Welcome to the PhAnToMe BioBike/SEED Server!
SEED Organisms Edition v5.2

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Lisp   BBL (text language)   VPL (graphical language)

What is BioBIKE?

  • Biological Integrated Knowledge Environment
  • A knowledge resource
    BioBIKE brings together available genomic, metabolic, and experimental data pertinent to a given research community
  • A programming environment
    BioBIKE provides a programming language accessible to biologists without programming experience.
    Built into it are concepts familiar to molecular biologists and powerful tools to manipulate and analyze biological data.
  • For a description of BioBIKE, see:
    Elhai J, Taton A, Massar JP, Myers JK, Travers M, Casey J, Slupesky M, Shrager J (2009). BioBIKE: A web-based, programmable, integrated biological knowledge base. Nucl Acids Res 37:W28-W32
General Help for VPL users
Learn more about the underlying software

The biologists and engineers who have contributed to BioBIKE so far include: Joe Anderson, Devaki Bhaya, Johnny Casey Victor Clarke, Jeff Elhai (NSF grant PI, guidance on visual interface), Dexter Gulick, Bob Haxo, Monica Jain, Michiko Kato, Ashvin Kumar, JP Massar (core engineering lead), John Myers (Javascript expert), Craig Noe, Tara Nulton, Marc Santoro, Karl Schweighofer, Peter Seibel (Ajax expert, 'Practical Common Lisp' author), Jeff Shrager, CTO of CollabRx, Mark Slupesky, Colin Smith, Mike Travers (knowledge framework and interface engineering lead), Arnaud Taton, Sumudu Watugala, and Robel Wolde.

The Frame system and Frame browser were conceived of and originally written by Mike Travers, with rewrites by JP Massar. The idea for a Web Server is Jeff Shrager's and a prototype implementation was done by Dan Siroker. JP Massar designed and implemented the existing Web Server, as well as much of the Biolingua-specific code, with ideas and coding assistance from Jeff Shrager, Mike Travers, Mark Slupesky, and Jeff Elhai.

The BBL language was designed by Jeff Elhai, JP Massar, and Peter Seibel with help from Mike Travers, Jeff Shrager and others.

The visual interface was designed by Jeff Elhai, JP Massar, Peter Seibel, Mike Travers, John Myers and others, and was implemented by John Myers, Johnny Casey, JP Massar, and others.

Thanks to Franz Inc. and LispWorks for contributions supporting both BioLisp and the BioBIKE server, which was developed using Lispworks and Franz's Allegro Common Lisp, and which runs on Franz's ACL8.1 and uses the AllegroServe engine.

Thanks also to Edi Weitz for Cl-ppcre, a Perl-compatible regular expression pattern matcher.

Thanks also to Virginia Commonwealth University and San Diego State University for hosting BioBIKE instances.

This work was supported by NSF grant DBI0850146 and by NASA's program in Astrobiology and Fundamental Biology.

USE THIS TOOL AT YOUR OWN RISK. Constantly being updated, it may become unavailable at any time for any reason. Morever, things are likely to change without warning and/or suddenly stop working altogether. We offer no guarantee nor promise of reliable service or support at this time. (But we give it our best effort).

All input and output are logged for debugging.