in the gaps by referring to sampletxt 2 Similarly please complete the descriptions for Isomerase of A and Isomerase of D Reactors on the other hand are implemented chemical reactions An example is defined below Table 2 3 Example descriptions of Reactors Type ces mh D nemes Span MichaelisUniUniReactor CELL CYTOPLASM fa je sa cuor MichaelisUniUniReactor CELL CYTOPLASM o esc en renuemo MichaelisUniUniReactor CELL CYTOPLASM fe on sc cuero Path is the location of the Reactor It is described in a fashion similar to the directory path in UNIX S ID is the Substrate or the starting substance of the chemical reaction S Path is its location P ID is the Product or the resulting substance of the chemical reaction P Path is its location C ID is
42. are divided up with single front slashes system1 system2 system3 and so forth and must be written as absolute paths This section cannot be left blank Note also that this section is case sensitive FQEN FQPN FQEN FullyQualifiedEntryName is a method to define the destinations for and Using this method the destination can be written as system0 system1 system2 ID where the path and the ID are separated with a colon If the path is CELL CYTOPLASM and the ID is ATP the FQEN would be CELL CYTOPLASM ATP FQEN cannot tell the difference among the System Substance and Reactor items FQPN adds these item name into the statement In FQPN the target is described as Type F QEN In the former example of ATP the target in FQPN will be Substance CELL CYTOPLASM ATP Note that FQPN is case sensitive Type Class path System Cell System Environment t System Cytoplasm CELL system Membrane ACELL Figure 6 System Section ID row Name row IDs are used as process orders inside the E CELL2 simulation software Thus if duplicate IDs are defined inside a System a warning message will be displayed and the former defined ID will be used only Note that ID must be defined as case sensitive Define the ID of the System location in the ID row and the name of the System in the Name row ID o Name E CELL The cell ENVIRONMENT The culture medium CYTOPLASM The cytoplasm Es
43. ates the execution of simulation for 500 seconds whereas line 13 designates the termination of the simulation 4 5 List of Script File Commands Command Accumulator class name TnpD r directory LoadRul e filename Stepl nterval second Updatel nterval count SaveCel State file name LoadCel State file name Run seconds St op Exi t New nterf ace interface name Contents Designates the default Accumulator class For details please refer to Chapter 4 Section 2 4 Has to be described before LoadRule Writes the temporary file generated during simulation to the path designated in the argument temp is designated at default Has to be described before LoadRule Loads the rule file designated in the argument Designates the integration time interval in seconds The default value is 0 001 Has to be described after LoadRule and before Run Designates the user interface update interval in natural numbers The default value is 100 The user interface is therefore updated once every 100 integration steps Has to be described after LoadRule and before Run Saves the simulation state in the designated file Has to be described after Run Loads the simulation state that is saved in the designated file Has to be describe after Run Executes simulation for the duration time within the simulation system designated in the argument Stops simulation Has no arguments Shuts down E CELL2 Has no arguments A co
44. bc D Complex of Ebc and D Figure 10 Substance Section Type row Class row Define Substance in the Type row with the type format in the Class row For current version only supports Substance as Class always input Substance as Class it will be automatically inserted if left blank Define the location S ystem of the Substance in the path row The format is identical to the Class Substance Substance Substance Substance SUbStance SUbStance Class substance aubstance aubstance aubstance Mame Substance 4 substance B substance C substance Li substance E Isomerase of amp Mame Dehydratase of B Isomerase of C Isomerase of D Figure 11 Substance Section path row System section with front slash seperators system1 system2 system3 Note that Substances with the same ID and Names in different Systems are treated as different elements in E CELL2 System Note also that this section is case sensitive Complex of E hc and D Type Class path Substance Substance ALELLICYTOPLASM substance 4 aubstance Substance ALELLACYTOPLASM eubstance Substance ALELLACYTOPLASM substance Substance ALELLICYTOPLASM substance Substance ALELLACYTOPLASM substance Substance ALELLALCYTOPLASM Type Class path substance Substance PCELLAICYTOPLASM E bc Dehydratase af B substance substance ACELLYCYTOPLASM E cd aubstance Substance ALELLICYTOPLASM SUBSTANCE Substance ALELLACYTOPLASM Figure 12 Substance Section ID row Name row
45. designated e File button menu If this menu is selected a directory selection dialog will appear with directories that can be selected and designated The selected directory name will be directly reflected in the input field on the left 5 2 Process Scheme 5 2 1 Designating the jar file J ava Archive file for imput Designate the input jar file via its path If a nonexistent file name is designated a warning message will be displayed upon execution and the import process will not be executed 5 2 2 Batch Process The import process will start when the Execute button is clicked A log will be displayed in the message window during the import process If an error occurs during the import process a warning message will be displayed and the process will be terminated This process creates a new directory with the name of the imported model under the installation directory of E CELL2 6 Export wizard tab Export Exports models that are created by this system so that they can be loaded by other E CELL2 users EZ EGELL Tool Launcher Execute Figure 7 Export Wizard 6 1 Required Input 6 1 1 Model name Designate the directory of the model to export by directly typing its location or by browsing for it using the File button on the right e File button menu If this menu is selected a directory selection dialog will appear with directories that can be selected and designated The selected directory
46. displayed In this case the coordinates on the bottom of the window will also not be displayed However if the area is enlarged the cross will appear Also if the Tracer in the enlarged state is clicked crosses will appear in the corresponding points To clear the gray cross please click anywhere outside the graph display area Also regions can be enlarged by dragging and creating rectangles with the right mouse button To cancel the enlarged state and return to the default state please double click on the right mouse button e Tracer Reactor Activities WM Eai Ebi Mf 12842 38 oo 1 881405 Figure 4 Tracer Expanded display Coordinates Display Area The coordinates of the gray cross that is displayed when the graph is left clicked will be displayed on the left On the other hand the coordinates of the mouse cursor will be displayed on the right Close Button Closes the TracerWindow Add Button Displays a new EntrySelector and then displays the newly selected Substance or Reactor in the Tracer S ave Button Saves the time series data that is displayed in the Tracer into a file The saved data is composed of 5 columns time instantaneous quantity average quantity maximum quantity and minimum quantity 3 4 EntrySelector EntrySelectors are used when selecting Substances or Reactors Please click on the folder icon in the System selection dialog on the left If the appropriate System has been
47. displayed please select the appropriate items from the Substance and Reactor selection dialog and then click on the OK button on the bottom By using the switch button on the top right what is selected by the Tracers Substance or Reactor can be selected beforehand en Entry Selector Figure 5 EntrySelector Switch Button Used for switching between Substance and Reactor when called by Tracers System Selection Dialog The System in a hierarchal structure is displayed To display the lower levels please click on the folder icon Substance Reactor Selection Dialog Substances or Reactors will be displayed If dragged multiple selections are possible Also if clicked while the Ctrl key is pressed separately located items can be selected OK Button Finalizes the selection Cancel Button Cancels the selection and closes the window 3 5 SubstanceWindow amp Substance CELELAGYTOPEASMAEB Figure 6 SubstanceWindow FIX Button If this button is checked the quantity will not change during simulation Quantity Display Area Displays the quantity number of molecules of the Substance When simulation is in a stopped state its numerical value can be changed by clicking this area Concentration Display Area Displays the concentration of the Substance When simulation is in a stopped state its numerical value can be changed by clicking this area 3 6 ReactorWindow Normal Display Mode i Reactor E ab l
