(Biological Integrated Knowledge Environment)

  • A knowledge base
    Brings together all available genomic, metabolic, and experimental data pertinent to a coherent research community

  • A programming environment
    A language accessible to biologists without programming experience, incorporating concepts familiar to molecular biologists.

  • Read about it: Nucleic Acids Research (2009) 37:W28-W32

BioBIKE Instances (and what they focus on)

CyanoBIKE (cyanobacteria)
      Public site [alternate]
          Cyanobacterial Community Web Site

GunneraBIKE (Gunnera transcriptome)
      Public site

PhAnToMe/BioBIKE (bacteria and their phages)
      Public site [alternate]
          Home of PhAnToMe

StreptoBIKE (Streptococcus)
      Public site [alternate]

StaphyloBIKE (Staphylococcus)
      Public site [alternate]

ViroBIKE (viruses)
      Public site [alternate]
          Viral Community Web Site

Rationale for BioBIKE

Basic new biological insights require making new sense out of basic biological information, and with increasing frequency, that information comes from genomes and other sources too large for the human mind to absorb unaided.

One solution is for biologists to become familiar with a few tools, such as Blast. This gets the researcher from one point to another, like flying high above the terrain. Some places are impossible to get to in this way.

Another solution is to procure the services of a computer programmer. This may produce new tools appropriate to the problem at hand, but it is like traveling in a darkened limosine, where the passenger directs the driver but with no first hand knowledge of the surrounding world.

BioBIKE offers a different solution, one where a computationally inexperienced researcher may ride leisurely through the data, observing its novelty and responding directly to it.

More rationale

Guided tours of BioBIKE

BioBIKE for Programmers

Breaking News

The National Science Foundation has funded a major project to create an on-line resource for the community annotation of bacteriophage genomes and metagenomes. This resource will use BioBIKE as its user interface. Read more here.

Hosted by The Center for the Study of Biological Complexity at Virginia Commonwealth University
Sponsored by the National Sciences Foundation, Grant DBI-0516378

Revised 26 October 2011
Contact Jeff Elhai