Essential resources
Other useful resources
Summer undergraduate research opportunities

Essential Resources

• BioBIKE portal
  
• Direct routes to CyanoBIKE instance and alternate route
  
• Direct route to PhAnToMe/BioBIKE instance
  
• BioBIKE meeting rooms - Use it to meet others in the class or in the project
      - Click "Presenter Login" if you have a password (instructions)
      - Click "Participant Login" if you don't (instructions)
• VCU Library
  Apart from its many other merits, the library enables you to reach electronic journal articles that would otherwise be restricted.

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
• Molecular Biology of the Cell (Bruce Alberts et al, 2002; 4th edition)
  Molecular Cell Biology text book. Free for searching but not browsing.
• 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
• Protein Data Base
  Large collection of data concerning protein structure and sequence
• Protein Explorer and help
  Site to display molecular structures, offering more power than FirstGlance, at the cost of a more complicated interface
• Proteopedia
  Repository of protein structures and educational tools
• Sequence analysis tools (courtesy of CBS, Technical University of Denmark)
  Collection of online DNA and protein analysis tools
• Sequence Logos (courtesy of Steven Brenner, U. California, Berkeley)
  Graphical representation of nucleotide or amino acid frequencies in aligned sequences
• 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.
• Taxonomy Browser (courtesy of National Center for Biotechnology Information)
  Enter the name of an organism and find out its classification. You can click on higher order taxons (e.g. families) to find other related organisms.

Summer Undergraduate Research Opportunities (2014 deadlines in parentheses)

VCU opportunities

• Center for the Study of Biological Complexity summer fellowships (Deadline March 10[?], mentor required)
  
• Undergraduate Research and Creative Scholarship Summer Fellowships (Deadline March 1, mentor required)
  
• Global Education Undergraduate Research Fellowships (Deadline March 1, mentor required)
  
• Undergraduate Fellowships for Clinical and Translational Research (Deadline March 1, mentor required)
  
• Undergraduate Fellowships for Community Engaged and Translational Research (Deadline March 1, mentor required)
  
• American Society for Microbiology Undergraduate Research Fellowship (Deadline February 1, mentor required)
  

Outside opportunities for undergraduate summer internships

• Search for National Science Foundation-sponsored Research Experiences for Undergraduates (various deadlines, all over the U.S.)
• Search for NASA-sponsored Research Experiences for Undergraduates (March 1[?], all over the U.S.)
• Search for various undergraduates research opportunities via Pathways to Science (various deadlines, all over the U.S.)
• Amgen Scholars Program in Science and Technology: US universities, European universities (deadlines usually February 3)
• Summer Undergraduate Research Program in Molecular and Computational & Quantitative Biology at Princeton University (February 1)
• Genomics Summer Research Opportunity at Broad Institute, Cambridge MA (January 31)
• Summer Internship Program in Biomedical Research at the National Institutes of Health (rolling, in progress)
• iSEED Undergraduate Summer Research Program at University of Buffalo (February 1)
• Summer Research Internship Program at University of Virginia (February 21)
• Undergraduate Training Program at Loma Linda University (rolling, from January 1)
• Noblis Summer Internship Program , Falls Church, VA (ongoing)