BioBike(nee. BioLingua ) is a

cloud-based Cloud computing is "a paradigm for enabling network access to a scalable and elastic pool of shareable physical or virtual resources with self-service provisioning and administration on-demand," according to International Organization for ...

, through-the-web programmable (

Paas Platform as a service (PaaS) or application platform as a service (aPaaS) or platform-based service is a cloud computing service model where users provision, instantiate, run and manage a modular bundle of a computing platform and applications, w ...

) symbolic biocomputing and

bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

platform that aims to make

computational biology Computational biology refers to the use of techniques in computer science, data analysis, mathematical modeling and Computer simulation, computational simulations to understand biological systems and relationships. An intersection of computer sci ...

, and especially intelligent biocomputing (that is, the application of

Artificial Intelligence Artificial intelligence (AI) is the capability of computer, computational systems to perform tasks typically associated with human intelligence, such as learning, reasoning, problem-solving, perception, and decision-making. It is a field of re ...

) accessible to research scientists who are not expert programmers.

Unique capabilities

BioBIKE is an integrated symbolic biocomputing and bioinformatics platform, built from the start as an entirely (what is now called) cloud-based architecture where all computing is done in remote servers, and all user access is accomplished through web browsers. BioBIKE has a built-in frame system in which all objects, data, and knowledge are represented. This enables code written either in the native

Lisp Lisp (historically LISP, an abbreviation of "list processing") is a family of programming languages with a long history and a distinctive, fully parenthesized Polish notation#Explanation, prefix notation. Originally specified in the late 1950s, ...

, in the visual programming language, or systems of rules expressed in the

SNARK Snark may refer to: Fictional creatures * Snark (Lewis Carroll), a fictional animal species in Lewis Carroll's ''The Hunting of the Snark'' (1876) * Zn'rx, a race of fictional aliens in Marvel Comics publications, commonly referred to as "Snarks ...

theorem prover to access the whole of biological knowledge in an integrated manner. For its time (released in 2002) it was unique in permitting users to create fully functional biocomputing programs that run on the back-end servers entirely through the web browser UI. (In modern terms it was one of the first PaaS (Platform as a Service) systems, predating even

Salesforce Salesforce, Inc. is an American cloud-based software company headquartered in San Francisco, California. It provides applications focused on sales, customer service, marketing automation, e-commerce, analytics, artificial intelligence, and ap ...

in this capability.) Initially this programming was carried out in raw Lisp, but Jeff Elhai's team at VCU, with NSF funding, created an entirely graphical programming environment on top of BioBIKE based upon the Boxer-style programming environments. Being a multi-headed, multi-threaded, multi-user, multi-tenancy cloud-based system, BioBIKE users were able to directly work together through their web browsers, remotely sharing the same listener and memory space. This permitted a unique sort of collaboration, discussed in Shrager (2007). A specialized offshoot of BioBIKE called "BioDeducta" includes SRI's

theorem prover, offering unique "deductive biocomputing" capabilities.

Implementation

BioBIKE is

open-source software Open-source software (OSS) is Software, computer software that is released under a Open-source license, license in which the copyright holder grants users the rights to use, study, change, and Software distribution, distribute the software an ...

implemented using the

Lisp programming language Lisp (historically LISP, an abbreviation of "list processing") is a family of programming languages with a long history and a distinctive, fully parenthesized Polish notation#Explanation, prefix notation. Originally specified in the late 1950s, ...

. Continuing development takes place by the BioBIKE team centered at

Virginia Commonwealth University Virginia Commonwealth University (VCU) is a Public university, public research university in Richmond, Virginia, United States. VCU was founded in 1838 as the medical department of Hampden–Sydney College, becoming the Medical College of Virgin ...

History

BioBIKE was originally called "BioLingua", and was developed by Jeff Shrager a
The Carnegie Inst. of Washington Dept. of Plant Biology
and JP Massar with funding fro
NASA's Astrobiology Division
Shrager and Massar wanted to create a web-based, multi-user Lisp Machine, specialized for

. Other early contributors to the project included Mike Travers, and Jeff Elhai o
VCU
Elhai obtained continuing funding from the

National Science Foundation The U.S. National Science Foundation (NSF) is an Independent agencies of the United States government#Examples of independent agencies, independent agency of the Federal government of the United States, United States federal government that su ...

for the project, which was renamed BioBIKE. Elhai and colleagues added BioBIKE's unique

visual programming language In computing, a visual programming language (visual programming system, VPL, or, VPS), also known as diagrammatic programming, graphical programming or block coding, is a programming language that lets users create computer program, programs by ...

. Shrager, meanwhile, collaborated with Richard Waldinger at SRI to build SRI's (

) theorem prover into BioBIKE, creating a deductive biocomputing system, called BioDeducta.

Instances

There used to be a number of BioBIKE verticals in different biological domains, including viral pathogens, cyanobacteria and other bacteria, Arabidopsis thaliana, and several others described in the references.

External links

BioBIKE Project home page

References