Charleston Computational Genomics Group

The goal of the Charleston Computational Genomics Group or C2G2 is to develop infrastructure and methodology to efficiently analyze genomic and bioinformatic data with the express purpose of training undergraduate students to excel as scientists, software engineers, computer scientists, and bioinformaticians.

Cluster Status
C2G2 portal is online. If you encounter technical difficulties please let us know.

Objectives

 * 1) Build cyberinfrastructure for Charleston area genomics and bioinformatics projects
 * 2) Develop novel software and algorithms for data mining, data acquisition, data storage, data management, data integration, data mining, data visualization.
 * 3) Train students in the genomic and bioinformatic sciences to be utilized at local and foreign institutions.
 * 4) Collaborate with Charleston area scientists studying genomic medicine, genome theory, gene expression, marine genomics, etc.

About

 * C2G2 is an academic group. Our primary interests are scientific discovery, algorithm and software research, and education.


 * It is our goal to provide opportunities and resources for collaboration and education between a diverse group of researchers in the Charleston area.


 * One of the benefits of being academics is that we can pursue projects for our interest and satisfaction. A good analogy is that we are building a car for computational genomics. But like any good car, it occasionally needs work and upgrades. Specifically, we ask that you consider adding in student bioinformatics support into your grants. These students work hard to provide the tools and support needed to run the analyses, and providing them with student employment through the year makes a big difference in their development and engagement. We also ask that you consider adding cloud storage to your grants.

People
The PI for the project is Paul Anderson of the College of Charleston Computer Science Department. Co-PIs are Andrew Shedlock of the College of Charleston Biology Department and Dennis Watsonof MUSC's Department of Pathology and Laboratory Medicine. Other members of the team are Starr Hazard, who handles MUSC's cluster and computation, Bob Wilson, Director of the Genomics Core at MUSC, and Robert Chapman at Hollings Marine Laboratory, Marine Resources Research Institute, South Carolina Department of Natural Resources.

2014 - present
Alex Jacobs, David Moore, Nick Levitt, Melinda Goforth

2013 - 2014
Jeremy Morgan, Connor Stanley, Matt Paul, and Tori McCaffrey.

Blogs
Matt Paul

Connor Stanley

Jeremy Morgan

Our vision and plans for genomics education in Charleston
In addition to this summer research program, we have several ongoing academic initiatives to prepare and expose students to this exciting new field. In the fall of 2013, Dr. Gavin Naylor and Dr. Paul Anderson are co-teaching an undergraduate honors Bioinformatics course. In addition, Dr. Andy Shedlock teaches a Vertebrate Genomics course for graduate and advanced undergraduate students, which includes a intensive laboratory experience (co-taught with Dr. Paul Anderson). In addition, we are consistently meeting to discuss ongoing research projects and encourage interested students to contact one of the PIs.

C2G2 Portals
The group maintains a web portal for accessing its suite of bioinformatics tools and resources: C2G2 Portal. We also maintain a R interface to the data at http://portal.cs.cofc.edu/rstudio/. Please contact Dr. Paul Anderson for account access.

Infrastructure
The C2G2 group currently maintains two compute clusters configured and optimized for computational genomics. The original commodity-based cluster is comprised of 4 nodes, with a total of 32 cores, 32 GB RAM per node, and 12 TB of raw storage. The recently awarded GEAR: CI grant has resulted in the purchase of a new high performance cluster comprised of 4 nodes, with a total of 96 cores, 96 TB of raw storage, 64 GB of RAM per node, and 4 Gb network connections. The C2G2 group also maintains cloud storage resources for the transfer, management, and organization of scientific data sets.

Project Goals
C2G2 Fall 2013

Documentation and related Links
To access the relevant literature, please contact [mailto:andersonpe2@cofc.edu Dr. Paul Anderson].

C2G2 Things you need to know

Galaxy_RNA-seq_Tutorial - For Galaxy-based RNAseq Tutorials

RNA Trimming

Running cummeRbund in R Studio

FAQ

Collaborator Project Page

Cloud Storage and Interface

NGS Analysis PDEF/FLi1

NGS Analysis lung cancer study

Meetings
10-25-2013

10-18-2013

09-27-2013

09-20-2013

09-13-2013

08-19-2013

08-16-2013

08-02-2013

07-29-2013

07-29-2013

07-09-2013

07-08-2013

06-28-2013

06-27-2013

06-21-2013

06-13-2013

06-13-2013

06-07-2013

Contact
C2G2@googlegroups.com

Support
This work is supported by the NSF EPSCoR Program of SC and the South Carolina Sea Grant Consortium.