BioBike(nee. BioLingua ) is a

cloud-based Cloud computing is the on-demand availability of computer system resources, especially data storage (cloud storage) and computing power, without direct active management by the user. Large clouds often have functions distributed over mult ...

, through-the-web programmable ( Paas) symbolic biocomputing and

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

platform that aims to make

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

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

Artificial Intelligence Artificial intelligence (AI) is intelligence—perceiving, synthesizing, and inferring information—demonstrated by machines, as opposed to intelligence displayed by animals and humans. Example tasks in which this is done include speech ...

) 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 A lisp is a speech impairment in which a person misarticulates sibilants (, , , , , , , ). These misarticulations often result in unclear speech. Types * A frontal lisp occurs when the tongue is placed anterior to the target. Interdental lispin ...

, in the visual programming language, or systems of rules expressed in the SNARK 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 customer relationship management (CRM) software and applications focused on sales, customer service, marketing automation, a ...

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 SNARK theorem prover, offering unique "deductive biocomputing" capabilities.

Implementation

BioBIKE is

open-source software Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. ...

implemented using the

Lisp programming language Lisp (historically LISP) is a family of programming languages with a long history and a distinctive, fully parenthesized prefix notation. Originally specified in 1960, Lisp is the second-oldest high-level programming language still in common us ...

. Continuing development takes place by the BioBIKE team centered at

Virginia Commonwealth University Virginia Commonwealth University (VCU) is a public research university in Richmond, Virginia. VCU was founded in 1838 as the medical department of Hampden–Sydney College, becoming the Medical College of Virginia in 1854. In 1968, the Virgini ...

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 Lisp machines are general-purpose computers designed to efficiently run Lisp as their main software and programming language, usually via hardware support. They are an example of a high-level language computer architecture, and in a sense, the ...

, 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 National Science Foundation (NSF) is an independent agency of the United States government that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National I ...

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) is any programming language that lets users create programs by manipulating program elements ''graphically'' rather than by specifying them ''textually''. A VP ...

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