BioCompute Object: Difference between revisions

Revision as of 13:20, 17 December 2018

Revision as of 08:10, 24 July 2019

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== Background ==

One of the biggest challenges in bioinformatics is documenting and sharing [[Scientific workflow system#Scientific workflows|scientific workflows]] in a such a way that the computation and its results can be peer-reviewed or reliably reproduced.<ref>{{cite journal|url=http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285|title=Ten Simple Rules for Reproducible Computational Research|first1=Geir Kjetil|last1=Sandve|first2=Anton|last2=Nekrutenko|first3=James|last3=Taylor|first4=Eivind|last4=Hovig|date=24 October 2013|publisher=|journal=PLOS Computational Biology|volume=9|issue=10|pages=e1003285|via=PLoS Journals|doi=10.1371/journal.pcbi.1003285|pmc=3812051}}</ref> Bioinformatic [[Pipeline (software)|pipelines]] typically use multiple pieces of software, each of which typically has multiple versions available, multiple input parameters, multiple outputs, and possibly platform-specific configurations. As with experimental parameters in a laboratory protocol, small changes in computational parameters may have a large impact on the scientific validity of the results. The BioCompute Framework provides an [[Object-oriented design|object oriented design]] from which a BCO that contains details of a pipeline and how it was used can be constructed, [[digitally signed]], and shared. The BioCompute concept was originally developed to satisfy FDA regulatory research and review needs for evaluation, validation, and verification of genomics data. However, the Biocompute Framework follows FAIR Data Principles<ref>{{Cite journal|last=Wilkinson|first=Mark D.|last2=Dumontier|first2=Michel|last3=Aalbersberg|first3=IJsbrand Jan|last4=Appleton|first4=Gabrielle|last5=Axton|first5=Myles|last6=Baak|first6=Arie|last7=Blomberg|first7=Niklas|last8=Boiten|first8=Jan-Willem|last9=Santos|first9=Luiz Bonino da Silva|date=2016-03-15|title=The FAIR Guiding Principles for scientific data management and stewardship|url=https://www.nature.com/articles/sdata201618|journal=Scientific Data|language=En|volume=3|doi=10.1038/sdata.2016.18}}</ref> and can be used broadly to provide communication and [[interoperability]] between different platforms, industries, scientists and regulators<ref>{{cite journal|url=https://www.biorxiv.org/content/early/2017/09/21/191783|title=Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results|first1=Gil|last1=Alterovitz|first2=Dennis A.|last2=Dean|first3=Carole|last3=Goble|first4=Michael R.|last4=Crusoe|first5=Stian|last5=Soiland-Reyes|first6=Amanda|last6=Bell|first7=Anais|last7=Hayes|first8=Charles Hadley H.|last8=King|first9=Elaine|last9=Johanson|first10=Elaine E.|last10=Thompson|first11=Eric|last11=Donaldson|first12=Hsinyi S.|last12=Tsang|first13=Jeremy|last13=Goecks|first14=Jonas S.|last14=Almeida|first15=Lydia|last15=Guo|first16=Mark|last16=Walderhaug|first17=Paul|last17=Walsh|first18=Robel|last18=Kahsay|first19=Toby|last19=Bloom|first20=Yuching|last20=Lai|first21=Vahan|last21=Simonyan|first22=Raja|last22=Mazumder|date=21 September 2017|publisher=|journal=bioRxiv|pages=191783|via=www.biorxiv.org|doi=10.1101/191783}}</ref>

== Utility ==