AbstractBiological model curation provides new insights by integrating biological knowledge-fragments, assessing their uncertainty, and analyzing the reliability of potential interpretations. Here we integrate published results about circadian clocks in Drosophila melanogaster while exploring economies of scale in biological model curation. Clocks govern rhythms of gene-expression that impact fitness, health, cancer, memory, mental functions, and more. Human clock insights have been repeatedly pioneered in flies. Flies simplify investigating complex gene regulatory networks, which express proteins cyclically using environmentally entrained interlocking feedback loops that act as clocks. Simulations could simplify research further. We found that very few computational models test their quality directly against experimentally observed time series scattered in the literature. We designed FlyClockbase for integrating such scattered data to enable robust efficient access for biologists and modelers. To this end we have been defining data structures that simplify the construction and maintenance of Versioned Biological Information Resources (VBIRs) that prioritize simplicity, openness, and therefore maintainability. We aim to simplify the preservation of more raw data and relevant annotations from experiments in order to multiply the long-term value of wet-lab datasets for modelers interested in meta-analyses, parameter estimates, and hypothesis testing. Currently FlyClockbase contains over 400 wildtype time series of core circadian components systematically curated from 86 studies published between 1990 and 2015. Using FlyClockbase, we show that PERIOD protein amount peak time variance unexpectedly exceeds that of TIMELESS. We hypothesize that PERIOD’s exceedingly more complex phosphorylation rules are responsible. Variances of daily event times are easily confounded by errors. We improved result reliability by a human error analysis of our data handling; this revealed significance-degrading outliers, possibly violating a presumed absence of wildtype heterogeneity or lab evolution. Separate analyses revealed elevated stochasticity in PCR-based peak time variances; yet our reported core difference in peak time variances appears robust. Our study demonstrates how biological model curation enhances the understanding of circadian clocks. It also highlights diverse broader challenges that are likely to become recurrent themes if models in molecular systems biology aim to integrate ‘all relevant knowledge’. We developed a trans-disciplinary workflow, which demonstrates the importance of developing compilers for VBIRs with a more biology-friendly logic that is likely to greatly simplify biological model curation. Curation-limited grand challenges, including personalizing medicine, critically depend on such progress if they are indeed to integrate ‘all relevant knowledge’.General Article SummaryCircadian clocks impact health and fitness by controlling daily rhythms of gene-expression through complex gene-regulatory networks. Deciphering how they work requires experimentally tracking changes in amounts of clock components. We designed FlyClockbase to simplify data-access for biologists and modelers, curating over 400 time series observed in wildtype fruit flies from 25 years of clock research. Substantial biological model curation was essential for identifying differences in peak time variance of the clock-proteins ‘PERIOD’ and ‘TIMELESS’, which probably stem from differences in phosphorylation-network complexity.We repeatedly encountered systemic limitations of contemporary data analysis strategies in our work on circadian clocks. Thus, we used it as an opportunity for composing a panoramic view of the broader challenges in biological model curation, which are likely to increase as biologists aim to integrate all existing expertise in order to address diverse grand challenges. We developed and tested a trans-disciplinary research workflow, which enables biologists and compiler-architects to define biology-friendly compilers for efficiently constructing and maintaining Versioned Biological Information Resources (VBIRs). We report insights gleaned from our practical clock research that are essential for defining a VBIRs infrastructure, which improves the efficiency of biological model curation to the point where it can be democratized.Statement of data availabilityStabilizing Versioned Variant of this file: QQv1r4_2017m07d14_LionBefore final publication FlyClockbase will be at https://github.com/FlyClockbase For review purposes FlyClockbase QQv1r4 will be provided as a zip-archive in the uploaded Supplemental Material; it is also available upon request from L. Loewe.AbbreviationsTable 1: Molecular core clock componentsTable 2: Concepts for organizing FlyClockbaseSupplemental MaterialAppendix: Supplemental Text and Tables (32 pages included in this file, QQv1v4)Supplemental Statistical Analysis (87 pages not included in this file, QQv1v4)R-Script zip file (>12K lines not included in this file, QQv1v4)FlyClockbase zip file (available upon request, QQv1v4)
State of the Art of Fuzzy Methods for Gene Regulatory Networks Inference
