Essential Resources

• BioBIKE portal
  
• Different routes to CyanoBIKE instances: usual, alternate,
  
• Alternate routes to ViroBIKE instances: usual alternate,
  
• Only route to PhAnToMe BioBIKE instance (at the moment): usual
  
• BioBIKE meeting rooms - Use it to meet others in the class or in the project
          Click "Presenter Login" if you have a password
          Click "Participant Login" if you don't
  

Other Useful Resources

• Abbreviations
  List of nucleotide, amino acid abbreviations, and genetic code
• Bioinformatics resources on web
  Annotated list of web-based programs for analyzing DNA and protein sequences
• Chi-squared calculator (courtesy of John Walker, Fourmilab)
  Chi-square test probability calculator
• Chi-squared table (courtesy of Alexei Sharov, Virginia Tech)
  Interpret Chi-square values for a given level of significance
• Codon usage tables (courtesy of Yasukazu Nakamura)
  Codon frequencies for large number of sequenced genomes
• DNA dot plots (courtesy of Colorado State U.)
  Compares two nucleic acid sequences
• GeneMark
  Predict open reading frames in DNA sequences
• Genetic code
  Useful on line reference to recall code, types of amino acids, and their abbreviations
• ICTVdB
  International Committee on the Taxonomy of Viruses Database: Descriptions of taxa, pictures
• Mycobacteriophage DataBase
  A site summarizing what is known concerning mycobacteriophages, particularly new phages analyzed by classes such as ours
• NCBI
  National Center for Biotechnology Information: Home of Blast, Entrez, much else
• PhAnToMe
  A loose group of those dedicated to the analysis of phage genomes. Not to be confused with the PhAnToMe BioBIKE instance
• Sequence analysis tools (courtesy of CBS, Technical University of Denmark)
  Collection of online DNA and protein analysis tools
• t-test calculator (courtesy of GraphPad)
  You provide either raw data or (mean, standard deviation, number of samples), it returns the t-test score and the probability of score arising if both samples were taken from the same population.
• t-test probability calculator (courtesy of Daniel Soper)
  You provide score from t-test and degrees of freedom, it returns probability of score arising if both samples were taken from the same population.
• VCU Library
  Apart from its many other merits, the library enables you to reach electronic journal articles that would otherwise be restricted.

Research Opportunities (Summer 2011 and perhaps beyond)

• Howard Hughes Medical Institute Science Education and Research Program (VCU)
  
• VCU Undergraduate Summer Fellowships (VCU)
  
• Research Experiences for Undergraduates (all over the U.S.)
• VCU Viral Genome Project (VCU). Apply here.