72:
152:
threads which execute in parallel with the computational back end. Functionality such as zooming, rotation, playing and pausing simulations, setting colors and viewing cross sections is available through the player, with a sample screenshot shown below.
147:
CompuCell3D is conducive for experimentation and testing biological models by providing a flexible and extensible package, with many different levels of control. High-level steering is possible through CompuCell Player, an interactive GUI built upon
164:
which contribute to extensibility, reducing coupling between independently operating modules. Optional functionality can be encapsulated through plugins, which are dynamically loaded at runtime through an XML configuration file reference.
160:
Biologo, which after lexical analysis and generation transparently converts to C++ extensions which can be compiled and dynamically loaded at runtime. The back end uses object-oriented
120:) which can model cell clustering, growth, division, death, adhesion, and volume and surface area constraints; as well as partial differential equation solvers for modeling
195:
290:
240:
24:
215:
Swat, Maciej H.; Thomas, Gilberto L.; Belmonte, Julio M.; Shirinifard, Abbas; Hmeljak, Dimitrij; Glazier, James A. (2012).
51:
105:
35:
128:. By integrating these models CompuCell3D enables modeling of cellular reactions to external chemical fields such as
280:
173:
157:
125:
176:, and fluid flows. The binaries and source code, as well as documentation and examples, are available at the
121:
285:
108:
for simulations of biocomplexity problems, integrating multiple mathematical models. These include the
109:
256:
236:
246:
228:
113:
117:
71:
251:
232:
216:
161:
274:
168:
CompuCell3D can model several different phenomena, including avian limb development,
149:
182:
For a list of more than 150 publications that used CompuCell3D please visit the
141:
137:
133:
60:
129:
260:
183:
112:(CPM) or Glazier-Graner-Hogeweg model (GGH) (originally developed by
23:
177:
93:
156:
Extending the back end is possible through an XML-based
124:
of external chemical fields and cell type automata for
104:(CC3D) is a three-dimensional C++ and Python software
172:
capillary development, adhesion-driven cell sorting,
217:"Multi-Scale Modeling of Tissues Using CompuCell3D"
89:
81:
50:
34:
8:
16:
70:
22:
15:
250:
196:List of systems biology modeling software
207:
7:
233:10.1016/B978-0-12-388403-9.00013-8
14:
291:Scientific simulation software
1:
184:CompuCell3D Publications page
106:problem solving environment
307:
46:
30:
21:
174:Dictyostelium discoideum
158:domain-specific language
136:, and responses such as
94:https://compucell3d.org/
221:Methods in Cell Biology
116:, François Graner and
110:cellular Potts model
178:CompuCell3D Website
18:
122:reaction–diffusion
99:
98:
298:
265:
264:
254:
212:
114:James A. Glazier
74:
69:
66:
64:
62:
26:
19:
306:
305:
301:
300:
299:
297:
296:
295:
281:Systems biology
271:
270:
269:
268:
243:
214:
213:
209:
204:
192:
162:design patterns
126:differentiation
118:Paulien Hogeweg
77:
59:
42:
12:
11:
5:
304:
302:
294:
293:
288:
283:
273:
272:
267:
266:
241:
206:
205:
203:
200:
199:
198:
191:
188:
97:
96:
91:
87:
86:
85:C++ and Python
83:
79:
78:
76:
75:
56:
54:
48:
47:
44:
43:
40:
38:
36:Stable release
32:
31:
28:
27:
13:
10:
9:
6:
4:
3:
2:
303:
292:
289:
287:
286:Biosimulation
284:
282:
279:
278:
276:
262:
258:
253:
248:
244:
242:9780123884039
238:
234:
230:
226:
222:
218:
211:
208:
201:
197:
194:
193:
189:
187:
185:
180:
179:
175:
171:
166:
163:
159:
154:
151:
145:
143:
139:
135:
131:
127:
123:
119:
115:
111:
107:
103:
95:
92:
88:
84:
80:
73:
68:
58:
57:
55:
53:
49:
45:
39:
37:
33:
29:
25:
20:
224:
220:
210:
181:
169:
167:
155:
146:
101:
100:
67:/CompuCell3D
65:/CompuCell3D
227:: 325–366.
102:CompuCell3D
41:4.2.4.3
17:CompuCell3D
275:Categories
202:References
142:haptotaxis
138:chemotaxis
134:resorption
82:Written in
52:Repository
130:secretion
261:22482955
190:See also
170:in vitro
252:3612985
90:Website
259:
249:
239:
61:github
257:PMID
237:ISBN
140:and
63:.com
247:PMC
229:doi
225:110
132:or
277::
255:.
245:.
235:.
223:.
219:.
186:.
150:Qt
144:.
263:.
231::
Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
