Featured Research

from universities, journals, and other organizations

Setting The Standard For Computer Models Of Life

Date:
December 6, 2005
Source:
European Molecular Biology Laboratory
Summary:
In the December 6 issue of Nature Biotechnology, scientists from 14 different organizations around the world, including the EMBL-European Bioinformatics Institute, propose a new quality standard for biochemical models. MIRIAM (for Minimum information requested in the annotation of biochemical models) will help researchers to reuse, modify and combine computer models of biochemical processes to gain a fuller understanding of life at the molecular and cellular level.

Biologists are making a concerted effort to catalogue all the molecular components of living things, from the smallest molecules and ions to the genetic code. These 'parts lists' help them to build computer models that simulate living processes. By combining models of simple processes they hope to understand and faithfully represent how entire biological systems - be they cells, organs, organisms or ecological niches - work. As well as contributing to the understanding of biology, this approach has numerous applications: for example, diseases can be simulated, and treatment regimens optimised.

"The computational systems biology community has made enormous progress in improving access to models," explains the EMBL-EBI's Nicolas Le Novθre, lead author of the paper. "We've begun to share programming languages for encoding them (e.g. systems biology markup language, www.sbml.org) and to build public repositories so we can share them (e.g. www.ebi.ac.uk/biomodels). The current challenge is quality control: systems biologists won't use publicly available models if they can't search them properly, of if a model's reuse is hampered by a tiny mistake in the way that it's encoded. MIRIAM is an attempt to address these issues."

MIRIAM has two parts: (1) a set of checks that match a model to its description ('reference correspondence', often a publication in a scientific journal), and (2) a set of 'annotation schemes'. The first of these documents the model's provenance: who created it, whether it's been modified, and a stable link to its full description; the second scheme links the components of the model to relevant bioinformatics resources: for example, a model of alcohol metabolism in the liver would be annotated with links to the protein databases for all the enzymes involved in this pathway, and database links to all the relevant metabolites. The aim of these annotation schemes is to make it easier for researchers to search models on the basis of their components, to contact the creators of the model if they need more information, and to track the history of a model if it has been modified.

MIRIAM's creators include representatives of four major repositories for models (BioModels Database, CellML Model Repository, DOQCS and SigPath), all of which are now in the process of making the models in their repositories MIRIAM compliant. "By adopting MIRIAM as a voluntary code of conduct, we will be able to provide our users with a reasonable level of quality assurance, so they'll be able to get on with the business of generating and testing new hypotheses instead of recoding someone else's old hypothesis," continues Le Novθre. "We also hope that journal editors will adopt MIRIAM as a quality control measure for papers that describe models. This approach has worked very well for other fields - for example the microarray community, by enabling authors, publishers and data providers to work together to improve access to meaningful biological information."

###

Source Article: N. Le Novθre et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol., 6 December 2005


Story Source:

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


Cite This Page:

European Molecular Biology Laboratory. "Setting The Standard For Computer Models Of Life." ScienceDaily. ScienceDaily, 6 December 2005. <www.sciencedaily.com/releases/2005/12/051206164025.htm>.
European Molecular Biology Laboratory. (2005, December 6). Setting The Standard For Computer Models Of Life. ScienceDaily. Retrieved August 2, 2014 from www.sciencedaily.com/releases/2005/12/051206164025.htm
European Molecular Biology Laboratory. "Setting The Standard For Computer Models Of Life." ScienceDaily. www.sciencedaily.com/releases/2005/12/051206164025.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