Test document — synVI paper

Welcome to the Sc2.0 sandbox. WeSynVI manuscript V12’d like this to be a place to post Q&A and protocols and basically anything useful to the Sc2 community.
For example, there are 7 papers in late stages of development we’d like to share. This would be a great place to put them for comments!

Build-a-Genome Network Workshop, Aug 14-16 Loyola University Maryland, Baltimore MD

The Build-a-Genome (BAG) course offers undergraduate students an exceptional opportunity to participate in the cutting-edge research of the Synthetic Yeast Project. BAG offers students an authentic laboratory experience where they perform fundamental techniques in synthetic genomics, present and critique their data, and troubleshoot experiments until successful. By completion of the course, students who worked on synthetic chromosome III became so fluent in molecular and synthetic biology techniques that they produced numerous synthetic chromosome “building blocks” and earned authorship on that milestone research paper. After being established at Johns Hopkins University, BAG franchises were established at Loyola University Maryland and Tianjin University in China. Thanks to funding from the National Science Foundation RCN-UBE program, the Build-a-Genome Network has now been established with the goal of broadening the number of colleges and universities that offer the BAG course.

A national workshop for the Build-a-Genome Network will be held from August 14th to 16th at Loyola University Maryland in Baltimore. This meeting will:

(1) Introduce new members to the Synthetic Yeast Project and the BAG workflow through a series of talks, hands-on bioinformatics exercises, and wet-lab activities.
(2) Discuss strategies for adapting the BAG course to diverse undergraduate institutions. We seek to preserve the most attractive features of the BAG course while confronting the logistical hurdles that may arise when implementing research-intensive courses at undergraduate institutions.
(3) Develop course learning objectives and assessment tools for different variations of the BAG course.

These activities will create a network of expertise and “ready-to-implement” frameworks, both of which will allow network participants to implement the BAG curriculum (or similar synthetic genomics projects) at a broad range of academic institutions. For more information please contact Rob Newman (rhnewman@ncat.edu), Eric Cooper (ecooper@hartwick.edu), or Lisa Scheifele (lzscheifele@loyola.edu).

First SAVI-sponsored joint US-China paper on Sc2.0 published

Two graduate students from Tianjin University, Qiuhui Lin and Jia Bin, from the laboratory of Yingjin Yuan at Tianjin University traveled to Johns Hopkins University where they worked in the lab of Jef Boeke for several months, in an effort to exchange scientific information, and develop new methods.  Working with postdoctoral fellow Leslie Mitchell and graduate students Jingchuan Luo and Zhuwei Xu they developed efficient and standardized methods for assembling “Minichunks” of 2.5-4 kb, stringing together Building Blocks previously made by JHU “Build A Genome” students. Then the “RADOM” method, which produces up to 10 kb fragments “in yeasto”, used the Build A Genome Class, led by Karen Zeller, as a testbed, and the workflow was implemented in BioStudioDb by Kun Yang.  The work is published in ACS SynBio and sponsored by the NSF SAVI program..
The RADOM method

The RADOM method