The Genome Consortium for Active Teaching NextGen Sequencing Group

GCAT-SEEKquence

The Genome Consortium for Active Teaching
NextGen Sequencing Group

 

In the spirit of the original microarray-based Genome Consortium for Active Teaching (GCAT) founded by Malcolm Campbell at Davidson College, we are a group of educators who seek to incorporate new, massively-parallel sequencing technologies into the undergraduate curriculum to provide our students with a hands-on opportunity to apply these revolutionary cutting-edge tools to investigate biology

Current News! (News Archive)

February 1, 2013 - GCAT-SEEK Awarded grant from the National Science Foundation for Workshops during summers 2013-2017 - Award # 1248096 - RCN-UBE - GCAT-SEEK: The Genome Consortium for Active Undergraduate Research and Teaching Using Next-Generation Sequencing. Applications for the workshop were distributed through the listserve - Please be sure to join the listserve to keep up to date with GCAT-SEEK opportunities.

May 24, 2012 -
Juniata College was selected by Howard Hughes Medical Institute to receive a $1,000,000 award entitled, "The Genomics Leadership Initiative at Juniata College." (http://www.hhmi.org/news/hhmicolleges20120524.html).  Vince Buonaccorsi is serving as PI of the Hughes award and our research coordination network was seen as highly meritorious by reviewers... an effective vehicle for implementing change in undergraduate education.  

The network has received:

• funding for summer faculty development workshops for the network
• funding for a very brainy computer capable of assembling large Illumina datasets for our collective use
• support for some shared bioinformatics software (TBA)

Congratulations to Vince and Juniata College!

April 1, 2012 - Undergraduate student Jordan Krebs of Lycoming College won 1st place at the Pennsylvania Academy of Sciences Annual Meeting at Cedar Crest College for his GCAT-SEEK-based research presentation entitled, "Genome Sequencing of Lycomia zaccaria gen. nov. sp. nov., Chryseobacterium haifense, and Kaistella koreensis and Comparison to Two Closely Related Genomes."

October 6, 2011
A few GCAT-SEEK infrastructure improvements:

1. The commercial software company SoftGenetics
   our first commercial sponsor, has provided a single two year license for their NextGENe program for the network at nominal cost ($2.5K). It is easy to use and will allow users to focus more on the biology, less on the technical details of the tools. For purchasing an annual single user license, SoftGenetics will provide the network with its NextGENe software for the processing of the sequencing data as well as an unlimited number of 90 day local licenses of the NextGENe Viewer/Browser which permit undergraduates to review, edit, and develop both text and graphical reports of data that has been processed on a centralized computer. Once the data is processed, typical data sets can be reviewed with the NextGENe viewer on 32‐bit Desk Top systems.
   The scheme we envision for undergraduates is:
   1. Sequence data is made available to a central processing unit via ftp download, email, or ground mail on an external hard drive, depending upon data volume.
      
   2. Via remote desktop, student or faculty users initiate analysis via NextGENe software analysis pipeline tool, which allows sequential processing of data. The user selects the application of interest, data/sequencing platform used, sets analysis parameters, and directory location of finished analysis.
      
   3. Local users can then download completed analysis to their local machines for data review, filtering, and other tertiary analysis or report generation.
2. Juniata ordered a server for GCAT-SEEK (8K, 16 processors, 64GB RAM, 3TB Hard Drive with automatic backup) that will allow members to run (via remote desktop) programs including NextGene (or whatever else would be helpful) on a Windows operating system and have a workspace to temporarily store projects. This was bought with some of the NSF-RCN money and some endowed equipment money the JC Bio dept had. Once we get it running, the idea is that projects will queue if there is something already running, and be processed sequentially. It should quickly handle small (metagenomic, prokaryotic genome) and medium (eukaryotic transcriptome, RNAseq) sized problems, but is still insufficient for de Novo assembly of large eukaryotic genomes, for example. If you are writing grants for your research program, I would certainly write a letter of support regarding availability of these facilities.