Navigation Links
Tips on how to build a better home for biological parts
Date:7/16/2008

Blacksburg, Va. Researchers at the Virginia Bioinformatics Institute (VBI) at Virginia Tech have compiled a series of guidelines that should help researchers in their efforts to design, develop and manage next-generation databases of biological parts. The stakes are high: the concept of biological parts is essential if methods developed in other fields of engineering are to be applied to biology. If successful, this approach will result in significant productivity gains for the biotechnology industry. The findings of the research, published in the Public Library of Science's open-access journal PLoS One, arose from a systematic analysis of the Registry of Standard Biological Parts, the most well developed collection of biological parts currently available to the synthetic biology research community.

Jean Peccoud, associate professor at the Virginia Bioinformatics Institute, remarked: "Our research group is very interested in providing the wider research community with design automation tools that will facilitate the engineering of biological systems. We needed to take a close look at the Registry of Standard Biological Parts in order to understand how GenoCAD, the platform we are developing to build and verify complex genetic constructs, should interface with this important community resource. In this process, we came to understand that repositories of biological parts represent a new generation of bioinformatics databases that pose a number of original and very interesting challenges." He added: "We believe that articulating the issues associated with these resources will help improve existing databases of biological parts. It will also assist in the development of new collections of parts for specialized applications such as bioenergy or biodefense."

The Registry of Standard Biological Parts is a publicly available resource and the focal point of the annual International Genetically Engineered Machine (iGEM) competition. iGEM undergraduate students engineer novel biological systems starting from BioBricks, the parts documented in the Registry of Standard Biological Parts. The BioBrick is an emerging standard for DNA fragments that facilitates the assembly of biological parts into more complex devices and systems by using a standardized fabrication process. The entire collection of parts associated with the Registry is distributed to all teams enrolled in the iGEM competition. The iGEM participants are expected to return the designs they made to the Registry at the end of the competition.

The new study by VBI researchers not only examined the information content of the Registry database but also the collection of publicly available DNA sequences or clones (BioBricks) that are used to make the biological devices and systems. The analysis of the Registry database and the associated DNA clones identified several key needs where improvements could be made. These included the following: (a) to distinguish basic parts and composite parts that can be broken down into smaller parts; (b) to set curation standards to document the sequences of basic parts by associating them with entries in bioinformatic or bibliographic databases; (c) to define and implement quality control standards that ensure the integrity of DNA clones; and (d) to provide editorial policies that could help build registries of biological parts with high-value and high-quality content.

Peccoud concluded: "The Registry of Standard Biological Parts has been a pioneering experiment for the synthetic biology community and lessons should be learned to improve this resource and design the next-generation registries of biological parts. This bottom-up approach to biology raises a number of challenging theoretical questions. Defining what is a biological part, for example, remains a problem that the entire synthetic biology community needs to solve. In this respect, recent initiatives led by the BioBrick foundation and others to organize forums that define technical standards for biological parts appear to be very timely and laudable."


'/>"/>

Contact: Barry Whyte
whyte@vbi.vt.edu
540-231-1767
Virginia Tech
Source:Eurekalert

Related biology news :

1. Building blocks of life
2. Researchers create system to build transplant tissue
3. New approach builds better proteins inside a computer
4. Rebuilding the evolutionary history of HIV-1 unravels a complex loop
5. Building blocks of life formed on Mars
6. Building disease-beating wheat
7. CSIC and UAB will build the most advanced superconductor cable for electricity network
8. GM, Coskata partnership builds on Oklahoma State University biofuels research
9. Building the future -- 21st century nano tools to repair the nervous system
10. Scientists rebuild ancient proteins to reveal primordial Earths temperature
11. International workshop to address capacity building for rainforest leaders
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/2/2016)... --  The Weather Company , an IBM Business (NYSE: ... in which consumers will be able to interact with IBM ... voice or text and receive relevant information about the product ... have long sought an advertising solution that can create a ... and valuable; and can scale across millions of interactions and ...
(Date:5/16/2016)... , May 16, 2016   EyeLock LLC , ... announced the opening of an IoT Center of Excellence ... and expand the development of embedded iris biometric applications. ... level of convenience and security with unmatched biometric accuracy, ... identity aside from DNA. EyeLock,s platform uses video technology ...
(Date:4/28/2016)... , April 28, 2016 First quarter 2016: ... up 966% compared with the first quarter of 2015 ... SEK 589.1 M (loss: 18.8) and the operating margin was 40% ... 0.32) Cash flow from operations was SEK 249.9 M ... revenue guidance is unchanged, SEK 7,000-8,500 M. The operating ...
Breaking Biology News(10 mins):
(Date:6/24/2016)... 2016  Regular discussions on a range of subjects including ... two entities said Poloz. Speaking at a lecture ... , he pointed to the country,s inflation target, which is ... "In certain areas there ... common economic goals, why not sit down and address strategy ...
(Date:6/24/2016)... (PRWEB) , ... June 24, 2016 , ... Researchers at ... most commonly-identified miRNAs in people with peritoneal or pleural mesothelioma. Their findings are the ... read it now. , Diagnostic biomarkers are signposts in the blood, lung fluid ...
(Date:6/23/2016)...   Boston Biomedical , an industry leader ... target cancer stemness pathways, announced that its lead ... Designation from the U.S. Food and Drug Administration ... gastroesophageal junction (GEJ) cancer. Napabucasin is an orally ... stemness pathways by targeting STAT3, and is currently ...
(Date:6/23/2016)... Houston Methodist Willowbrook Hospital has signed ... to serve as their official health care provider. ... will provide sponsorship support, athletic training services, and ... volunteers, athletes and families. "We are ... and to bring Houston Methodist quality services and ...
Breaking Biology Technology: