Literature DB >> 25328913

An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities.

Matthew Fenwick1, Colbert Sesanker2, Martin R Schiller3, Heidi Jc Ellis, M Lee Hinman, Jay Vyas, Michael R Gryk.   

Abstract

Scientists are continually faced with the need to express complex mathematical notions in code. The renaissance of functional languages such as LISP and Haskell is often credited to their ability to implement complex data operations and mathematical constructs in an expressive and natural idiom. The slow adoption of functional computing in the scientific community does not, however, reflect the congeniality of these fields. Unfortunately, the learning curve for adoption of functional programming techniques is steeper than that for more traditional languages in the scientific community, such as Python and Java, and this is partially due to the relative sparseness of available learning resources. To fill this gap, we demonstrate and provide applied, scientifically substantial examples of functional programming, We present a multi-language source-code repository for software integration and algorithm development, which generally focuses on the fields of machine learning, data processing, bioinformatics. We encourage scientists who are interested in learning the basics of functional programming to adopt, reuse, and learn from these examples. The source code is available at: https://github.com/CONNJUR/CONNJUR-Sandbox (see also http://www.connjur.org).

Entities:  

Keywords:  Clojure; Haskell; Java; LISP; NMR; bioinformatics; component; functional-programming

Year:  2012        PMID: 25328913      PMCID: PMC4197993          DOI: 10.1109/ITNG.2012.21

Source DB:  PubMed          Journal:  Proc Int Conf Inf Technol New Gener


  6 in total

1.  Random phase detection in multidimensional NMR.

Authors:  Mark W Maciejewski; Matthew Fenwick; Adam D Schuyler; Alan S Stern; Vitaliy Gorbatyuk; Jeffrey C Hoch
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-26       Impact factor: 11.205

2.  Randomization improves sparse sampling in multidimensional NMR.

Authors:  Jeffrey C Hoch; Mark W Maciejewski; Blagoje Filipovic
Journal:  J Magn Reson       Date:  2008-05-21       Impact factor: 2.229

3.  Nonuniform sampling and spectral aliasing.

Authors:  Mark W Maciejewski; Harry Z Qui; Iulian Rujan; Mehdi Mobli; Jeffrey C Hoch
Journal:  J Magn Reson       Date:  2009-04-16       Impact factor: 2.229

4.  CONNJUR spectrum translator: an open source application for reformatting NMR spectral data.

Authors:  Ronald J Nowling; Jay Vyas; Gerard Weatherby; Matthew W Fenwick; Heidi J C Ellis; Michael R Gryk
Journal:  J Biomol NMR       Date:  2011-03-16       Impact factor: 2.835

5.  BioJava: an open-source framework for bioinformatics.

Authors:  R C G Holland; T A Down; M Pocock; A Prlić; D Huen; K James; S Foisy; A Dräger; A Yates; M Heuer; M J Schreiber
Journal:  Bioinformatics       Date:  2008-08-08       Impact factor: 6.937

6.  VENN, a tool for titrating sequence conservation onto protein structures.

Authors:  Jay Vyas; Michael R Gryk; Martin R Schiller
Journal:  Nucleic Acids Res       Date:  2009-08-05       Impact factor: 16.971

  6 in total
  4 in total

1.  Parser Combinators: a Practical Application for Generating Parsers for NMR Data.

Authors:  Matthew Fenwick; Gerard Weatherby; Heidi Jc Ellis; Michael R Gryk
Journal:  Proc Int Conf Inf Technol New Gener       Date:  2013

2.  The genomic CDS sandbox: An assessment among domain experts.

Authors:  Ayesha Aziz; Kensaku Kawamoto; Karen Eilbeck; Marc S Williams; Robert R Freimuth; Mark A Hoffman; Luke V Rasmussen; Casey L Overby; Brian H Shirts; James M Hoffman; Brandon M Welch
Journal:  J Biomed Inform       Date:  2016-01-15       Impact factor: 6.317

3.  cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.

Authors:  Toshiki Takeuchi; Atsuo Yamada; Takashi Aoki; Kunihiro Nishimura
Journal:  Source Code Biol Med       Date:  2016-08-17

4.  How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications.

Authors:  Bohdan B Khomtchouk; Edmund Weitz; Peter D Karp; Claes Wahlestedt
Journal:  Brief Bioinform       Date:  2018-05-01       Impact factor: 11.622

  4 in total

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