48. e cleared If any changes were to be made to the saved data A warning message will be displayed before altering the data 7 1 Spreadsheet Editor Simple editor to edit CSV files in tab format D Few File Spreadsheet M IILIMULIIISMRTILIPBXTELIIILERVTITRETETLPTABTE2I ETE EERERMES 0080 080 0 8080808 0 I E Figure 8 Spreadsheet Editor Right clicking inside the cell displays the following menu e Insert Insert row Inserts a new row onto that position e Delete Delete row Deletes the row of that position e Add Add new row Adds a new row under the selected row 7 2 Text Editor Simple editor for editing files in text format M ne M es Lam Ed i Figure 9 Text Editor 7 3 Message Viewer Message window to display errors and process logs Read only em Messages A O x File O9 37 27 Input sample er 09 37 27 Output sample er inc Temporary file 09 37 27 gt gt Executing command c E CELL2 Lib Perl Bin perl exe C E CELL2 BIN TOOLS4i1 08 37 27 Return value 09 37 27 lt lt finished 09 37 27 Script C E CELL2 BIN TOOLS calcqty pl 09 37 27 Input sample er inc 09 37 27 Output sample er inc qty Temporary file ol 09 37 27 gt gt Executing command c E CELL2 Lib Perl Bin perl exe C E CELL2 BIN TOOLS ci 09 37 27 Return value 0 at 9 37 27 lt lt finished 08 37 27 Deleted sample er inc 02 37 27 Command C E CELL2
49. e of the E CELL2 System itself In order to create a Reactor object the Reactor Description file RD file must be written with the actual commands and the required data such as the equation and the parameters inside The RD file gets converted to C and dll modules executable with E CELL2 System RD files can also be converted to a Reactor Spec Sheet in Latex format l Postern Reactor Two kinds of Reactors exist Regular Reactors and Postern Reactors While regular reactors use integrating functions to solve multi derivative equations postern reactors are separated from these integrating functions and used in cases where derivative equations are not suitable for calculating the Substance amount The two reactors realize due to the multi step calculation architecture after the React step in the regular reactor is executed the calculation will be performed in the Postern Step Postern Reactors can be used in the following case e n cases where the substance amount is controlled as discrete in cases where the substance amount is very low e n cases where the substance amount can be defined directly without the integrating functions For reactors describing the transcription start point or in cases where all substance value reduce to half because of a mitosis e In cases the reaction is described as an algebraic function Suitable for RapidEquilibrium Reactions or for Osmotic Calculations While regular reactors calculate the reaction
50. e refer to Chapter 2 3 Custom Install CD ROM version Custom Install is for users with some of the software above already installed The E CELL2 26 package to be installed will have the same function as installed by quick install imi E CELL2 Installer Ioj x Select install type Quick install Recommended Automatically inetalls the following products E Cell Verz zb JZRET 3 1 Uh Active Perl 5 5 1 Borland C 5 5 1 Total disk space 188 MB Custom install selects the features to be installed Read Manual Your OS type is WindowshT 2000 RP or later The name of the directory to install must contain only printable US ASCII characters The use of Spaces or non ls ASCII characters e g Japanese characters is not allowed Figure 6 E CELL2 26 Installer Click on Custom Install Select the third party software and the packages to install from below E CELL2 Installer 2 Figure 7 E CELL2 26 Installer Select from below e Newly install e Do not install but reconfigure environment e Do not install Click Next to go on For Do not install but reconfigure environment please follow the instructions of the software C TEMPYE CELL L IBYPERLSBIN perl exe C THP E CELL2 L B PERL BIN per exe ipee The following message will be displayed to check the list E E CELL2 Installer 3 Figure 9 E CELL2 26 Installer If the above informat
51. ed for operation of tasks such as reading and writing files operating on other interfaces and executing and stopping simulation If a rule file is loaded the name of the loaded rule file will be displayed after the Rule under the menu If a script file is loaded Script and the script file name will be displayed following the rule file fas E Cell Control Panel File New interface Windows Help Rule sample eri Script sample ecs Figure 1 ControlP anel Pull down menu list File Load Rule Loads a rule file Load Script Loads a script file Load Cell State Loads a Cell State Save Cell State Saves the Cell State Quit Shuts down the E CELL2 System NewInterface Tracer Displays a TracerWindow Substance Window Displays a SubstanceWindow Reactor Window Displays a ReactorWindow Windows Message Window X Displays a MessageWindow Preference Window Displays a PreferenceWindow Start Button Executes simulation Stop Button Stops simulation Step Button Executes a step of simulation Time Counter Displays the elapsed time inside the simulation system in seconds 3 2 FileSelector FileSelector windows are displayed for selecting files when reading or writing files Files can usually be selected by first clicking the directory name until the file display area becomes the appropriate directory and then by clicking the appropriate file and the OK button on the bottom To write in a new file please click on the
52. ed in C E CELL2 standard RD in a standard installation When creating Reactor Description files it would probably be helpful if the descriptions in these files are used for reference By using the modeling launcher to create C source codes and header files from Reactor Description files and then by compiling them Reactor DLLs are created Please press the Execute button to create the DLL If there are no syntax errors in the C code for the RD file and if the Borland C Compiler has been properly set a DLL will be created Messages will be displayed in the message window during the compilation process zs i bless File rei rei rei or ee rchorch a orch rho rchorch ee ee rok a r e ee ee gt gt Executing command C E CELL test make reactor bat MAKE Version 6 2 Copyright c 1887 2000 Borland becd c 1 7 5R0 5R00 I SRCR L L BIMSWIN BCC DDLL REACTOR SROR MyHic Borland C 5 5 1 for Wini Copyright fc 1333 2000 Borland srcrimymichael isuniuni reactor cpp ilink32 Ted c x L BIN WIN BCE c d32 obj MyMichael isllnillniReactor obi MyM i cha Turbo Incremental Link 5 00 Copyright cj 1937 2000 Borland Return value I amp x finished MyMichaelisliilluiReactor dll is already exists in Makefile gt gt Executing command C XE DCELL testBEmake reactor bat MAKE Version 5 2 Copyright c 1987 2000 Borland hcca2 c I SRC SRCD I SRCR DDLL REACTOR SR
53. eer file eri file conversion will be executed A warning message will be displayed if the selected spreadsheet do not exist 2 f the Spreadsheet is not selected er file selection is required for it will become the input for the scheme 3 Selecting er files or their paths o If the Spreadsheet is selected Spreadsheet eer file eri file conversion will be executed according to the data inputted The output will be directory name spreadsheet name ERI extension A warning message will be displayed if the selected spreadsheet do not exist o If the Spreadsheet is not selected er file is required for it will be the input for the scheme er file gt eri file conversion will be executed A warning message will be displayed if the selected er file do not exist 4 f neither er files nor the directory are selected Spreadsheet er file gt eri file conversion will be executed according to the data inputted The output will be directory name spreadsheet name ERI extension under the Model directory set at the preference window If neither the spreadsheet file nor er files are selected a warning message will be displayed If either Translate immediately after editing spreadsheet or Translate immediately after editing er file is checked the eri conversion process will start immediately after each editing window is closed 3 2 2 Set output rule file and directory Set the filename or the directory name for the out
