Literature DB >> 29058018

[Big Data Revolution or Data Hubris? : On the Data Positivism of Molecular Biology].

Gabriele Gramelsberger1.   

Abstract

Genome data, the core of the 2008 proclaimed big data revolution in biology, are automatically generated and analyzed. The transition from the manual laboratory practice of electrophoresis sequencing to automated DNA-sequencing machines and software-based analysis programs was completed between 1982 and 1992. This transition facilitated the first data deluge, which was considerably increased by the second and third generation of DNA-sequencers during the 2000s. However, the strategies for evaluating sequence data were also transformed along with this transition. The paper explores both the computational strategies of automation, as well as the data evaluation culture connected with it, in order to provide a complete picture of the complexity of today's data generation and its intrinsic data positivism. This paper is thereby guided by the question, whether this data positivism is the basis of the big data revolution of molecular biology announced today, or it marks the beginning of its data hubris.

Keywords:  automation; base-calling algorithms; big data; genome sequencing; human genome project; validation

Mesh:

Year:  2017        PMID: 29058018     DOI: 10.1007/s00048-017-0179-2

Source DB:  PubMed          Journal:  NTM        ISSN: 0036-6978


  56 in total

1.  Zero-mode waveguides for single-molecule analysis at high concentrations.

Authors:  M J Levene; J Korlach; S W Turner; M Foquet; H G Craighead; W W Webb
Journal:  Science       Date:  2003-01-31       Impact factor: 47.728

2.  The accuracy of DNA sequences: estimating sequence quality.

Authors:  G A Churchill; M S Waterman
Journal:  Genomics       Date:  1992-09       Impact factor: 5.736

3.  Outcome signature genes in breast cancer: is there a unique set?

Authors:  Liat Ein-Dor; Itai Kela; Gad Getz; David Givol; Eytan Domany
Journal:  Bioinformatics       Date:  2004-08-12       Impact factor: 6.937

4.  A new insight into Sanger's development of sequencing: from proteins to DNA, 1943-1977.

Authors:  Miguel García-Sancho
Journal:  J Hist Biol       Date:  2010       Impact factor: 1.326

5.  What is a gene? - Revisited.

Authors:  Raphael Falk
Journal:  Stud Hist Philos Biol Biomed Sci       Date:  2010-11-09

6.  A sequence assembly and editing program for efficient management of large projects.

Authors:  S Dear; R Staden
Journal:  Nucleic Acids Res       Date:  1991-07-25       Impact factor: 16.971

7.  A sequencing method based on real-time pyrophosphate.

Authors:  M Ronaghi; M Uhlén; P Nyrén
Journal:  Science       Date:  1998-07-17       Impact factor: 47.728

8.  The history of the genetic sequence databases.

Authors:  T F Smith
Journal:  Genomics       Date:  1990-04       Impact factor: 5.736

9.  Structure and base sequence in the cohesive ends of bacteriophage lambda DNA.

Authors:  R Wu; A D Kaiser
Journal:  J Mol Biol       Date:  1968-08-14       Impact factor: 5.469

Review 10.  The sequence of sequencers: The history of sequencing DNA.

Authors:  James M Heather; Benjamin Chain
Journal:  Genomics       Date:  2015-11-10       Impact factor: 5.736

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