Literature DB >> 24290918

Accelerating in silico research with workflows: a lesson in Simplicity.

Paul Walsh1, John Carroll, Roy D Sleator.   

Abstract

Bioinformatics is the application of computer science and related disciplines to the field of molecular biology. While there are currently several web based and desktop tools available for biologists to perform routine bioinformatics tasks, these tools often require users to manually and repeatedly co-ordinate multiple applications before reaching a result. In an effort to reduce time and error, workflow tools have been developed to automate these tasks. However, many of these tools require expert knowledge of the techniques and supporting databases which more often than not lies outside the scope of most biologists. Herein, we describe the development of sequence information management platform (Simplicity), a workflow-based bioinformatics management tool, which allows non-bioinformaticians to rapidly annotate large amounts of DNA and protein sequence data.
© 2013 Published by Elsevier Ltd.

Keywords:  Bioinformatics; Computational biology workflow; Genomics; Simplicity; Usability; annotation

Mesh:

Year:  2013        PMID: 24290918     DOI: 10.1016/j.compbiomed.2013.09.011

Source DB:  PubMed          Journal:  Comput Biol Med        ISSN: 0010-4825            Impact factor:   4.589


  16 in total

Review 1.  Under the microscope: From pathogens to probiotics and back.

Authors:  Roy D Sleator
Journal:  Bioengineered       Date:  2015       Impact factor: 3.269

2.  Functional Screening of the Cronobacter sakazakii BAA-894 Genome reveals a role for ProP (ESA_02131) in carnitine uptake.

Authors:  Audrey Feeney; Roy D Sleator
Journal:  Bioengineered       Date:  2015-04-27       Impact factor: 3.269

3.  Draft Genome Sequences of Six Different Staphylococcus epidermidis Clones, Isolated Individually from Preterm Neonates Presenting with Sepsis at Edinburgh's Royal Infirmary.

Authors:  P Walsh; M Bekaert; J Carroll; T Manning; B Kelly; A O'Driscoll; X Lu; C Smith; P Dickinson; K Templeton; P Ghazal; R D Sleator
Journal:  Genome Announc       Date:  2015-05-14

4.  Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software.

Authors:  Brendan Lawlor; Paul Walsh
Journal:  Bioengineered       Date:  2015-05-21       Impact factor: 3.269

5.  Draft Genome Sequence of a Streptococcus agalactiae Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland.

Authors:  K A Kropp; A Lucid; J Carroll; V Belgrudov; P Walsh; B Kelly; C Smith; P Dickinson; A O'Driscoll; K Templeton; P Ghazal; R D Sleator
Journal:  Genome Announc       Date:  2014-09-04

6.  Draft Genome Sequence of a Staphylococcus warneri Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland.

Authors:  K A Kropp; A Lucid; J Carroll; V Belgrudov; P Walsh; B Kelly; C Smith; P Dickinson; A O'Driscoll; K Templeton; P Ghazal; R D Sleator
Journal:  Genome Announc       Date:  2014-09-04

7.  Analysis of the role of the Cronobacter sakazakii ProP homologues in osmotolerance.

Authors:  Audrey Feeney; Christopher D Johnston; Rodney Govender; Jim O'Mahony; Aidan Coffey; Roy D Sleator
Journal:  Gut Pathog       Date:  2014-05-24       Impact factor: 4.181

8.  Draft Genome Sequence of a Serratia marcescens Strain Isolated from a Preterm Neonatal Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.

Authors:  K A Kropp; A Lucid; J Carroll; V Belgrudov; P Walsh; B Kelly; C Smith; P Dickinson; A O'Driscoll; K Templeton; P Ghazal; R D Sleator
Journal:  Genome Announc       Date:  2014-09-11

9.  Draft Genome Sequence of an Enterococcus faecalis Strain Isolated from a Neonatal Blood Sepsis Patient.

Authors:  K A Kropp; A Lucid; J Carroll; V Belgrudov; P Walsh; B Kelly; C Smith; P Dickinson; A O'Driscoll; K Templeton; P Ghazal; R D Sleator
Journal:  Genome Announc       Date:  2014-09-11

10.  Draft Genome Sequence of a Staphylococcus aureus Isolate Taken from the Blood of a Preterm Neonatal Blood Sepsis Patient.

Authors:  K A Kropp; A Lucid; J Carroll; V Belgrudov; P Walsh; B Kelly; K Templeton; C Smith; P Dickinson; A O'Driscoll; P Ghazal; R D Sleator
Journal:  Genome Announc       Date:  2014-09-11
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