54. emical reaction equation Reactor e Nodes of Substance connected by a Reactor constitute a directed graph Figure 1 Substance Reactor Model e Cellular organelles are described via the location System of substances System Figure 2 Substance Reactor Model inside a System Please note that the concept of a substance Substance includes not only chemical molecules ions and radicals but also voluntary physical properties such as osmotic pressure and cell volume Negative values however cannot be described In E CELL it is assumed that the intracellular concentration of a substance is uniform throughout the cell To handle diffusion it is therefore necessary to prepare multiple systems each with varying substance quantities To simulate various intracellular phenomena in E CELL both rate flux based reactions such as enzymatic reactions and rapid reactions such as chemical equilibrium can be implemented Flux based i e can be solved as differential equations chemical reactions are handled inside E CELL as follows e Changes the rate of chemical reaction equations using a standard Regular Reactor e Solves the ordinary differential equations using the Runge Kutta method e Michaelis Menten reactions are examples of rate equations Chemical equibrium based I e can be solved as algebraic equations chemical reactions are handled as follows e Manipulates the quantity of Substances directl
55. enu Tracer is selected when creating a Tracer window which represents the quantity of Substances or the activity of Reactors SubstanceWindow is selected when opening windows for displaying and manipulating Substances ReactorWindow is selected when opening windows for displaying Reactors E E Cell Gontral Panel File New Interface Windows Rule MessageVWvindow Preferencevvindow Elapsed Time s o Figure 17 Windows menu The items MessageWindow and PreferenceWindow are included in the Windows menu MessageWindow is used when opening windows for displaying messages from E CELL2 P referenceWindow is selected when setting the width of a simulation time step and the timing of Tracer window updating Fran ETE Figure 18 Help menu The item Version Information is included in the Help menu If selected the version information will be displayed The menus have been explained above To load Rule Intermediate Files please select File lmenu Load Rule A file selection window will be displayed Please click on the name of the file that ends with the eri extension which indicates that it is a Rule Intermediate File then select Open Figure 19 File selector window for Rule Intermediate Files If the designated file is loaded normally Condition Good will be displayed in the Message Window ib ECELL2 Console
56. ersion As similar with other sections the Include section can be placed many times at any position This function is usable in cases where general lines that must be included The Include Section need not be included if there are no files that need to be imported The lemmatizing words are Type and Filename Define Include as Type and the actual filename under Filename The above example is importing the file simple er 3 Saving and Converting Spreadsheets 3 1 Saving Spreadsheets To convert to ERI file which can be read in the E CELL2 System the input file must be in a tab separated text format that the converting software can recognize To create such a text file it is desired to use the spreadsheet creating function of the ModelingLauncher or general software such as Microsoft Excel A sample for the ss file can be found under the standard directory with the txt extensions In the basic install the directory will be C E CELL2 standard ModelingLauncher which can be used for creating rule files can be executed with the ModelingLauncher shortcut or from Programs gt E CELL2 ModelingLauncher in the Start menu Refer to Chapter 6 for more details 3 2 Converting to ERI format In order to perform simulations with the E CELL2 System it is required to convert the ss files or the er files into eri format Launch the ModelLauncher select the Rule tab and select Choose from the File button on the right em EGELL
57. etween the symbol until the end of the line are comments that will be ignored 4 3 Sample Script File A sample script file is shown below TnpLi r C XE CELL2Xt enp LoadRul e sanpl e eri New nterface Tracer tracel AddTrace Subst ance CELL CYTCPLASM A AddTrace Reactor CELL CYTCPLASM R1 SaveA 45 New nterf ace Subst anceW ndow t est sw Subst ance CELL CYTCPLASM A There have been a few changes made from the E CELL1 System What indicates the path of the Reactors is included in the startup batch file ECELL2 BAT or ECELL2BB BAT It has been made to describe the PATH when loading Therefore the ReactorP ath command cannot be used TmpDir is a directory for saving temporary files If the command does not exist the temp directory under E CELL2 s installation directory is used If the directory designated for TmpDir does not exist the E CELL2 System will terminate when executing simulation 4 4 Explanation of Sample Script File The first line designates the target location for writing the temporary files whereas the second line designates the rule file to be loaded Lines 4 to 7 display a TracerWindow called Tracel and are carry out a few settings Line 5 designates the addition of a Substance called A to the Tracer whereas line 6 designates the addition of a Reactor called R1 Line 7 designates the saving of the state of the Tracer after 45 seconds Lines 9 and 10 open a SubstanceWindow Line 12 design
58. ew Reactors necessary for executing your own simulation model 5 Operating E CELL2 The goal of this section is to master the basic operation of E CELL2 using the Rule Intermediate Files and Reactors that have been created A Control Panel will first appear when E CELL2 is started ES E Cell Control Panel File New Interface Windows Help Rule sample en Script sample ecs Figure 14 Control Panel of E CELL2 The pull down menus will be explained first amp E A y I iontral F 3 nal File New Interface Windows Help Load Rule Load Script oad Cell State Save Cell State Quit sun Figure 15 File menu The items Load Rule Load Script Load Cell State Save Cell State and Quit are included in the File menu Load Rule is selected when loading Rule Intermediate F iles Load Script is selected when loading scripts for automating the operation of E CELL2 Load Cell State is selected when resuming simulation by loading files that include the progress data of a cell state Save Cell State is selected when saving files that record the progress data of a cell state Quit is selected when terminating E CELL 2 m E Cell Control Panel File N ce Windows Help Rule Tracer Substancevvindow Figure 16 New Interface menu Elat ReactorWindow The items Tracer SubstanceWindow and ReactorWindow are included in the New Interface m
59. fficient of the Substrate in S Coeff Mame Isomerization of Dehydration af B Isomerization af C Isomerization of D Bonding of Ebc and D a ID o path o Coett rs es p O ee e EL EL E d TL fCELLAL YTOPLASM 1 5E CELL CYTOPLAS CELL CYTOPLAS zu oy TI C I n 1 C za Figure 24 Reactor Section P ID row P path row P Coeff row P ID and P Path defines the Product ID and its path of the System location In the reaction below ADP and GOP are the products under CYTOPLASM in the reaction Define the Stoichiometric coefficient of the Product in P Coeff s path CELL CYTOPLASM CELL CYTOPLASM PCELLAL YTOPLASM fLELLAC YTOPLASM fLELLAC YTOPLASM fLELLAC YTOPLASM c Coe P path FP Caoeff CELL CYTOPLASM 18D yJCELL CYTOPLASM 1 E cd l 1l EB o oL ee ee ee ee ee TSE ACELLACYTOPLASM 1 rs ee ee NENNEN TCEbc D j CELL CYTOPLASM 1 LX l1 Figure 25 Reactor Section C ID row C path row C ID defines the catalysts influencing Substrates and Products inside the reaction C Path defines the Catalyst System location Path In default the ID and the Path for the catalysts will be identical with the reaction s ID and Path S Coeff PID P peh P coef C I UC pah IPLASM 15B CELL CYTOPLASM 1 E ab CELL CYTOPLASM IPLA SM Sc PCELLIC YTOPLASM E 6c PCELLIAL YTOPLASM D IPLASM 1S0 ACELLICYTOPLASM E cd CELL C
60. file name display area then directly input the file name and click on the OK button File Selecto Figure 2 FileSelector File Display Area Displays a list of the files and directories that are currently selectable By clicking on the displayed file name the file name in the file display area on the bottom becomes that of the clicked one By clicking on the OK button the file can be selected Files can also be selected by double clicking the file names If a displayed directory name is clicked the directory displayed in the file display area on the top becomes that of the clicked one File Name Display Area Displays the file name currently selected By clicking on the displayed area the file name can be directly inputted If the return key or the OK button is clicked after input The file will be selected File Type List Displays the regular expression for restricting the files that are displayed in the file display area using filters In the default settings only the files with the appropriate extensions such as ecs will be displayed To change filters please click on the file type list and select a different file type OK Button If clicked the file currently displayed in the file name display area will be selected Cancel Button If clicked file selection will be canceled and the window will close 3 3 Tracer Tracers display the quantity of Substances or the activity of Reactors using 2 dimensional grap
