Navigation Links
New method for estimating parameters may boost biological models
Date:3/6/2012

Modeling biological systems can provide key insights for scientists and medical researchers, but periodic cycles that repeat themselves so-called oscillatory systems pose some key challenges. Researchers at North Carolina State University have developed a new method for estimating the parameters used in such models which may advance modeling in research areas ranging from cancer to fertility.

"These oscillatory systems are found in everything from mechanisms in cells that allow a cell to replicate itself to the sleep-wake cycle in mammals," says Dr. Cranos Williams, an assistant professor of electrical and computer engineering at NC State and co-author of a paper describing the work. "The method we've developed should expedite the development of more accurate parameters, which can be used to create more precise and predictable models of oscillatory biological systems." Understanding such oscillatory systems is important for research into cancer, cardiac health, fertility and many other fields, he adds.

Modeling a biological system relies, in part, on defining parameters for that system, which correspond to how the system functions under normal conditions. Once those parameters are established, they can be used to create a model to predict the system's response under different conditions.

To estimate parameters in simpler systems, researchers measure the concentration of the system's components. In a cell, for example, researchers would measure the concentration of its proteins, among other things. Researchers then try to identify the parameters that would result in the closest 'fit' to those concentrations when plugged into the model.

A measure known as an objective function is used to quantify the quality of the 'fit' to the measured concentrations. Simple systems often result in an objective function that looks like a bowl, with the lowest point of the bowl corresponding to the parameters that provide the best or "optimal" fit. All other parameter values correspond to higher points that arc up from the bottom of the bowl. These points correspond to increasingly poor matches to the measured component concentrations as you move further away from the bottom. Robust optimization routines are well adapted to sliding down the sides of these mathematical bowls to identify a functional set of parameters corresponding to the best fit. It can be virtually impossible to identify the optimal set of parameters, but you can often get very close.

But the cyclical nature of oscillatory systems makes it difficult to identify this functional set of parameters, even when using the most robust optimization routines. This is because the repetitive nature of these systems transforms the bowl into something that looks more like a mountain range, with many hills and valleys. This makes it more complicated and time-consuming to work your way toward accurate parameters.

Since these oscillatory systems present a problem for most optimization algorithms, Williams and NC State Ph.D. student Seyedbehzad Nabavi focused on developing methods that would manipulate the surface characteristics of the objective function itself. This new approach factors in the frequency of the concentrations within the system or how often each concentration is repeated to generate a new objective function that mitigates the impact of system oscillations.

"By generating a new objective function that factors in the frequency of the system oscillations, we are able to eliminate many of the hills and valleys, resulting in a surface with the same optimal point, but that is easier to search," Williams says. "This makes it easier for optimization routines to identify a functional working set of parameters that can then be used to predict the activity of the modeled system."

The paper, "A Novel Cost Function for Parameters Estimation in Oscillatory Biochemical Systems," will be presented at the IEEE SoutheastCon in Orlando, Fla., March 15-18. Nabavi is lead author on the paper.


'/>"/>

Contact: Matt Shipman
matt_shipman@ncsu.edu
919-515-6386
North Carolina State University
Source:Eurekalert  

Related biology news :

1. More effective method of imaging proteins
2. New methods for better purification of wastewater
3. New 3-D stem cell culture method published in JoVE
4. New method for stronger dental implants
5. Noninvasive method accurately and efficiently detects risk of Down syndrome
6. Researchers develop new method for creating tissue engineering scaffolds
7. New methodology assesses risk of scarce metals
8. Powerful drugs surprising, simple method could lead to better treatments
9. ISU scientist helps find structure of gene-editing protein named Method of the Year
10. Penn scientists pioneer new method for watching proteins fold
11. Researchers develop new method of cleaning toxins from the oilsands
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
New method for estimating parameters may boost biological models
(Date:4/11/2017)... 11, 2017 NXT-ID, Inc. (NASDAQ:   ... announces the appointment of independent Directors Mr. Robin D. ... Board of Directors, furthering the company,s corporate governance and expertise. ... Gino Pereira , ... forward to their guidance and benefiting from their considerable expertise ...
(Date:4/4/2017)... NEW YORK , April 4, 2017   ... solutions, today announced that the United States Patent and ... The patent broadly covers the linking of an iris ... the same transaction) and represents the company,s 45 th ... our latest patent is very timely given the multi-modal ...
(Date:3/29/2017)... , March 29, 2017  higi, the health ... in North America , today announced ... and the acquisition of EveryMove. The new investment and ... set of tools to transform population health activities through ... lifestyle data. higi collects and secures data ...
Breaking Biology News(10 mins):
(Date:10/12/2017)... Diego, CA (PRWEB) , ... ... ... (https://www.onramp.bio/ ) has launched Rosalind™, the first-ever genomics analysis platform specifically ... all bioinformatics complexity. Named in honor of pioneering researcher Rosalind Franklin, who ...
(Date:10/11/2017)... ... October 11, 2017 , ... The ... endogenous context, enabling overexpression experiments and avoiding the use of exogenous expression plasmids. ... is transformative for performing systematic gain-of-function studies. , This complement to loss-of-function ...
(Date:10/11/2017)... ... 2017 , ... ComplianceOnline’s Medical Device Summit is back for its 4th year. ... San Francisco, CA. The Summit brings together current and former FDA office bearers, regulators, ... government officials from around the world to address key issues in device compliance, quality ...
(Date:10/11/2017)... -- VMS BioMarketing, a leading provider of patient support solutions, has ... (CNE) network, which will launch this week. The VMS CNEs ... professionals to enhance the patient care experience by delivering peer-to-peer ... care professionals to help women who have been diagnosed and ... ...
Breaking Biology Technology: