BioBike Documentation Index

BioBike

(Until recently, BioBike was called "BioLingua". See the old BioLingua home page for an explanation of the name change)

All contents Copyright 2002-2009 The BioBike Team

About BioBike BioBike FAQ Servers Introductory BioLisp Contacts

Live Tutorials Advanced Materials System Documents Lisp Resources Acknowledgements

Registered BioBike Servers:

Try out the BioBike demo server(no password required)
Log into the main BioBike Server (password required)

(You may request an account on the non-demo servers by writing to Jeff Shrager (jshrager@stanford.edu). We strongly recommend trying out the demo server before requesting a full BioBike account. The demo server is identical to the main server, although less stable, and your work is not backed up.)

About BioBike:

The BioBike FAQ
Introduction: The BioBike Vision (What is this thing?)
Programming the BioBike system
The BioBike paper in Bioinformatics [link out to Oxford U. Press site].
A commentary appearing in the June 6, 2005 issue of The Scientist describes our collaboration with the HyBrow team at Penn State.
The (Re)Birth of the Knowledge Operating System [PDF] (appearing at the International Lisp Conference, Stanford, June, 2005)
Why Lisp?

News!

20090511: A new BioBike paper, entitled "BioBIKE: A Web-based, Programmable, Integrated Biological Knowledge Base" (by Jeff Elhai, Arnaud Taton, and others) appears in a special issue of Nucleic Acids Research (NAR) on biocomputational web servers. This paper focuses on the VPL and other accomplishments since the last major paper (the 2005 BioInformatics paper). Click here to access this Open Source paper.
20080302: A new BioBike Google Group has been created. Anyone can join it. Click [here] to visit the new group.
20071205: The paper "The Evolution of BioBike: Community Adaptation of a Biocomputing Platform " has just appeared in Studies in History and Philosophy of Science (v38, pp642-656). You can see a preprint Here [PDF], or ask Jeff Shrager for a PDF of the final version that appeared in the journal.
20071025: A new tutorial on Lisp Macros has been added to the Live Tutorials set. You can see it by [clicking here], but it's really supposed to be run live from inside BioBike. (See instructions below on how to do this.)
20070404: The latest BioBike paper just appeared in the Open Source journal PLoS One; Deductive BioComputing (Shrager, Waldinger, Stickel, and Massar) describes the way that SRI's SNARK theorem prover can be used inside the BioBike platform to do complex biological reasoning.
20061215: A walk through tour and engineering-level description of the new BBL visual programming language (vBBL) has been posted. This is more-or-less a teaser as vBBL hasn't been released yet, but it gives you some idea of how it looks and works.
20060904: A new "success story" about BioBike just appeared on the LispWorks web site
20060830: I've just completed yet another BioBike paper, this one for a special issue of the Journal of the History and Philosophy of Science. Here's a preprint in PDF.
20060815: Richard Waldinger, Mark Stickel, JP Massar and I just completed a new paper on "Deductive Biocomputing". This describes using SNARK, SRI's First Order theorem prover, combined with BioBike to enable "intelligent" (deduction-based) biological computation. Here's a preprint in PDF.
20060606: Richard Waldinger (SRI) presented a paper entitled "Deductive Discovery and Composition of Resources" which describes BioDeducta (BioBike + Snark). The paper appears in the proceedings of the conference: Reasoning on the Web 2006 (RoW06). Here's a link to the conference proceedings pdf for that paper.
20060228: Numerous biobike tutorials are now available! Many of these are Live Tutorials, which are intended to be run live from within BioBike.
20050523: A paper describing the greater "KnowOS" (a knowledge operating system) vision (of which BioBike is the main instance) was delivered at the International Lisp Conference at Stanford in June. See About BioBike above for a link to the paper.
20050606: A commentary appearing in the June 6, 2005 issue of The Scientist describes our collaboration with the HyBrow team at Penn State.
20050523: A paper describing the greater "KnowOS" vision (of which BioBike is the main instance) will be delivered at the International Lisp Conference at Stanford in June. See About BioBike below for a link to the paper.
20050112: The BioBike paper has appeared in BioInformatics! Click here to access the paper at the OUP site.

Introductory BioLisp Materials and Tutorial Examples:

The Introductory Materials and Tutorial Examples are slowly being merged. Many of the tutorials are being turned into Live Tutorials (described below).

A Tour of BioBike Users interested in a demo will want to begin here.
(Also available as a Live Tutorial, see below.)

Live Tutorials:

These are intended to be run live from within BioBike. To get to the Live versions of Live Tutorials, log into BioBike demo server and select "Help...", then "Live Tutorials", and choose from the list list of live tutorials that appears. Outside a running BioBike, these are just normal HTML pages, but they may not fully work if you just read them straight from here; for example some images might not appear correctly. Also, please note that some of these are still under construction.

A Tour of BioBike: Getting one's feet wet with BioLisp and the BioBike Listener
Lisp I: Evaluation: The basics of Lisp evaluation.
Lisp II: Data and Iteration: Lisp data structures and iteration (loops).
How Blast Works: How sequence alignment (i.e., Blast) works.
Functions: This is what makes Lisp Special!
Lisp Macros: How to Define Entirely New Languages in Lisp
Tables: Working with data tables
Biocomputing I: Comapring gene function across organisms using annotation and microarrays
Graph R&R: Representation and Reasoning about Graphs
GO Analysis I: Simple symbolic biocomputing based on the Gene Ontology
Microarray Analysis: Simple microarray data clustering
Metabolic Simulation I: Introduction to dynamic analysis of metabolic pathways
Metabolic Simulation II: Dynamic pathway analysis using the Gene Ontology knowledge base
Regulation Simulation: Simulating the cell cycle (based upon a 2004 PNAS publication)
Natural Language I: Extracting biological relationships from PubMed I
Functional Phylogeny: Exploring phylogeny based upon gene function
Model Discovery I: Reverse engineering of regulatory networks
Reasoning Intro: Introduction to automated reasoning using Snark
Basic BioReasoning: Re-understanding the Elhai problem as a reasoning
Regulatory Reasoning: Using Snark to reason about the cell cycle (not done!)

Advanced Materials:

Common Lisp Resources:

Core Documentation:

Acknowledgments:

The biologists, students, and engineers who have contributed to this project so far include: Jeff Shrager (PI), JP Massar (core engineering lead), Mike Travers (knowledge framework and interface engineering lead), Jeff Elhai, Mark Slupesky, Julian Brooke, Devaki Bhaya, Arthur Grossman, Bob Haxo, Monica Jain, Ashvin Kumar, Pat Langley, Andrew Pohorille, Marc Santoro, Karl Schweighofer, Dan Siroker, Colin Smith, Arnaud Taton, Serdar Uckun, and Sumudu Watugala.
Thanks to Franz Inc. and LispWorks for software contributions.

This work has been supported by NASA'S program in Astrobiology and Fundamental Biology through a Biological Science Research Program grant, and by grant BDI-0516378 from the NSF Biological Databases and Informatics program, and by grant EEC-0234104 from the NSF/NIH Bioinformatics and Bioengineering Summer Institute program.

Wisp Lizard (by Rebecca Agin)

Email contacts:

Principal Investigator: Jeff Shrager
Questions and issues are posted on the BioBike Google Group, which anyone can join it. Click [here] to visit this group.

About BioBike	BioBike FAQ	Servers	Introductory BioLisp	Contacts
Live Tutorials	Advanced Materials	System Documents	Lisp Resources	Acknowledgements

BioBike

(Until recently, BioBike was called "BioLingua". See the old BioLingua home page for an explanation of the name change)