61. file selection window RE3ECELL2 Tool Launcher File Help z IE es Execute Figure 10 Reactor tab Please open the file MyMichaelisMentenUniUni rd Reactor Description files RD files are usually created as files with the rd extension Reactors are defined and described in these files Fes GXE GELL2Xsetandard RD My Michaelis UniUniReactorrd CTesct File B4CLASSNAME MyM i chael isUniUni Reactor BEASELLASS FluxReactar BALITH R Yusuke Saito BEMAIL tob4Qbysilstc kelo ac ip ADATE 29 6 1999 ISVERSIUM E CELL Reactor AVERSION ecs v 3 0 1 BBRIEF DESCRIPTION Unireactant enzyme activity of which kinetics can be described by th e e Henri Michaelis Menten equat ian BDESCRIPTIUM reactor class for unireactant enzyme activity where kinetics can be desc ribedz X by the Henri Michaelis Menten equation derived from rapid equilibrium assumptions Yvspace 0 2cm This reactor is applicable to the following reaction sequence begin center SEtS rightleftharpoons Ik 1 Tk 11 ES rjehtarrow tk 1prIETPT Figure 11 Example of a Reactor Description file When creating Reactor Description files please note that the file name minus the extension has to directly become CLASSNAME as shown for this file Except for their class names the contents of MyMichaelisUniUniReactor rd and MichaelisMentenUniUniReactor rd are identical The description files for the standard reactors would be locat
62. for FluxReactor or in any case where the IDs start out with an the behavior is non guaranteed 5 Definitian af Volume environment Definition of volume cytaplasm Figure 22 Reactor Section init act row For Reactor activities that get calculated 1 step after the another these Reactor activity values need to be set at the start of the simulation init act row is to input those initial values where in defining Reactors pointed in the Volumelndex of the System section it is always required This init act will be used initially as Reactor activity values before starting the simulation The Volume to be used in every reaction inside the model will be set as 0 at the first step initial point of the simulation if no value exist here disabling the simulation The initial Volume in the example below is defined in the ConstantP arameterReactor of the Reactor defining volume inside the 5 ystem Hath Mame CELL CYTOPLASM Ean 0 iomenrslonofa S LL i CELL CYTOPLASM Dehydration of B ma D BB m CELL CYTOPLASM Esc owed SC CELL CYTOPLASM ES omereaton orb SD CELL CYTOPLASM EG Ebc D Bonding of Ebc and D E o TL LIE Ci Figure 23 Reactor Section S ID row S path row S Coeff row S ID and S Path defines the Substrate ID and its path of the System location In the reaction below ATP and Glc are the substrates under CYTOPLASM in the reaction Define the stoichiometric coe
63. hese metabolic pathways Although this model aims at the reconstruction of only the metabolic pathways it is expected that hemoglobin transport will be included in a future model cmt PT PGK eg GM This metabolic model of the Human erythrocyte cell was constructed by assistant professor Nakayama professor Tomita and their colleagues at Keio University Although only the metabolic model of a normal human erythrocyte is introduced in this demonstration models of anemia caused by genetic disorders are also currently being simulated Please contact assistant professor Nakayama ynakayam sfc keio ac jo for further information To observe an actual simulation of the erythrocyte cell please select Program E CELL2 erythrocyte from Start or click on the icon in your desktop E CELL2 loaded with the erythrocyte model will start If E CELL2 finds the file default ecs in the same directory as ECELL2 BAT it reads the file default ecs and attempts to start simulation Because a default ecs file has already been prepared for the erythrocyte model shown in Fig 4 the demonstration will automatically start The file Erythrocyte v236 eri describes the parameters and initial values for this simulation Files with the ecs extension usually are scripts for automating E CELL2 and include instructions for operating E CELL2 For details please refer to Section 2 3 and Section 3 4 The simulation of the erythrocyte model shown in Fig
64. hs Up to 8 series of data can be displayed in a single Tracer window dm Tracer Reactor Activities iim I Ty D pa x L l E h E DE ee jd RED GT bee o d ceo dutem eins mc rna Ma i mcm T rom nd e re en d Figure 3 Tracer Tracer A list of the Substances and Reactors displayed in the Tracer will be displayed The color of the radio button on the left of the name corresponds to the color of the graph on the bottom Switching between the display non display of the graphs is possible by left clicking the button By right clicking the button a SubstanceWindow will be displayed if it is a Substance and a ReactorWindow if it is a Reactor In a single Tracer up to 8 Substances or Reactors can be displayed Graph Display Area Simulation results will be displayed as graphs The vertical axis represents the number of molecules or concentration whereas the horizontal axis represents time If left clicked in the graph area a gray cross with its vertex at the point that was clicked will be displayed If there are multiple TracerWindows being displayed the gray crosses will be displayed in the same coordinates for all of them Please note that there are a few points to be careful about regarding synchronous cross cursors For example if the scales of 2 windows differ by a lot even if a cross is displayed in one of the Tracers the coordinates of the cross may be near 0 in the other Tracer and therefore may not be
65. iles If the conmand does not exist the tenp directory under E CELL2 s install ation directory is use Li ne 2 Desi gnates the Rule I nternedi ate File eri file to be oaded Li ne 4 8 Infornati on regarding a Tracer Li ne 4 7 AddTrace is declared only i nsi de a Tracer The Substances or Reactors witten in the argunents are added for di spl ay by the Tracer The argunents nust incl ude not onl y the ID but al so the Systemand Type that it bel ongs Li ne 8 The Substances di splayed in this Tracer are saved after 500 seconds in E CELL ti ne It is decl ared onl y i nsi de a Tracer Line 9 A blank lineis necessary after a New nterface Li ne 10 Updates the Tracer every 100 steps Li ne 12 Executes si nul ati on for 501 seconds Li ne 13 Saves the state of the cell nodel to the file sanpl e after500s cs Li ne 14 Stops the si nul ati on Please save the file above with a suitable name such as toy ecs However please do not use non US ASCII characters Please save it under the directory C YE CELL 2Ystandard which is the directory that includes sample eri If E CELL2 has been installed under a directory other than this please choose the proper target directory accordingly Please start the standard reactor version of E CELL2 After it starts please select Load Script from the File menu in the Control Panel and load the ecs file that has just been created The Logger mechanism which has been
66. ill be used in the eri if none is inputted in Conc Note that having no Volumelndex for System sections with substances result with the System Volume equal to 0 Conc value can be fixed Fix function T oubstance amp J 1000000 Te 06 means 1 10 EUER SA is fixed aB substance B U SL substance C 0 aL substance D U SE substance E U E ab Isomerase of 4 q83 Fix 00 E hc Denydratase of B U 02 Accumulator E cd Isomerase of C 0 0 E de Isamerase af D D 1 C Ebc D Complex of E bc and D Figure 15 Fix function Fix function manipulates the Substance Column so that the substance will not get the influence of the Reactor to fix the inputted Qty or the Conc value To fix these values input Fix under the Qty Conc value IL Mame AM E bc Dehydratase of B e UUE O02 Accumulator iImpleAccumulat E cd Isomerase of C 0 01 E de Isomerase of D 0 01 Figure 16 Substance Part Arg tag row Accumulator describes the method in rounding off the decimal points Defining Accumulator for Arg tag selects the method Arg coeff describes the specifics in selecting the actual rounding method choosing multiple methods for calculations have no proof in accuracy Mame CONT Arg_tag Dehydratase of B Q00E O02 Accumulator Simpleaccumulator Isomerase af C 0 01 Isomerase of D 0 01 Complex of E bc and D 0 Figure 17 Substance section Arg coeff row Select the capsulated Accumulator Class for rounding decimal points in Subs
