Preprints (not yet peer-reviewed)

424 downloads
1,931 views

This essay proposes mathematical answers to meta-scientific questions including "how much knowledge is produced by research?", "how rapidly is a field making progress?", "what is the expected reproducibility of a result?", "what do we mean by soft science?", "what...

["Computational Biology","Evolutionary Studies","Science Policy","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.1968v3
32 downloads
85 views

Life science ontologies play an important role in semantic web. In the fish and fisheries research field, it is imperative to have an ontology that can automatically provide information for biological objects annotations and links to relevant data pieces. As such,...

["Aquaculture, Fisheries and Fish Science","Bioinformatics","Computational Science"]
doi:10.7287/peerj.preprints.3020v1
83 downloads
75 views

Emerging infectious diseases caused by fungal taxa are increasing and are placing a substantial burden on economies and ecosystems worldwide. Of the emerging fungal diseases, chytridomycosis caused by the fungus Batrachochytrium dendrobatidis (hereafter Bd) is...

["Ecology","Microbiology","Mycology","Computational Science"]
doi:10.7287/peerj.preprints.3017v1
184 downloads
478 views

In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for...

["Biochemistry","Bioinformatics","Biophysics","Pharmacology","Computational Science"]
doi:10.7287/peerj.preprints.2857v2
173 downloads
200 views

Generating heatmaps of genes datasets have been known to be a graphical representation of data where the individual values contained in a matrix are represented as colors. Herein, we describe AFCMHeatMap a shiny web App that integrates quantitative interaction...

["Bioinformatics","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2961v1
104 downloads
381 views

The use of online data repositories and the establishment of new data standards that require data to be computer-parsable so that algorithms can reason over them have become increasingly important with the emergence of high-throughput technologies, Big Data and...

["Biodiversity","Bioinformatics","Computational Biology","Zoology","Computational Science"]
doi:10.7287/peerj.preprints.2429v2
102 downloads
1,055 views

Background. The goals of this study were (1) to present the set of data evaluating running biomechanics (kinematics and kinetics), including data on running habits, demographics, and levels of muscle strength and flexibility made available at Figshare (DOI: 10.6084/m9.figshare.4543435);...

["Bioengineering","Neuroscience","Kinesiology","Computational Science"]
doi:10.7287/peerj.preprints.2888v1
60 downloads
327 views

Background. High talker variability (i.e. multiple voices in the input) has been found effective in training non-native phonetic contrasts in adults. A small number of studies suggest that children also benefit from high-variability phonetic training with some...

["Psychiatry and Psychology","Computational Science"]
doi:10.7287/peerj.preprints.2870v2
95 downloads
311 views

Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects...

["Bioinformatics","Ecology","Microbiology","Computational Science"]
doi:10.7287/peerj.preprints.2879v1
262 downloads
404 views

This document summarizes a series of authoritative views on research data management, sharing and citation, developed in Expert Groups, Working Groups, and other activities organized through FORCE11 (http://force11.org), an international community of over 2,000...

["Translational Medicine","Science Policy","Human-Computer Interaction","Computational Science"]
doi:10.7287/peerj.preprints.2836v1
30 downloads
186 views

Hydrolysis of ATP by Na+/K+-ATPase, a P-Type ATPase, catalyzing active Na+ and K+ transport through cellular membranes leads transiently to a phosphorylation of its catalytical α-subunit. Surprisingly, 3-dimensional molecular structure analysis of P-type ATPases...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2812v1
867 downloads
779 views

The past influences the present and future; for example, in computational chemistry, simplifying assumptions and approximations important in the pre-computing era remains relevant today in allowing simulation of larger systems with reasonable amount of computer...

["Biochemistry","Bioengineering","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.365v4
56 downloads
169 views

Colony counting to estimate colony forming units (CFUs) is a standard microbiology procedure used for determining the number of viable microbes in a system. Typically this process is done manually, which is time consuming, tedious, and sometimes error prone. Alternate...

["Microbiology","Medical Genetics","Computational Science"]
doi:10.7287/peerj.preprints.2792v1
15 downloads
151 views

Basic idea of science is reproducibility of phenomena and experiments. Reproducibility of data analyses and reports is becoming more and more important. It requires structured organization of data, augmented with enought metadata for future re-use of data. Our...

["Bioinformatics","Genomics","Plant Science","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2791v1
148 downloads
348 views

As part of a recent workshop entitled "Imagining Tomorrow's University”, we were asked to visualize the future of universities as research becomes increasingly data- and computation-driven and identify a set of principles characterizing pertinent opportunities...

["Ethical Issues","Science and Medical Education","Science Policy","Computational Science"]
doi:10.7287/peerj.preprints.2781v1
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