The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks
Abstract
Understanding of the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed a modeling/simulating tool called CellDesigner. CellDesigner primarily has capabilities to visualize, model, and simulate gene-regulatory and biochemical networks. Two major characteristics embedded in CellDesigner boost its usability to create/import/export models: 1) solidly defined and comprehensive graphical representation (systems biology graphical notation) of network models and 2) systems biology markup language (SBML) as a model-describing basis, which function as intertool media to import/export SBML-based models. In addition, since its initial release in 2004, we have extended various capabilities of CellDesigner. For example, we integrated other systems biology workbench enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, supported by integration with SBML ODE Solver, enabling users to simulate through our sophisticated graphical user interface. Users can also browse and modify existing models by referring to existing databases directly through CellDesigner. Those extended functions empower CellDesigner as not only a modeling/simulating tool but also an integrated analysis suite. CellDesigner is implemented in Java and thus supports various platforms (i.e., Windows, Linux, and MacOS X). CellDesigner is freely available via our Web site.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Using process diagrams for the graphical representation of biological networks
Kitano, H., Funahashi, A., Matsuoka, Y., & Oda, K. (2005) · Nature Biotechnology · doi:10.1038/nbt1111 · Cited by 483
Self-citation
Cited by
The systems biology graphical notation.
Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1558 · Cited by 903
Self-citationBioModels—15 years of sharing computational models in life science
Malik-Sheriff, R. S., Glont, M., Nguyen, T. V. N., Tiwari, K., Roberts, M. G., Xavier, A., Vu, M. T., Men, J., Maire, M., Kananathan, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1055 · Cited by 361
Gama-Castro, S., Salgado, H., Peralta-Gil, M., Santos-Zavaleta, A., Muniz-Rascado, L., Solano-Lira, H., Jimenez-Jacinto, V., Weiss, V., Garcia-Sotelo, J. S., Lopez-Fuentes, A., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1110 · Cited by 353
GSK3 and p53 - is there a link in Alzheimer's disease?
Proctor, C. J., & Gray, D. A. (2010) · Molecular Neurodegeneration · doi:10.1186/1750-1326-5-7 · Cited by 80
“Figure 3E shows the mean levels and standard deviations from 100 simulations and it can be seen that this is similar to the results of a deterministic simulation (see Figure 3F) using Cell Designer [32].”
ResultJSBML 1.0: providing a smorgasbord of options to encode systems biology models
Rodriguez, N., Thomas, A., Watanabe, L., Vazirabad, I. Y., Kofia, V., Gómez, H. F., Mittag, F., Matthes, J., Rudolph, J., Wrzodek, F., et al. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv341 · Cited by 37
Metadata
- Authors
- Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N., & Kitano, H.
- Venue
- Proceedings of the IEEE
- Published
- 2008-08
- Volume
- 96
- Issue
- 8
- Pages
- 1254-1265
- ISSN
- 0018-9219 (ISSN-L)
- 1558-2256
- OpenAlex
- W2038264484
- Cited by
- 464
- References
- 1
- FWCI
- 8.81
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. https://app.cochat.ai/papers/10.1109/jproc.2008.925458
- The paper
- Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N., & Kitano, H. (2008). CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. Proceedings of the IEEE. https://doi.org/10.1109/jproc.2008.925458
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