67. ion is correct click OK to proceed Any new software will be installed at this point License Agreement for the third party software will be displayed for each software to newly install If you agree with the license please click Yes and select the installation directory to go on with the install C YE CELL YL ib becd5 B in C E CELL2ML ib Per Bin E CELL Lib JRE 1 9 1_05 Bin 170 E CELL2 1 ib boc55 include x L G wE DELL2I ibXibech5 ib C XE CELL2 I ib bech5 1 erann ananuna Sennen annnm Figure 10 E CELL2 26 Installer While installing BCC the following will be displayed In Windows NT 2000 perform path settings in HKEY CURRENT USER in Windows 98 perform path settings in Autoexec bat Also creates bcc32 cfg and ilink32 cfg for BCC editable Click Next to proceed r eae n ren E bs Figure 11 Windows Click OK and restart Windows to reflect the above settings This is the end of the installation procedure For basic operations please refer to Chapter 2 4 Quick Install Network version Please download the E CELL2 Ver2 26 Quick Install module ecell226web all in one exe Execute the module and please install according to the directions of the wizard If install is complete the install guidance screen for Borland C will be displayed Borland C is required for creating Reactors so therefore please download and install following the instructions Notice B
68. ivePerl if the executable module ts located under a folder that includes a spacefe g Program Files the environment will not be properly set and E CELL2 will thus be unexecutable To execute E GELL2 after completing the environment settings a reboot is necessary for the contents of the settings to be reflected in the system Common Acquisition of Java Runtime Environment 1 3 1 Operating manual i rating manua Acquisition of Borland G 3 9 pe g Only for those Acquisition of ActivePerl 3 6 1 Operating manual creating Reactors Environment settings Tor E CELL Ver 26 Operating manual Figure 13 Guidance window of the setup This is the end of the installation procedure For basic operations please refer to Chapter 2 Chapter 2 Tutorial 1 Features of E CELL2 In this chapter the features and operation methods of E CELL2 26 will be outlined For details regarding the theoretical background of E CELL please refer to the tutorial available at E CELL Org http www e cell org To model a cell the abstraction of its components is necessary In E CELL the Substance Reactor Model has been adopted for describing the structures of a cell and the chemical reactions inside a cell This model has the following features e The state of a cell is regarded as a set of quantity of substances Substance e he activity of a cell is represented by a change in the quantity of a Substance using a ch
69. l be created as comment lines In order to use the character at the start of the line as a non comment line use or include a space before it 5 at non starting positions will be treated as normal characters For line headers without these keywords the line will be treated as continuance from the previous line While converting to Spec Sheet in order to add a new line type YY e Certain Keywords can be omitted if they are not required General Keywords e CLASSNAME e BASECLASS e AUTHOR e EMAIL 6 DATE e WWERSION e BRIEF DESCRIPTION GLASSNAME line is to define the Reactor Classname The filename of the Reactor MUST BE CLASSNAME inany case GBASECLASS line is to defi ne the base class for that class In nost cases Fl uxReactor is def i ned UTHOR GEMVL DATE lines are to defi ne those i nf ornati on i nto the reactor BRIEF DESCRIPTION line is a single lined definition of the Reactor The details of these keywords are passed on to the E CELL2 System Keywords for the Reactor Spec Sheet DESCRIPTION EQUATION SUBSTANCE NOTES ESCRI PT ON ine is to define the full description of that Reactor GQAT ON line is to define the equation in LaTeX displaymath format Thus 1 Write Equation 2 Xbegi n di spl aynath Write Equation end di spl aynat h 3 M Write Equation Y choose any of the above JeUBSTANCE line is to defi ne the Substance fromSubstrate Product Catalyst
70. le C E CELL2 standarditoy File ER file File Execute Figure 9 Selection of toy txt If the Execute button is clicked a Rule File toy er and a Rule Intermediate File toy eri will be created The creation of Rule Files and Rule Intermediate Files have been explained in this section Please proceed to the next section on creating Reactors 4 Creating User defined Reactors for E CELL2 To describe a chemical reaction that is not included in the standard reactors one must design and create a Reactor for E CELL2 4 Outline of Reactors Reactors calculate the temporal changes in the quantity of Substances The source code is described in C language Writing a Reactor in E CELL means writing a Reactor describing Reactor Description RD file e g filename rd n an RD file the specifications of the Reactor and the contents of the processes to be executed are written Using rd2ch pl and rd2tex pl RD files are converted into tex files i e Reactor Spec Sheets in LaTeX format and dll files i e Dynamic link libraries in an E CELL loadable format RD files are created by arranging lines consisting of pairs of keywords and values RD files can roughly be divided into the following three parts e General information e Reactor Spec Sheet e Reactor Source Code When creating Reactor Description files please conform to the following rules Keywords consist of capital letters or
71. le selection dialog will open and users are to select the target file to open The selected file will be displayed in the input field 2 Edit existing files Edit A file selection dialog will open and users are to select the target file to edit The selected file will be displayed in the input field 3 Create new file New This will create new spreadsheet files to be edited The selected file will be displayed in the input field 3 1 3 eri file ERI file Select the eri file or the path itself by directly typing its location or by browsing for the target by the File button on the right If the path is omitted the Model directory set at the Preference window will be used If only the path is designated files will be created with the input spreadsheet or the er file name with an ERI extension Model directory set at the preference window will be used if the field is left blank A warning message will be displayed on overwriting existing files The process will terminate with a warning message if the set directory do not exist e File menu The following can be performed 1 Select the target file Choose A file selection dialog will open and users are to select the target file to open The selected file will be displayed in the input field 3 2 Process Scheme 3 2 1 Select the spreadsheet or er file for input Choose the input file under the following rules 1 If the Spreadsheet is selected Spreadsheet
72. mmand for creating new interfaces Requires 2 arguments the type of the interface and the name of the interface Commands Declared within Newlnterface Command Contents Designates the size and the display coordinates of the interface However because it only takes one argument it is described like the following X1 x Y1 4 X2 4 Y2 However X1 and Y1 denote the width and height Geonet ry X1 x Y 1 4 X2 4 Y2 respectively Also X2 and Y2 denote the x coordinate and y coordinate for the top left corner of the window If it is the top left becomes the base If it is the bottom right becomes the base The difference between E CELL1 is that if the location of the window is designated in the above rule but does not fit in the Windows screen the location of the screen will automatically be fixed so that it does fit in the Windows screen Commands for Each Interface e Tracer Command Contents Adds the Substance or Reactor written in the argument to the Tracer for display The argument has to include not only the ID but also the System and Type that it belongs to and uses FOPN Saves the state of the Tracer at a certain time Has the same effect as clicking the Save button in the TracerWindow In the first argument the time in which the state will be recorded is provided in seconds In the second argument the directory for saving the data is designated If omitted becomes Data Add
73. n quantity NOTE 0 0 0 0 0 O 100000000000000064 624 314 66 624 6 O 20000000000000016 1247 938 65 1247 630 O 300000000000000192 1871 1562 5 1871 1254 O 40000000000000032 2495 2186 19 2495 1877 0 50000000000000032 3118 2809 73999999999968 3118 2501 O 600000000000000384 3742 3433 15 3742 3125 O 700000000000000512 4365 4056 4 4365 3748 0 80000000000000064 4988 4679 5 4988 4371 0 90000000000000064 5611 5302 47999999999936 5611 4994 1 00000000000000064 6234 5925 27 6234 5617 1 0999999999999896 6856 6547 95 6856 6240 1 19999999999997856 7479 7170 48 7479 6862 1 29999999999996 768 8101 7192 86 8101 7485 Omissi on ll To suspend simulation and save the states of the substances for the whole model please select Save Cell State from the File menu in the ControlP anel Please save the file with an appropriate name with the cs extension The states of the models saved here can be loaded by selecting Load Cell State from the same File menu Simulations can thus be resumed from the states that have been saved 2 8 Shutting Down the E CELL2 System If Quit is selected from the File menu in the ControlP anel a confirmation dialog will be displayed If the OK button is clicked the E CELL2 System will shut down 2 9 E CELL2 Batch Mode and Loggers E CELL2 provides a batch mode that is executable from command lines Please start the command prompt MS DOS prompt and then move to the directory
74. n error On the other hand if the step size is decreased the time necessary for simulation will be longer but will result in a decrease in error 2 6 Displaying Simulation Results In the default settings user interfaces are updated once every 100 integration calculations This interval can be changed in the ecs file 2 6 1 Using Tracers Tracers display the simulation results as a 2 dimensional graph In the vertical axis the changes in the quantity concentration of Substances or the changes in the activity of Reactors are displayed In the horizontal axis on the other hand the time is displayed To display a new TracerWindow please select Tracer from the NewInterface in the ControlPanel To display a new Substance or Reactor in the Tracer please click on the Add button at the bottom An EntrySelector will then be displayed Please select the appropriate Substance or Reactor Please note that what Substances describe does not necessarily refer to molecules of strict chemical terminology It may be voluntary particles such as ions and radicals However in this manual we will use the term molecule for convenience The selected Substances and Reactors will be displayed with the colored square checkboxes in the Traces display area If simulation starts in this state the state of the Substance or Reactor will be represented by a graph of the same color as the square next to the checkbox 2 6 2 Using SubstanceWindows To dis
75. name will be directly reflected in the input field on the left 6 2 Process Scheme 6 2 1 Designation of the model to export Designate the directory of the model to export If a nonexistent file name is designated a warning message will be displayed upon execution and the export process will not be executed 6 2 2 Batch Process The export process will start when the Execute button is clicked A log will be displayed in the message window during the export process If an error occurs during the export process a warning message will be displayed and the process will be terminated This process creates a model archive file in jar format under the installation directory of E CELE 7 Editor Viewer Window Two simple editors and one viewer window Is included in this launcher e Spreadsheet Editor e Text Editor for er and rd files e Message Viewer Each window has a common command set of the following 1 Save File Saves the edited or displayed text onto a file If the file was newly created a file selection dialog will open during save The editing file will be the save target elsewise When in message viewer mode the displayed text file will be saved A file selection dialog will always appear in this mode A warning message will be displayed on overwriting existing files 2 Refresh Performs an undo and refreshes the data back to its saved or last opened position When in message viewer mode any displayed message will b
76. network of chemical reactions has now been depicted as static graph However to actually start simulation the rules that define the parameters for each reaction e g initial values rates and how the reactions proceed i e which chemical reaction equations to choose have to be decided When creating models for E CELL simulation rules called Rule Files which are distinguished by the er extension are described using text editors Then using tools included with E CELL files that can be directly read by E CELL called Rule Intermediate Files are created Rule Intermediate Files are usually distinguished by the eri extension Because it is difficult for beginners of E CELL to describe Rule Files from scratch tools for creating Rule Files from spreadsheet files are also provided to support the Rule File creation process 3 1 Creating Spreadsheets Here the methods for creating spreadsheets for simulation and converting them to Rule Intermediate Files for E CELL2 will be outlined The minimum operating procedures necessary for creating Rule Files using the modeling launcher which is included with E CELL2 will be explained To start the modeling launcher please select P rogram E CELL2 ModelingLauncher from Start or click on the icon in your desktop fey ECELL2 Tool Launcher al xl File Help Spreadsheet file E ERMle 0 0 0 0 0 0 0 0 00 0 Execute Figure 7 Window
77. ng reacti on sequence begi n cent er E 5 ri ghtl eftharpoons k 1 k_ 1 ES Yri ghtarrow k 1p EJPS Yend cent er vspace 0 3cn GQATI ON v2 amp f ract K cF LE S HK n53130 S SUBSTANCE Substrate 1 1 SUBSTANCE Product 1 1 SUBSTANCE Catal yst 1 1 9SUBSTANCE Effector O O PARAMETER Kn Float nol l Mchaelis Constant of Substrate PARAMETER KcF Float nol l Catalytic Constant Forward REACT FUNC Fl oat S substrate O eoncent rat i on Float E catal yst 0 quanti t y Float velocity KcF E S Float Den Kn S vel oci ty Den pr ocess vel oci t y 2 General information related keywords o CLASSNAME The class name of this Reactor the file name minus the rd extension o BASECLASS The name of the base class inherited by this class o AUTHOR The name of the author o EMAIL The e mail address of the author o DATE The creation date of this Reactor o YWERSION The version of the E CELL System the version of this Reactor o BRIEF DESCRIPTION A brief description of this Reactor 3 Reactor Spec Sheet related keywords o DESCRIPTION A detailed description of this Reactor o EQUATION The equation of this Reactor described under the LaTeX displaymath environment in either of the following methods 1 Description of a mathematical expression 2 begindisplaymath Description of a mathematical expression gt end Bisplaymath 3
78. nvolved in the Simulation The definition for each item is as follows Name Definition Default if left blank Type Substance required Class Substance can be omitted optional Path required ID ID of the in target required Name Name of the in target ID Qty 0 Conc Qty Arg tag value in orders Accumulator optional required if Arg tag Is ge included Figure 9 Substance Section Lemmatizing Names path ID Name CELL CYTOPLASM SA substance A CELL CYTOPLASM SB Substance B CELL CYTOPLASM SC Substance C CELLACYTOPLASM SD Substance D JCELL CYTOPLASM SE Substance E PCELLACY TOPLAS E ab Isomerase of amp ses path I Mame CELL CYTOPLASM Ebe Dehydratase of B ACELLALYTOPLASM E cd Isomerase of C CELL CYTOPLASM Ede Isomerase of D CELL CYTOPLASM C E
79. ocess will start when the Execute button is pressed Log will be displayed in the message window during the conversion process The process will terminate with a warning message if an error occurs during the process If the error occurred when loading script error details will be displayed in the message window Note that the Makefile for creating Reactor modules is required for this conversion process to succeed A warning message will be displayed if this Makefile do not exist under the DLL output directory set at the Preference window Please also make sure that the permission settings for the Makefile is set in writable mode for the list of the Reactor modules DLL to be created will be appended to the file under the DLLFILESR section This process creates the Reactor source files in the format set at Output source Extension in the Preference window The extensions for the header files are always h Reactor Source files and DLL files will be saved under the directories set at the Preference window 5 Import wizard tab Import Imports models that are created externally to this system em ECELLZ Tool Launcher Execute Figure 6 Import Wizard 5 1 Required Input 5 1 1 Model name Designate the location of the jar file of the model to import via its path by directly typing its location or by browsing for it using the File button on the right The installation directory of E CELL2 will be chosen if only a file name is
80. of the modeling launcher 1 Please try loading the sample Rule File for E CELL2 Please click on the File button in the Spreadsheet file column select Edit and open the file selection window Then please search and load sample txt ac XE CELLZXs tandard sample tx t Spreads Temm D 1 System Cel Def 120 Svstem Envi ronment po OET meatu ENIM Def Svstem Cytoplasm et aes ec a RST E 25 Membrane ENVIR N ConstantP ENVIRONMENT NoD ConstantP CELL ZCYT VOLUME CELL CYT SA pese oo RHET Substance B Rosen I RUE substance C 0 Substance CELLZCYT Substance D 0 CELL CYT Substance E NENNEN NNI VCELL GYT E ab Isomerase 0 83027003 Fix Name CONC Arg fag Arg coeff ACELL CYT E be Dehydrata 0 02 Accumulator Si i Es damned 00 RURCCERE o qme MM ee a s a a a a a al a a a a a a a a a a a a a a a a a a a s a a a a a a a a a a a a a a a a a a a a a a a a a Figure 8 Window of the modeling launcher 2 After finishing editing please save the file by choosing Save or Save As from the File menu 3 2 Creating Rule Files and Rule Intermediate Files The procedures for converting spreadsheets into Rule Files and Rule Files into Rule Intermediate Files will be explained Please refer to Chapter 4 for details regarding Rule Files Please start the modeling launcher and load sample txt and toy txt
81. on in the Control Panel and then select Save Cell State from the File menu a Cell State File Files describing the state of the whole cell model have the cs extension Please save it under a suitable directory Files in this format can be loaded by selecting Load Cell State from the File menu in the Control Panel It is thus possible for simulation to be resumed from a saved state Automation using script files In large scale simulation the manual operation of its various tasks is a troublesome process In E CELL simulation can be automated by using a mechanism called script which loads the commands described in the script into E CELL Script files are usually distinguished by the ecs extension The directions on how to write the script files will be explained briefly here The format differences between the script files of E CELL1 and E CELL will also be explained First please take a look at the following file The numbers in the beginning of each line are line numbers Ol TnpDLr C XE CELL2 tenp 02 LoadRul e sanpl e eri 03 04 Newnterface Tracer ABC 05 AddTr ace Subst ance CELL CYTCPLASM SA 06 AddTr ace Subst ance CELL CYTCPLASM SB 07 AddTr ace Subst ance CELL CYTCPLASM SC 08 SaveAt 500 10 Updatel nterval 100 12 Run 501 13 SaveC State sanpl e af ter500s cs 14 Stop Line 1 Desi gnates the directory for saving tenporary files TnpO r is a directory for saving tenporary f
82. orland i required for creating and customizing models After registering from the Compiler link for Windows Ver5 5 in the Borland Software Corporation site please download and then install To execute Setting of Borland G after completing the install the environment settings Is necessary for the contents of the settings IA click of a link displays the warning of security depending on the browser of use Then please choose Run this program from its current location Setting of Borland C 3 0 Operating manual Figure 12 Guidance window of the setup This is the end of the installation procedure For basic operations please refer to Chapter 2 5 Custom Install Network version Please download the E CELL2 Ver2 26 Custom Install module ecell226web minimal set exe Execute the module and please install according to directions of a wizard If install is complete install guidance for the third party software and E CELL2 26 will be displayed Therefore please install according to the guidance E CELL2 Ver2 26 Installer yo execute E GCELLZ Java Runtime Environment is required Please download this trom the following URL and then install Borlandi c js also required Tor creating and customizing models Therefore please download and then install this alse After all the necessary software have been installed please proceed to Environment settings for E GELL2 Ver 26 Please note that for Borland and Act
83. play or change the quantities of substances SubstanceWindows are used To display a S ubstanceWindow please select SubstanceWindow from the NewInterface menu in the ControlP anel An EntrySelector will then be displayed Please select the appropriate Substance If the OK button is clicked a SubstanceWindow will be displayed In the SubstanceWindow the ID and the substance name are displayed from the top Below this the number of molecules is displayed on the left and the concentration on the right If simulation is in a stopped state these two values can be directly changed After clicking on the displayed values to be changed and inputting new numbers please press the return key to actually change the values The number of molecules can be changed also by using the up and down buttons on the bottom 2 6 3 Using ReactorWindows To observe the rates of reactions and the substrates and products that are involved ReactorWindows are used To display a ReactorWindow please select ReactorWindow from the NewInterface menu in the ControlP anel An EntrySelector will then be displayed Please select the appropriate Reactor If the OK button is clicked a ReactorWindow will be displayed In the ReactorWindow the Reactor class entry name and the name of the reaction will be displayed from the top Below these the activity per second will be displayed This is in a simple display mode To observe the substrates and products involved
84. please press the Close button Please try changing the quantity of a Substance and then observe its effects on the system adr EE Cu l L i i E Figure 26 Behavioral change of a system caused by a change in the quantity of a Substance In this example Substance D has been suddenly increased It can be observed that the increased Substance compensated by the other reactions in the system gradually decreases Similarly the activity of Reactors can also be displayed in detail Please select ReactorWindow from the NewInterface menu in the Control Panel s Entry selector oi SUHSantE Cie Reactor Figure 27 Entry Selector window for ReactorWindow As was the case with SubstanceWindow please click on the System displayed in the left panel and search for the target Reactors Please click on the Ok button after selecting the Reactors ET um e Reactor E ab 0 Figure 28 ReactorWindow In this window the name of the selected Reactor the type of reaction equation used and the activity of the reaction is displayed If the Show lists button is pressed more details will be displayed If the Close button is pressed the window will close Please try pressing the Show lists button m Reactor E ab U Figure 29 ReactorWindow in the expanded state Besides the information above the initial values for each parameter and information regarding the s
85. public items used If FluxReactor h is included in the file Reactor h Reactant h and RootS ystem h are all automatically included in the file are need not to be included Note that Stepper h used in E CELL1 is not used in E CELL2 If not including FluxReactor h including StandardHeaders h is desired in ordered to include the former three header files PTl ON C line is to defi ne new nethods and nacros The data here wll be appended to the top of the cpp file N TI ALI FUNC line is to define the C code to be executed only once at the initialization point This line can be used to set the non changing elements and to check parameter ranges REACT FUNC line is to defi ne the process that nust be done for each cal cul ati on step As def aul t 1 Calculate Reaction Velocity 2 Alter the substance value according to the Velocity if including the FluxReactor process nethod can be used to easily performthe 2 task Argunent for the process nethod is the nol ecul ar reacting anount per second in Fl oat The activity that the reactor handle is the value per single step but the value shown in the reactor window are values per second KEYWORD tex Cpp h format required CLASSNAME O O O l O BASECLASS O O O O AUTHOR O 1 1 EMAIL O I 1 DATE O 1 1 9M ERSION O O O BRIEF DESCRIPTION O DESCRIPTION O TEX EQUAION O TEX l YSUBSTANCE O O 2 9P ARAMETER O O O O 2 NOTES O TEX NCLUDE FILE H
86. put eri files according to the data inputted ERI files with inputted filename and directory if any will be created If left blank the file will be created under the Model directory set at the preference window If the selected filename do not exist a new file will be created with that name A warning message will be displayed if the selected directory do not exist 3 2 3 Batch Process Clicking the Execute button starts the conversion process The log of the process will be displayed in the message window during the process with errors if any where the process will be terminated at that point If the error occurred while script execution the error details will be in the message window e If Save spreadsheet file in the Preference window is not checked the spreadsheet file of input will be deleted in the spreadsheet gt er conversion process e If Save er file in the Preference window Is not checked the er file will be deleted in the eer file gt eri file conversion process 4 Reactor wizard tab Reactors Creates the Reactor source files C C and header files and DLL from rd files ECELLZ Tool Launcher Figure 5 Reactors Wizard 4 1 Required Input 4 1 1 rd file RD file Select the rd file via its path by directly typing its location or by browsing for the target by the File button on the right If the path is omitted the RD directory under Model set at the Preference window will be used
