BCB Graduate Student Organization Resources

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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
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