Protein Modeling Lab
Children's Hospital Research Foundation
& University of Cincinnati
Introduction to Bioinformatics
The Protein Modeling Lab was primarily built in order to enhance graduate level training in bioinformatics. However, it is also being used to facilitate specialized training in modeling of biomolecular systems and bioinformatics at various levels at the University of Cincinnati and Children's Hospital Research Foundation. For example, the Modeling Lab is being used for hands-on type of classes and case studies taught as part of the Introduction to Functional Genomics and Introduction to Bioinformatics courses for Biomedical Engineering graduate program in bioinformatics. The syllabus for the latter course is available here (see also the links above and my web pages for more general info). The setup of our computational facilities is briefly described below.
CITRIX cluster:
| Protein Lab 1 | Protein Lab 2 | Protein Lab 3 |
| DL360, 2CPUs, 4GB RAM
DS Modeling 1.1, Matlab, GhostMiner, Tooldiag, BioAdviser, MOIL, LOOPP, VMD, Modeller, Autodock |
DL360, 2CPUs, 4GB RAM
DS Modeling 1.1, Matlab, GhostMiner, Tooldiag, BioAdviser, MOIL, LOOPP, VMD, Modeller, Autodock |
DL380, 2CPUs, 4GB RAM
DS Modeling 1.1, Matlab, GhostMiner, Tooldiag, BioAdviser, MOIL, LOOPP, VMD, Modeller, Autodock, Arena |
In order to connect with the CITRIX cluster you will need to install CITRIX client, which can be dowloaded for free at www.citrix.com. If you do have your client installed you may directly open a login session on any the machines above. Please, use your username, password and domain name as provided by the administrator of the Citrix accounts. Major applications installed on each machine are listed above (CITRIX uses load balancing and when using your domain account you will be directed to the machine which is least overloaded). You may contact me directly if you experience problems.
LINUX cluster:
| Protein Lab 4 | Protein Lab 5 | Protein Lab 6 |
| DL380, 2CPUs, 4GB RAM
PBS queuing system |
The LINUX cluster is still under construction. However, one central server with a queuing system that enables spawning jobs on our cluster consisting of additional 12 CPUs at present is available. More applications will be installed soon. Stay tuned for more news.
The Protein Modeling Lab was created using funds from a grant from the Ohio Board of Regents to Dr. R. Brackenbury. We would like to further acknowledge the support from the Division of Biomedical Informatics and Children's Hospital Research Foundation for providing space and technical support.
Author: Jarek Meller