87. tance and define in Arg coeff Below are the selectable choices Accumulator Class Rounding Decimal Points Integer and decimal parts are stored separately Only the integer part will be used for the results while under calculations the decimal parts will be added up until the sum crosses the 1 0 border to be added on to the integer part Variation Integer Decimal Initial 0 0 0 8 0 0 8 0 8 1 0 6 2 ReserveAccumulator SimpleAccumulator m values for calculations 1386 18 digits alpha 15 digits in RoundDownAccumulator Round down decimal points RoundUpAccumulator X Round up decimal points RoundOffAccmulator Round off decimal points Store separately integer and decimal parts and handle the latter as MonteCarloAccumulator random numbers and round off Ex if the actual change is 3 4 The change will be 6096 wise 3 and 40 wise 4 2 4 Reactor Section The Reactor Section is to select the environment variables such as the reactions using substances defined in the Substance sections inter relationships and volume In this section the Reactor will be stoichiometrically defined with the involved Substances Below are the specifications Name Definition Default if left blank Type Reactor required Class kinetic equations required Path Reactor Path required ID Reactor ID required Name Name of the Reaction ID init act Initial Reactor Activity omittable unless defined in Volumelndex S ID S ubstrate ID required
88. that E CELL2 has been install to In a standard install C E CELL2Ystandard is the location of the startup batch of E CELL2 for the standard reactor model The E CELL2 startup batches for each model are located in CXE CELL model name If ECELL2BB BAT h is typed a list of the options will be displayed The options are the same as in GUI mode Please refer to Section 2 1 ECELL2BB BAT is the batch file for MS DOS and describes the PATH of the directory that the dynamically linked Reactor libraries DLL are housed in In PATH the designation of a DLL housing folder e g DLLRB for batch mode is necessary To execute simulation in batch mode it is necessary to include the f option when loading the script file ecs If simply typed ECELL2BB BAT it will load default ecs For details on script files please refer to Section 4 in this chapter ECELL2BB BAT f filenane ecs The following are the contents of ECELL2BB BAT SET PATHSAV P ATH PATH BIN WIN BCC DLLRB P ATH ecell2b exe r DLLRB 9d 92 94 9 6 9g B 90 PATH PATHSAV If the Logger mechanism implemented from E CELL2 is used it is possible to record the cell state continuously during simulation This function was implemented for use in batch mode For details on its usage please refer to Section 4 5 List of Script File Commands 3 Interfaces 3 1 ControlP anel The ControlP anel which is the main interface for the E CELL2 System is us
89. the Catalyst or the chemical substance that promotes or represses the reaction C Path is its location In the Arg tag column the constant names that are defined differently according to the type of Reactor are inputted In the Arg coeff column the constant values that correspond to the Arg tag are inputted Reactor Reactor Reactor Reactors whose IDs begin with are back door Reactors used for describing reactions that cannot be described by differential equations In the Toy model EQ Ebc D is the algebraic equation based back door Reactor Ebc4SD lt C Ebc D is a reversible reaction that consists of a reaction that produces C Ebc D from Ebc and SD and a reaction that decomposes C Ebc D Therefore it cannot be solved by differential equations Thus RapidEquibriumP Reactor for rapid equilibrium is used here Pr obl ens gt 1 Please conpl ete the descri pti ons for the reaction i n Reactor D Please refer to Section 4 2 4 for details regarding Reactors If all of the above operations have been finished please save toy txt and start working on creating Rule Files The actual operations for creating Rule Files from spreadsheet files will be explained using the model launcher Please click on the File button in the spreadsheet file column and then open the file selection window by selecting Choose Please search and load toy txt em EC SIE Taai Piha File Help Spreadsheet fi
90. tools such as notepads The file names correspond to each Substance and Reactor Information on the time instantaneous value average value maximum value minimum value instantaneous concentration average concentration maximum concentration and minimum concentration are listed The procedures for carrying out simulation have been explained so far in this chapter Please refer to the chapters that follow Chapter 3 for details regarding each item Chapter 3 Basic Operation Introduction In this chapter the basic operation of the E CELL2 System will be explained It will be assumed that users have already mastered the overall operating procedures for E CELL2 which have been explained in Chapter 2 Tutorial Please refer to Chapter 2 if necessary Two modes a GUI mode and a batch mode exist in E CELL2 In this chapter most of the explanations will be on the former mode GUI mode In Section 2 Basic Operation the startup and shutdown of the E CELL2 System in GUI mode will be explained briefly first Operations in batch mode will be explained in Section 2 9 E CELL2 Batch Mode and Loggers Loggers newly implemented for the E CELL2 System are mechanisms that continuously save simulation results in real time Details of the operation procedures will be explained in Section 3 Interfaces Script files which improve the operation of E CELL2 will be explained in detail in Section 4 E CELL2 Script Files
91. ubstances participating in the reaction will be displayed To return the window to the Original size please press the Hide lists button To close the window please press the Close button _ m Preferences Figure 30 PreferenceWindow PreferenceWindow will be explained next To display this window please select PreferenceWindow from the Windows menu in the Control Panel This window is provided to control the width of a simulation time step Unit sec and how often the Tracer window is updated If the time step is short the accuracy of computation increases at the expense of increases in the time necessary for simulation On the other hand if the time step is long the time necessary for simulation decreases but the accuracy of computation also decreases which therefore makes its results less reliable In the initial settings a computation step is set at 0 001 seconds whereas the frequency of window updating is set at once per 100 steps Because this window is a modal dialog other windows may not be operated until Ok or CANCEL is pressed arming CELL MEMBREAME na volume index is specified warning CELL no volume index is specified Warning ICELL MEMBRAMNE no volume index is specified warning CELLUMEMBRANE na volume index is specified ENVIRONMENT volume index is ENVIRGMMERNT VOLUME checking cell configuration Reactor initialization succeeded condition Good Figure 31 MessageWindow
92. y using a back door Postern Reactor e Phenomena such as rapid equilibrium and changes in osmotic pressure are examples of this type of reaction From the standpoint of software engineering E CELL2 has the following features The part written in C will be described first This part the so called heart of E Cell2 corresponds to the view of the world Ontology that shows how E CELL2 describes a cell Such components are called classes in the field of object oriented modeling The computation mechanisms necessary for simulation are implemented by the interactions between the classes Messagelnterface Root ystem Cell SNS Cytopasm 47777 1777 mm s Fa Environment 4 Each Reactor P He i 2t Inhentance Monolithic LL ENT Membrane Pointer or Reference Windows DLL Figure 3 Internal structure of E CELL2 The differences between E CELL2 and the Linux based E CELL1 are listed below Multiple class inheritance has been abolished in E CELL2 e Friend functions have also been abolished in E CELL2 e he Integrator and Accumulator classes have been integrated into the Substance class e he Stepper class has been integrated into the System class e A modeling launcher has been implemented These changes were made to improve the portability of E CELL1 which only works on Linux The GUI Graphic User Interface and the modules for interpreting the script files for automating the operation

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