RT Journal Article
SR Electronic
T1 Bio-compute objects - a step towards evaluation and validation of bio-medical scientific computations
JF PDA Journal of Pharmaceutical Science and Technology
JO PDA J Pharm Sci Technol
FD Parenteral Drug Association (PDA)
SP pdajpst.2016.006734
DO 10.5731/pdajpst.2016.006734
A1 Simonyan, Vahan
A1 Goecks, Jeremy
A1 Mazumder, Raja
YR 2016
UL http://journal.pda.org/content/early/2016/12/13/pdajpst.2016.006734.abstract
AB The unpredictability of actual physical, chemical, and biological experiments due to the multitude of environmental and procedural factors is well-documented. What is systematically overlooked, however, is that computational biology algorithms are also affected by multiplicity of parameters and have no lesser volatility. The complexities of computation protocols and interpretation of outcomes is only a part of the challenge: there are also virtually no standardized and industry accepted metadata schemas for reporting the computational objects that record the parameters used for computations together with the results of computations. Thus, it is often impossible to reproduce the results of a previously performed computation due to missing information on parameters, versions, arguments, conditions, and procedures of application launch. In this publication we describe the concept of biocompute objects developed specifically to satisfy regulatory research needs for evaluation, validation, and verification of bioinformatics pipelines. We envision generalized versions of biocompute objects called biocompute templates that support a single class of analyses but can be adapted to meet unique needs. To make these templates widely usable, we outline a simple but powerful cross-platform implementation. We also discuss the reasoning and potential usability for such concept within larger scientific community through the creation of a biocompute object database consisting of records relevant to US Food and Drug Administration (FDA). A biocompute object database record will be similar to a GenBank record in form; the difference being -- instead of describing a sequence, the biocompute record will include information related to parameters, dependencies, usage and other related information related to specific computations. This mechanism will extend similar efforts and also serve as a collaborative ground to ensure interoperability between different platforms, industries, scientists, regulators, and other stakeholders interested in bio-computing.