Posted by endy

It's been three years since the BIOFAB Emeryville pilot project completed. Most of the original data links and servers are now broken or inoperable and cannot be easily fixed. Here is a world-readable external link [hosted by Google] to all our sequence and activity data files:

All data and work products from BIOFAB Emeryville remain now and forever public domain.

Posted by Vivek_Mutalik

Palo Alto and Berkeley, Calif. – March 10, 2013 An unprecedented collaboration among academia, industry, government and civil society has resulted in the launch of a professional-grade collection of public domain DNA parts that greatly increases the reliability and precision by which biology can be engineered.

Posted by kcosta

BIOFAB has developed a method that allows for reliable functional coupling of prokaryotic transcription and translation control elements with user-specific coding sequences for genes of interest. The BIOFAB team engineered a collection of standard biological parts that implements the method across a range of transcription and translation levels, and with native and also a phage RNA polymerase. For the genes tested in the system so far, BIOFAB achieved >90% predictability of gene expression to within a two-fold protein concentration of the target window. Team Leader Vivek Mutalik announced the work during Cambridge Healthtech Institute's Third Annual Engineering Genes, Vectors, Constructs and Clones Conference on January 9, 2012.

Posted by kcosta

DNA2.0 today announced that the first collection of biological building blocks characterized by the BIOFAB International Open Facility Advancing Biotechnology (BIOFAB) are now available for use in the design and assembly of genes within DNA2.0’s Gene Designer software. The free-to-use BIOFAB genetic parts are distributed as virtual sequences in the newly minted gene marketplace embedded within DNA2.0’s gene design and assembly application. This “app store” for molecular biology and biotechnology provides scientists and bioengineers access to powerful preassembled and validated DNA elements for making genetic constructs with Gene Designer. DNA2.0 becomes the first commercial vendor to provide access—through a few clicks of a mouse—to the initial collection of biological parts developed by BIOFAB.

Posted by kcosta

We'll hold an ad hoc BIOFAB Community Meeting this Saturday 18 June 2011 at Stanford, immediately following SB5.0. The meeting will commence at Stanford’s Y2E2 Building, Room 299. Coffee will be available at 8:30, we’ll start at 9. The building address is 473 Via Ortega, Stanford CA 94305. Free parking is available right next to building.

Posted by kcosta

Following a discussion by the workgroup for Data Standards in Synthetic Biology, which met in June 2010 during the Second Workshop on Biodesign Automation, several participants (including a number of BIOFAB and SynBERC investigators) published a Nature Biotechnology letter to the editor arguing that articles reporting synthetic gene networks should always disclose the complete sequence of all constructs described. They note that without such information, it is challenging if not impossible to reproduce and build upon others' work, which is a central tenet of the engineering of biology. The full letter, entitled "Essential information for synthetic DNA sequences" and published January 10, 2011, is at Nature Biotechnology.

Posted by kcosta

SynBERC investigators Drew Endy and Vivek Mutalik represented the BIOFAB: International Open Facility Advancing Biotechnology at the BIO Pacific Rim Summit on December 12, 2010 in Honolulu, Hawaii. The very specialized workshop on advancements in synthetic biology was open to all attendees of the large annual meeting focused on Industrial Biotechnology and Bioenergy. Endy, Mutalik, and BioBricks Foundation Executive Director Holly Million highlighted the BIOFAB's progress toward producing thousands of free, standardized DNA parts.

The first BIOFAB Community Meeting took place on July 19-20, 2010 at the Joint BioEnergy Institute in Emeryville, CA. The BIOFAB welcomed interested users from SynBERC and the broader synthetic biology community to participate in the day and a half meeting that brought together international experts to help us respond to needs in technical development, open innovation, and social ramifications of standardized biology.

Webcast: Day one

Webcast: Day two

The BIOFAB has produced the first in a series of Human Practices reports on scientific, organizational, and political topics central to responsibly fulfilling its core operational mandates. The first report takes up the question “What is a part?” in biology. The report overviews foundational questions that animate the BIOFAB’s research program, interfacing those questions with a range of strategic opportunities and challenges.

Posted by kcosta

The BIOFAB's first datasheet provides information about three previously uncharacterized promoters that we obtained from the MIT Registry of Standard Biological Parts. We will use such datasheets to formally capture and share information about the parts that we build and characterize (see Canton et. al., 2008). We hope that all users, ranging from theoretical biophysicists to highschool students, will help us to develop quality measurements based upon their needs and application. An understanding of quality will help to define specific objectives for the build-out of our operational capacities.