
arXiv: 1404.0444
ANIMO (Analysis of Networks with Interactive MOdeling) is a software for modeling biological networks, such as e.g. signaling, metabolic or gene networks. An ANIMO model is essentially the sum of a network topology and a number of interaction parameters. The topology describes the interactions between biological entities in form of a graph, while the parameters determine the speed of occurrence of such interactions. When a mismatch is observed between the behavior of an ANIMO model and experimental data, we want to update the model so that it explains the new data. In general, the topology of a model can be expanded with new (known or hypothetical) nodes, and enables it to match experimental data. However, the unrestrained addition of new parts to a model causes two problems: models can become too complex too fast, to the point of being intractable, and too many parts marked as "hypothetical" or "not known" make a model unrealistic. Even if changing the topology is normally the easier task, these problems push us to try a better parameter fit as a first step, and resort to modifying the model topology only as a last resource. In this paper we show the support added in ANIMO to ease the task of expanding the knowledge on biological networks, concentrating in particular on the parameter settings.
FOS: Computer and information sciences, cs.CE, METIS-304060, parameter synthesis, Molecular Networks (q-bio.MN), q-bio.MN, Experimental data, Computational modeling, QA75.5-76.95, EWI-24659, FMT-TOOLS, Computational Engineering, Finance, and Science (cs.CE), biological networks, Electronic computers. Computer science, FOS: Biological sciences, QA1-939, Quantitative Biology - Molecular Networks, Computer Science - Computational Engineering, Finance, and Science, IR-91060, signal transduction, Mathematics
FOS: Computer and information sciences, cs.CE, METIS-304060, parameter synthesis, Molecular Networks (q-bio.MN), q-bio.MN, Experimental data, Computational modeling, QA75.5-76.95, EWI-24659, FMT-TOOLS, Computational Engineering, Finance, and Science (cs.CE), biological networks, Electronic computers. Computer science, FOS: Biological sciences, QA1-939, Quantitative Biology - Molecular Networks, Computer Science - Computational Engineering, Finance, and Science, IR-91060, signal transduction, Mathematics
| selected citations These citations are derived from selected sources. This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | 10 | |
| popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network. | Average | |
| influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | Average | |
| impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network. | Top 10% |
