IEEE Transactions on Computational Biology and Bioinformatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) is a bimonthly journal that publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology. Read the full scope of TCBB
IEEE Transactions on Computational Biology and Bioinformatics (TCBB) will move to the OnlinePlus publication model starting with 2015 issues!
From the March/April 2015 Issue
ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes
By Yongguo Mei, Adria Carbo, Stefan Hoops, Raquel Hontecillas, and Josep Bassaganya-Riera
Modeling and simulations approaches have been widely used in computational biology, mathematics, bioinformatics and engineering to represent complex existing knowledge and to effectively generate novel hypotheses. While deterministic modeling strategies are widely used in computational biology, stochastic modeling techniques are not as popular due to a lack of user-friendly tools. This paper presents ENISI SDE, a novel web-based modeling tool with stochastic differential equations. ENISI SDE provides user-friendly web user interfaces to facilitate adoption by immunologists and computational biologists. This work provides three major contributions: (1) discussion of SDE as a generic approach for stochastic modeling in computational biology; (2) development of ENISI SDE, a web-based user-friendly SDE modeling tool that highly resembles regular ODE-based modeling; (3) applying ENISI SDE modeling tool through a use case for studying stochastic sources of cell heterogeneity in the context of CD4+ T cell differentiation. The CD4+ T cell differential ODE model has been published  and can be downloaded from biomodels.net. The case study reproduces a biological phenomenon that is not captured by the previously published ODE model and shows the effectiveness of SDE as a stochastic modeling approach in biology in general and immunology in particular and the power of ENISI SDE.
Editorials and Announcements
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- TCBB celebrates its 10th Anniversary. Editor-in-Chief Ying Xu says, "The emergence and maturation of increasingly more and powerful molecular measurement technologies such as next generation sequencing and chromosome conformation capture allow scientists to tackle biological problems at the depth and breadth that we have never seen before. At the same time the enormity and complexity of the data generated using these technologies raised tremendous challenges to computational scientists to develop more effective techniques to store, transmit, organize, process, analyze and mine the data, and to construct models to assist interpreting the data. Since its creation ten years ago, TCBB has been playing a major role in bridging the world of computing and the world of biology. I want to congratulate what the journal has done in providing biologists with the most powerful computational tools to help address their data and modeling needs. I fully expect that TCBB will continue to play increasingly significant roles in attracting more computational scientists to address the ever increasing needs for new and more powerful computational techniques and to introduce to new comers the important and challenging computational biology problems in a timely fashion."
- Subscribe to TCBB in 2014. Click for more information. (PDF)
- Editorial from the Editor-in-Chief by Y. Xu (January/February 2015)
- Reviewer Appreciation Editorial by Y. Xu (July/August 2014)
- EIC Editorial by M.-F. Sagot (March/April 2011)
- EIC Editorial by M.-F. Sagot (January/February 2011)
- Special Section on BIBM 2013 (March/April 2015)
- Selected Papers from ACM-BCB 2013 (Jan/Feb 2015)
- Special Section on BIOKDD2013 (Sept/Oct 2014)
- 12th Asia Pacific Bioinformatics Conference (July/August 2014)
- Pattern Recognition in Bioinformatics (May/June 2014)
- Special Section on Bioinformatics Research and Applications (May/June 2014)
- Bioinformatics and Computational Systems Biology (July/August 2012)
- High Performance Computational Systems Biology (May/June 2012)
- Special Section on Bioinformatics Research and Applications (July/August 2011)
- Special Focus on Bioinformatics and Systems Biology (March/April 2011)
- Special Section on Bioinformatics Research and Applications (Oct-Dec 2010)
Call for Papers
- Special Issue on Big Data Processing in Computational Biology and Bioinformatics (PDF)
Submission Deadline: April 20, 2015
- Special Issue on Emerging Security Trends for Biomedical Computations, Devices, and Infrastructures (PDF)
Submission Deadline: August 15, 2015
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TCBB is a joint publication of the IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.
Published in cooperation with: IEEE Control Systems Society
Indexed in MEDLINE®/PubMed® & ISI