Cells are tightly packed with structures and molecules that carry out the day-to-day operations of living. Understanding how cellular design dictates function is essential to understanding life and disease, in the brain, heart, or elsewhere. MCell (Monte Carlo cell) is a program that uses spatially realistic 3-D cellular models and specialized Monte Carlo algorithms to simulate the movements and reactions of molecules within and between cells—cellular microphysiology.

Model design, editing, and visualization are integral to microphysiological simulations. DReAMM (Design, Render, and Animate MCell Models) can be used to import and edit meshes from 3-D reconstruction and computer-aided-design software, and subsequently tailor the meshes to represent pieces of cells in MCell simulations. In addition, it is used to visualize MCell simulation results, including the locations and states of participating meshes and molecules.

[[Using These Tutorials]] . [[MainMenu]] . [[Other Tutorials|http://www.mcell.psc.edu]]

A TiddlyWiki is like a blog because it's divided up into neat little chunks, but it encourages you to read it by hyperlinking rather than sequentially: if you like, a non-linear blog analogue that binds the individual microcontent items into a cohesive whole.\n\n[[developed by JeremyRuston|http://tiddlywiki.com/]]

http://www.mcell.psc.edu

InterfaceOptions are displayed when you click the 'options' button on the right. They are saved in a cookie on your browser, making them sticky between visits. RegExpSearch allows more complex search expressions; CaseSensitiveSearch does as it's name implies. The user name for edits should be set //before// starting to edit things (ouch. another bug). AutoSave and SaveBackups give the option of automatically saving changes and whether to generate backup files. You can also choose to GenerateAnRssFeed.

PSCDX is software that is based on [[OpenDX|http://www.opendx.org/]]with added features and bug fixes. It is specifically tailored to enhance the performance of the ~DReAMM program for visualizing and editing complicated meshing objects.

A row of ToolbarButtons appears to the right of a entry title. The buttons are:\n\n * ''close'' - close the current entry\n * ''link to this entry''- puts a link direct to the current entry into the Web address (URL) bar\n * ''references'' - displays all the entries that link to the current entry

// define defaults for cookie-based option values\nif (config.options.txtTOCSortBy==undefined) config.options.txtTOCSortBy="modified";\nif (config.options.txtTOCListSize==undefined) config.options.txtTOCListSize=12;\nif (config.options.chkTOCShow==undefined) config.options.chkTOCShow=true;\n\n// define macro "tableOfContents" to render controls\nversion.extensions.tableOfContents = {major: 2, minor: 1, revision: 0, date: new Date(2005,9,6)};\nconfig.macros.tableOfContents = { label: "contents" };\n\nconfig.macros.tableOfContents.css = '\s\n.TOC { padding:0.5em 1em 0.5em 1em; }\s\n.TOC a { padding:0em 0.25em 0em 0.25em; color:inherit; }\s\n.TOCList { width: 100%; font-size:8pt; margin:0em; }\s\n';\n\nconfig.macros.tableOfContents.html = '\s\n<div style="text-align:right">\s\n <span style="float:left">\s\n <a href="JavaScript:;" id="TOCMenu" class="button" style="padding: 0em;"\s\n onclick="onClickTOCMenu(this)" title="show/hide table of contents">%label%</a>\s\n </span>\s\n <a href="JavaScript:;" id="TOCSmaller"\s\n onclick="resizeTOC(this)" title="reduce list size">&#150;</a>\s\n <a href="JavaScript:;" id="TOCLarger"\s\n onclick="resizeTOC(this)" title="increase list size">+</a>\s\n <a href="JavaScript:;" id="TOCMaximize"\s\n onclick="resizeTOC(this)" title="maximize/restore list size">=</a>\s\n</div>\s\n';\n\nconfig.macros.tableOfContents.handler = function(place,macroName,params) { \n var parsedParams = new Array();\n parsedParams['label']=this.label;\n parsedParams['inline']=false;\n while (params.length>0) {\n if (params[0]=="label:none")\n parsedParams['label']="";\n else if (params[0].substr(0,6)=="label:")\n parsedParams['label']=params[0].substr(6);\n if (params[0].substr(0,7)=="prompt:")\n parsedParams['prompt']=params[0].substr(7);\n if (params[0].substr(0,8)=="padding:")\n parsedParams['padding']=params[0].substr(8);\n if (params[0].substr(0,7)=="margin:")\n parsedParams['margin']=params[0].substr(7);\n if (params[0].substr(0,5)=="sort:")\n parsedParams['sortby']=params[0].substr(5);\n if (params[0].substr(0,5)=="date:")\n parsedParams['date']=params[0].substr(5);\n if ((params[0]=="size:auto")||(params[0]=="size:0"))\n parsedParams['autosize']=true;\n else if (params[0] && (params[0].substr(0,5)=="size:"))\n parsedParams['requestedSize']=params[0].substr(5);\n if (params[0].substr(0,6)=="width:")\n parsedParams['width']=params[0].substr(6);\n if (params[0]=="hidelist")\n parsedParams['hidelist']=true;\n if (params[0]=="showtabs")\n parsedParams['showtabs']=true;\n if (params[0]=="inline")\n parsedParams['inline']=true;\n params.shift(); \n }\n setStylesheet(config.macros.tableOfContents.css,"tableOfContents");\n var newTOC=createTiddlyElement(place,parsedParams['inline']?"span":"div",null,"TOC",null)\n if (parsedParams['margin']) { newTOC.style.margin=parsedParams['margin']; }\n if (parsedParams['padding']) { newTOC.style.padding=parsedParams['padding']; }\n if (parsedParams['label']!="") newTOC.innerHTML=config.macros.tableOfContents.html.replace(/%label%/,parsedParams['label']);\n var newTOCList=createTOCList(newTOC,parsedParams)\n refreshTOCList(newTOCList);\n document.getElementById('sidebarTabs').style.display=(parsedParams['showtabs'])?"block":"none";\n if (!store.blanketNotifications.find(reloadTOCLists))\n store.addNotification(null,reloadTOCLists); // reload listbox after every tiddler change\n}\n\n// IE needs explicit global scoping for functions/vars called from browser events\nwindow.onChangeTOCList=onChangeTOCList;\nwindow.onDblClickTOCList=onDblClickTOCList;\nwindow.reloadTOCLists=reloadTOCLists;\nwindow.refreshTOCList=refreshTOCList;\nwindow.onClickTOCMenu=onClickTOCMenu;\nwindow.resizeTOC=resizeTOC;\n \nfunction createTOCList(place,params)\n{\n var theList = createTiddlyElement(place,"select",null,"TOCList",params['prompt'])\n theList.onchange=onChangeTOCList;\n theList.ondblclick=onDblClickTOCList;\n theList.style.display=config.options.chkTOCShow ? "block" : "none" ;\n theList.sortBy=config.options.txtTOCSortBy;\n theList.dateFormat="DD MMM YYYY";\n theList.requestedSize=config.options.txtTOCListSize;\n if (params['sortby'])\n { theList.sortBy=params['sortby']; theList.noSortCookie=true; }\n if (params['date'])\n { theList.dateFormat=params['date']; }\n if (params['autosize'])\n { theList.autosize=true; theList.noSizeCookie=true; }\n if (params['requestedSize'])\n { theList.requestedSize=params['requestedSize']; theList.noSizeCookie=true; }\n if (params['width'])\n { theList.style.width=params['width']; }\n if (params['hidelist'])\n { theList.style.display ="none" ; theList.noShowCookie=true; }\n return theList;\n}\n\nfunction onChangeTOCList()\n{\n var thisTiddler=this.options[this.selectedIndex].value;\n if ((this.size==1)&&(thisTiddler!=''))\n displayTiddler(document.getElementById('sidebar'),thisTiddler,0,null,null,false);\n refreshTOCList(this);\n return false;\n}\n\nfunction onDblClickTOCList()\n{\n var thisTiddler=this.options[this.selectedIndex].value;\n if (thisTiddler!='')\n displayTiddler(document.getElementById('sidebar'),thisTiddler,0,null,null,false);\n return false;\n}\n\nfunction reloadTOCLists()\n{\n var all=document.all? document.all : document.getElementsByTagName("*");\n for (var i=0; i<all.length; i++)\n if (all[i].className=="TOCList")\n { all[i].selectedIndex=-1; refreshTOCList(all[i]); }\n}\n\nfunction refreshTOCList(theList)\n{\n var selectedIndex = theList.selectedIndex;\n if (selectedIndex==-1) selectedIndex=0;\n var sortBy = theList.sortBy;\n\n if (selectedIndex==0) sortBy=theList.sortBy; // "nnn tiddlers" heading\n if (selectedIndex==1) sortBy='title';\n if (selectedIndex==2) sortBy='modified';\n if (selectedIndex==3) sortBy='modifier';\n if (selectedIndex==4) sortBy='tags';\n if (selectedIndex==5) sortBy='missing';\n if (selectedIndex==6) sortBy='orphans';\n if (selectedIndex==7) sortBy='system';\n if (selectedIndex>7)\n {\n if (theList.options[theList.selectedIndex].value=='')\n expandTOC(theList);\n return;\n }\n theList.sortBy = sortBy;\n if (!theList.noSortCookie)\n { config.options.txtTOCSortBy=sortBy; saveOptionCookie("txtTOCSortBy"); }\n\n // get the list of tiddlers\n var tiddlers = store.getTiddlers(sortBy);\n if (sortBy=="missing") tiddlers = store.getMissingLinks();\n if (sortBy=="orphans") tiddlers = store.getOrphans();\n if (sortBy=="tags") tiddlers = store.getTags();\n if (sortBy=="system")\n {\n tiddlers=new Array();\n var temp = store.getTaggedTiddlers("systemTiddlers");\n for (var t in temp) if (temp[t].title!=undefined) tiddlers.pushUnique(temp[t].title,true);\n var temp = store.getTaggedTiddlers("systemConfig");\n for (var t in temp) if (temp[t].title!=undefined) tiddlers.pushUnique(temp[t].title,true);\n for (var t in config.shadowTiddlers) tiddlers.pushUnique(t,true);\n tiddlers.sort();\n }\n\n var indent=String.fromCharCode(160)+String.fromCharCode(160);\n\n // clear current list contents\n while (theList.length > 0) { theList.options[0] = null; }\n theList.saved=null;\n\n // add heading and control items to list\n var i=0;\n var theHeading=tiddlers.length+' tiddlers:';\n if (sortBy=='missing') theHeading=tiddlers.length+' missing tiddlers:';\n if (sortBy=='orphans') theHeading=tiddlers.length+' orphaned tiddlers:';\n if (sortBy=='tags') theHeading=tiddlers.length+' tags:';\n if (sortBy=='system') theHeading=tiddlers.length+' system tiddlers:';\n theList.options[i++]=new Option(theHeading,'',false,false);\n theList.options[i++]=new Option(((sortBy=="title" )?">":indent)+' [by title]', '',false,false);\n theList.options[i++]=new Option(((sortBy=="modified")?">":indent)+' [by date]', '',false,false);\n theList.options[i++]=new Option(((sortBy=="modifier")?">":indent)+' [by author]','',false,false);\n theList.options[i++]=new Option(((sortBy=="tags" )?">":indent)+' [by tags]', '',false,false);\n theList.options[