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BCB Graduate Student Organization Resources
Next-Gen Sequencing Expertise. Sponsored by BCB IGERT training grant.
- BCBGSO/Lab collaborates with Dr. Andrew Severin, the manager of the Genome Informatics Facility at Iowa State University. This server was purchased using a grant from the Plant Sciences Institute.
- Athena Server. Contact Akshay Yadav for an account.
- Processor: Dual Intel Xeon E5649 2.53GHz
- Memory: 48GB (12X4GB), 1333MHz Dual Ranked LV RDIMMs
- Storage: 1TB, 7200rpm SATA
- High-Performance Computing. Contact Andrew Severin for an account.
- 1 node on Lightening3 machine at Iowa State University. The node provides access to 32 cores and 128GB of RAM. Users are limited to only 1 processor (with 8 cores) at a time.
Note: This is SMP multi-core system where each core has 4GB of RAM available.
- Laptops check-out* for BCB students. Contact Carla Mann to request a laptop.
- Total 5 Apple iBooks with OS X Leopard (10.5.x) based laptops
- Total 2 Dell Inspiron Mini 10 netbooks with Microsoft Windows XP.
- Total 17 (9 Microsoft Windows Vista based + 8 Ubuntu 10.04 (Lucid Lynx) based) laptops with following configuration.
Bioinformatics Software packages available:
- BLAST: Basic Local Alignment Search Tool
- NCBI-toolkit: For writing efficient sequence comparison algorithms
- mpiBLAST: Parallel implementation of BLAST
- HMMER: Sequence comparison/alignment using Hidden Markov Models
- ClustalW: Sequence Alignment
- GROMACS: Molecular dynamics simulation package
- EMBOSS: European Molecular Biology Open Software Suite
- TIGR Assembler: Genome assembly
- MeV: Microarray Analysis Tool
- Glimmer: Gene finder for microbial genomes
- FASTA: Database search program for protein/nucleotide sequences
- MrBayes: Bayesian inference of phylogeny
- Phylip: Package for inference of phylogenies
- T_Coffee: Multiple sequence alignment package
- Bioperl/BioPython: Programming libraries