Charleston Computational Genomics Group

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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.

Contents

Galaxy and HPC Cluster

We maintain a high performance computing cluster for novel computational and scientific research. If you are interested in collaborating with the Anderson Research Lab and wish to use the cluster resources, please contact Dr. Paul Anderson (andersonpe2@cofc.edu).

The cluster resources include a customized instance of Galaxy, Hadoop, Rstudio, and other data science related software. The cluster resources are continuously expanding, so exact number of RAM, processors, and storage are subject to change, but they include large networked file system solutions, multiple processor nodes, and expanded RAM for high memory programs.

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. Focusing on algorithms for heterogenous large biological datasets.
  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 support for hardware improvements. As a computer science lab, expanding our capacity is an ongoing expense that is analogous to a web lab needed to consistently order supplies.

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, Jack Meagher

2013 - 2014

Jeremy Morgan, Connor Stanley, Matt Paul, and Tori McCaffrey.

Prior Student 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). Dr. Paul Anderson teaches Introduction to Data Science in the fall and often Data Mining and Artificial Intelligence in the spring. We 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

(Disclaimer: this is almost always out of date) The C2G2 group currently maintains s compute cluster configured and optimized for computational genomics. 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 150+ cores, 96 TB of raw storage, >64 GB of RAM per node, and 4 Gb network connections. The Anderson Lab also maintains a physical lab including room for 8 concurrent students.

REU

Please see http://omics.cofc.edu for more information on our new NSF REU program in bioinformatics and genomics.

Portals

Galaxy: http://freyja.cs.cofc.edu/c2g2

Rstudio: http://freyja.cs.cofc.edu/rstudio/

Documentation and related Links

Please note that there are a lot of resources available on the web, and that Google should be used liberally.

Uploading files to the cluster: https://github.com/pauleanderson/galaxy-upload-helper/blob/master/README.md

Using MATLAB: https://docs.google.com/document/d/132t5kqLE8oJqCErJCB0Ih1426kZHsY1CfhphoNsVK0I/edit?usp=sharing

Using Git: https://docs.google.com/document/d/1ARZvfK_Bn2FOjT3GQPvevpG3s0Oja_tCRIFajbWkU8c/edit?usp=sharing

Linux Handbook: https://docs.google.com/document/d/1AxPilo45UUb6B70gYaUu9-59txzgYRKftqVra8FUMz8/edit?usp=sharing

For full access to Anderson Lab Documentation, please contact Dr. Paul Anderson.

Old 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

andersonpe2@cofc.edu

Support

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

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