Featured Research

from universities, journals, and other organizations

MSI Releases 'Moleculizer': A New Approach To Simulation Of Intracellular Biochemical Networks

Date:
January 10, 2005
Source:
The Molecular Sciences Institute
Summary:
The Molecular Sciences Institute has announced the release of a new approach to simulation of intracellular biochemical networks in the January edition of Nature Biotechnology. The research article, entitled "Automatic generation of cellular reaction networks with Moleculizer 1.0," describes MSI's discrete stochastic event simulator, which keeps track of the thousands of complex species formed from pathway proteins as it simulates reactions between them by a standard Monte Carlo method.

Berkeley, CA - January 6, 2005 - Dr. Roger Brent, President and Director of Research at the Molecular Sciences Institute (MSI), announced today the release of a new approach to simulation of intracellular biochemical networks in the January edition of Nature Biotechnology.

The research article, entitled "Automatic generation of cellular reaction networks with Moleculizer 1.0," describes MSI's discrete stochastic event simulator, which keeps track of the thousands of complex species formed from pathway proteins as it simulates reactions between them by a standard Monte Carlo method. A distinguishing aspect of Moleculizer is its ability to generate protein complexes and reactions as they are needed, as opposed to generating all potential complexes and reactions all at once, a task that requires tremendous computational resources.

"Moleculizer is a powerful tool that meets a very real need for biologists," explained Dr. Brent. "It is a critical step forward in our quest to provide an accurate simulation of intracellular biochemical networks."

"I've designed Moleculizer to be intuitive for biologists," said Dr. Larry Lok, a mathematician who conceived and programmed Moleculizer. "Its parallel simplifications in simulation setup and output provide data in a way that is meaningful and useful to biological researchers."

Moleculizer was developed in the context of MSI's "Alpha Project", an ambitious experimental and computational effort to understand the quantitative behavior of a cell signaling pathway in yeast. The Alpha Project is funded by the National Institutes of Health's National Human Genome Research Institute, which designated MSI as a Center of Excellence in Genomic Research. The CEGS program supports multi-investigator, interdisciplinary research teams to develop novel and innovative genomic research projects.

"Moleculizer is exactly the sort of development that one wants to see from multidisciplinary work," explained Dr. Brent. "The mathematical and algorithmic skills that Dr. Lok brought to the problem could only come from one with his strengths, but the work is important because it addresses a problem arising directly from the biology."

Dr. Daniel Gillespie, a pioneer in stochastic methods for modeling chemical kinetics stated, "Dr. Lok has succeeded in adapting and creatively extending earlier developed techniques for stochastically simulating chemical reactions so that they can be used to study real cellular systems, where the huge numbers of potential species and reaction channels makes things very difficult."

Computer simulations can be powerful tools in contemporary molecular biology research, aiding scientists in analyzing data and in testing hypotheses with simulated outcomes before testing them experimentally. The predictive capabilities of computer simulations can also aid biologists in viewing cellular activity over a period of time, by taking advantage of the power of computers to generate the thousands of potential protein complexes and reactions that cells are able to generate.

The Molecular Sciences Institute is an independent nonprofit research laboratory that combines genomic experimentation with computer modeling. Work at MSI aims to weave physics, engineering, computer science, and mathematics together with biology and chemistry to enable precise, quantitative, prediction of the future behaviors of biological systems.

In keeping with the MSI's support for an open source biology, Moleculizer will be made freely available under the GNU Lesser General Public License.

Nature Biotechnology is "a monthly journal covering the science and business of biotechnology. It publishes new concepts in technology/methodology of relevance to the biological, biomedical, agricultural and environmental sciences as well as covers the commercial, political, ethical, legal, and societal aspects of this research."


Story Source:

The above story is based on materials provided by The Molecular Sciences Institute. Note: Materials may be edited for content and length.


Cite This Page:

The Molecular Sciences Institute. "MSI Releases 'Moleculizer': A New Approach To Simulation Of Intracellular Biochemical Networks." ScienceDaily. ScienceDaily, 10 January 2005. <www.sciencedaily.com/releases/2005/01/050110115414.htm>.
The Molecular Sciences Institute. (2005, January 10). MSI Releases 'Moleculizer': A New Approach To Simulation Of Intracellular Biochemical Networks. ScienceDaily. Retrieved August 2, 2014 from www.sciencedaily.com/releases/2005/01/050110115414.htm
The Molecular Sciences Institute. "MSI Releases 'Moleculizer': A New Approach To Simulation Of Intracellular Biochemical Networks." ScienceDaily. www.sciencedaily.com/releases/2005/01/050110115414.htm (accessed August 2, 2014).

Share This




More Computers & Math News

Saturday, August 2, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Google Mystery Barge Headed For The Scrap Yard

Google Mystery Barge Headed For The Scrap Yard

Newsy (Aug. 1, 2014) We may never know what was going on inside one of Google's mystery barges in Portland, Maine as it's now headed for the scrap yard. Video provided by Newsy
Powered by NewsLook.com
Escaping Email: Inspired Vision or Pipe Dream?

Escaping Email: Inspired Vision or Pipe Dream?

AP (Aug. 1, 2014) Dustin Moskovitz is plotting an escape from email, using his communications expertise in an attempt to change the way people connect at work, where the incessant drumbeat of email has become an excruciating annoyance. (Aug. 1) Video provided by AP
Powered by NewsLook.com
Google (Kind Of) Complies With 'Right To Be Forgotten Law'

Google (Kind Of) Complies With 'Right To Be Forgotten Law'

Newsy (July 31, 2014) Google says it is following Europe's new "Right To Be Forgotten Law," which eliminates user information upon request, but only to a certain degree. Video provided by Newsy
Powered by NewsLook.com
Tesla, Panasonic Ink Deal To Make Huge Battery 'Gigafactory'

Tesla, Panasonic Ink Deal To Make Huge Battery 'Gigafactory'

Newsy (July 31, 2014) The deal will help build a massive battery factory that Tesla says will produce 500,000 lithium batteries by 2020. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins