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The soybean crop, Glycine max (L.) Merr., is consumed by humans, Homo sapiens, worldwide. While the respective bodies of literature and -omics data for each of these organisms are extensive, comparatively few studies investigate the molecular biological processes occurring between the two. We are interested in elucidating the network of protein-protein interactions (PPIs) involved in human-soybean allergies. To this end, we leverage state-of-the-art sequence-based PPI predictors amenable to predicting the enormous comprehensive interactome between human and soybean. A network-based analytical approach is proposed, leveraging similar interaction profiles to identify candidate allergens and proteins involved in the allergy response. Interestingly, the predicted interactome can be explored from two complementary perspectives: which soybean proteins are predicted to interact with specific human proteins and which human proteins are predicted to interact with specific soybean proteins. A total of eight proteins (six specific to the human proteome and two to the soy proteome) have been identified and supported by the literature to be involved in human health, specifically related to immunological and neurological pathways. This study, beyond generating the most comprehensive human-soybean interactome to date, elucidated a soybean seed interactome and identified several proteins putatively consequential to human health.

The coronavirus disease 19 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prompted the development of diagnostic and therapeutic frameworks for timely containment of this pandemic. Here, we utilized our non-conventional computational algorithm, InSiPS, to rapidly design and experimentally validate peptides that bind to SARS-CoV-2 spike (S) surface protein. We previously showed that this method can be used to develop peptides against yeast proteins, however, the applicability of this method to design peptides against other proteins has not been investigated. In the current study, we demonstrate that two sets of peptides developed using InSiPS method can detect purified SARS-CoV-2 S protein via ELISA and Surface Plasmon Resonance (SPR) approaches, suggesting the utility of our strategy in real time COVID-19 diagnostics. Mass spectrometry-based salivary peptidomics shortlist top SARS-CoV-2 peptides detected in COVID-19 patients’ saliva, rendering them attractive SARS-CoV-2 diagnostic targets that, when subjected to our computational platform, can streamline the development of potent peptide diagnostics of SARS-CoV-2 variants of concern. Our approach can be rapidly implicated in diagnosing other communicable diseases of immediate threat.

Summary Synthetic proteins with high affinity and selectivity for a protein target can be used as research tools, biomarkers, and pharmacological agents, but few methods exist to design such proteins de novo. To this end, the In-Silico Protein Synthesizer (InSiPS) was developed to design synthetic binding proteins (SBPs) that bind pre-determined targets while minimizing off-target interactions. InSiPS is a genetic algorithm that refines a pool of random sequences over hundreds of generations of mutation and selection to produce SBPs with pre-specified binding characteristics. As a proof of concept, we design SBPs against three yeast proteins and demonstrate binding and functional inhibition of two of three targets in vivo. Peptide SPOT arrays confirm binding sites, and a permutation array demonstrates target specificity. Our foundational approach will support the field of de novo design of small binding polypeptide motifs and has robust applicability while offering potential advantages over the limited number of techniques currently available., Graphical Abstract, Highlights • InSiPS engineers synthetic binding proteins (SBPs) using primary protein sequence • SBPs are designed to a bind a target protein and avoid “off-target” interactions • Binding and functional inhibition of two of three target proteins in yeast is demonstrated • Our new approach offers advantages over alternative tools that rely on 3D models, Biological Sciences; Bioinformatics; Protein Family Determination

This paper presents VelocityOLAP (VOLAP), a distributed real-time OLAP system for high-velocity data. VOLAP makes use of dimension hierarchies, is highly scalable, exploits both multi-core and multi-processor parallelism, and can guarantee serializable execution of insert and query operations. In contrast to other high performance OLAP systems such as SAP HANA or IBM Netezza that rely on vertical scaling or special purpose hardware, VOLAP supports cost-efficient horizontal scaling on commodity hardware or modest cloud instances. Experiments on 20 Amazon EC2 nodes with TPC-DS data show that VOLAP is capable of bulk ingesting data at over 600 thousand items per second, and processing streams of interspersed insertions and aggregate queries at a rate of approximately 50 thousand insertions and 20 thousand aggregate queries per second with a database of 1 billion items. VOLAP is designed to support applications that perform large aggregate queries, and provides similar high performance for aggregations ranging from a few items to nearly the entire database.

The big data software stack based on Apache Spark and Hadoop has become mission critical in many enterprises. Performance of Spark and Hadoop jobs depends on a large number of configuration settings. The manual tuning procedure is expensive and brittle. There have been efforts to develop online and off-line automatic tuning approaches to make the big data stack more autonomic, but many researchers noted that it is important to tune only when truly necessary because many parameter searches can reduce rather than enhance performance. Autonomic systems need to be able to accurately detect important changes in workload characteristics, predict future workload characteristics, and use this information to pro-actively optimise resource allocation and frequency of parameter searches. This paper presents the first study focusing on workload change detection, change classification and workload forecasting in big data workloads. We demonstrate 99% accuracy for workload change detection, 90% accuracy for workload and workload transition classification, and up to 96% accuracy for future workload type prediction on Spark and Hadoop job flows simulated using popular big data benchmarks. Our method does not rely on past workload history for workload type prediction.

The need for larger-scale and increasingly complex protein-protein interaction (PPI) prediction tasks demands that state-of-the-art predictors be highly efficient and adapted to inter- and cross-species predictions. Furthermore, the ability to generate comprehensive interactomes has enabled the appraisal of each PPI in the context of all predictions leading to further improvements in classification performance in the face of extreme class imbalance using the Reciprocal Perspective (RP) framework. We here describe the PIPE4 algorithm. Adaptation of the PIPE3/MP-PIPE sequence preprocessing step led to upwards of 50x speedup and the new Similarity Weighted Score appropriately normalizes for window frequency when applied to any inter- and cross-species prediction schemas. Comprehensive interactomes for three prediction schemas are generated: (1) cross-species predictions, where Arabidopsis thaliana is used as a proxy to predict the comprehensive Glycine max interactome, (2) inter-species predictions between Homo sapiens-HIV1, and (3) a combined schema involving both cross- and inter-species predictions, where both Arabidopsis thaliana and Caenorhabditis elegans are used as proxy species to predict the interactome between Glycine max (the soybean legume) and Heterodera glycines (the soybean cyst nematode). Comparing PIPE4 with the state-of-the-art resulted in improved performance, indicative that it should be the method of choice for complex PPI prediction schemas.

Computing a spanning tree (ST) and a minimum ST (MST) of a graph are fundamental problems in graph theory and arise as a subproblem in many applications. In this article, we propose parallel algorithms to these problems. One of the steps of previous parallel MST algorithms relies on the heavy use of parallel list ranking which, though efficient in theory, is very time-consuming in practice. Using a different approach with a graph decomposition, we devised new parallel algorithms that do not make use of the list ranking procedure. We proved that our algorithms are correct, and for a graph [Formula: see text], [Formula: see text], and [Formula: see text], the algorithms can be executed on a Bulk Synchronous Parallel/Coarse Grained Multicomputer (BSP/CGM) model using [Formula: see text] communications rounds with [Formula: see text] computation time for each round. To show that our algorithms have good performance on real parallel machines, we have implemented them on graphics processing unit. The obtained speedups are competitive and showed that the BSP/CGM model is suitable for designing general purpose parallel algorithms.

Motivation: Interactions between amino acids are important determinants of the structure, stability and function of proteins. Several tools have been developed for the identification and analysis of such interactions in proteins based on the extensive studies carried out on high-resolution structures from Protein Data Bank (PDB). Although these tools allow users to identify and analyze interactions, analysis can only be performed on one structure at a time. This makes it difficult and time consuming to study the significance of these interactions on a large scale. Results: SpeeDB is a web-based tool for the identification of protein structures based on structural properties. SpeeDB queries are executed on all structures in the PDB at once, quickly enough for interactive use. SpeeDB includes standard queries based on published criteria for identifying various structures: disulphide bonds, catalytic triads and aromatic–aromatic, sulphur–aromatic, cation–π and ionic interactions. Users can also construct custom queries in the user interface without any programming. Results can be downloaded in a Comma Separated Value (CSV) format for further analysis with other tools. Case studies presented in this article demonstrate how SpeeDB can be used to answer various biological questions. Analysis of human proteases revealed that disulphide bonds are the predominant type of interaction and are located close to the active site, where they promote substrate specificity. When comparing the two homologous G protein-coupled receptors and the two protein kinase paralogs analyzed, the differences in the types of interactions responsible for stability accounts for the differences in specificity and functionality of the structures. Availability and implementation: SpeeDB is available at http://www.parallelcomputing.ca as a web service. Contact: d@drobilla.net Supplementary Information: Supplementary data are available at Bioinformatics online.

In contrast to queries for on-line transaction processing (OLTP) systems that typically access only a small portion of a database, OLAP queries may need to aggregate large portions of a database which often leads to performance issues. In this paper we introduce CR-OLAP, a scalable Cloud based Real-time OLAP system based on a new distributed index structure for OLAP, the distributed PDCR tree. CR-OLAP utilizes a scalable cloud infrastructure consisting of multiple commodity servers (processors). That is, with increasing database size, CR-OLAP dynamically increases the number of processors to maintain performance. Our distributed PDCR tree data structure supports multiple dimension hierarchies and efficient query processing on the elaborate dimension hierarchies which are so central to OLAP systems. It is particularly efficient for complex OLAP queries that need to aggregate large portions of the data warehouse, such as "report the total sales in all stores located in California and New York during the months February-May of all years". We evaluated CR-OLAP on the Amazon EC2 cloud, using the TPC-DS benchmark data set. The tests demonstrate that CR-OLAP scales well with increasing number of processors, even for complex queries. For example, for an Amazon EC2 cloud instance with 16 processors, a data warehouse with 160 million tuples, and a TPC-DS OLAP query stream where each query aggregates between 60% and 95% of the database, CR-OLAP achieved a query latency of below 0.3 s which can be considered a real time response. Collaboration with the IBM on alleviating performance bottlenecks for OLAP queries.OLAP queries may aggregate large portions of the database, creating bottlenecks.We study the use of parallel computing on scalable clouds to accelerate queries.Our system, CR-OLAP, is based on a new scalable distributed index structure.CR-OLAP uses dynamic cloud elasticity to improve performance.

The progressive elucidation of positive protein-protein interactions (PPIs) as wet-lab techniques continue to improve in both throughput and precision has increased the number and quality of known PPIs across the spectrum of life. Creating high quality datasets of positive PPIs is critical for training PPI prediction algorithms and for assessing the performance of PPI detection efforts. We present the Positome, a web service to acquire sets of positive PPIs based on user-defined criteria pertaining to data provenance including interaction type, throughput level, and detection method selection in addition to filtration by multiple lines of evidence (i.e. PPIs reported by independent research groups). The Positome provides a tunable interface to obtain a specified subset of interacting PPIs from the BioGRlD database. Both intra- and inter-species PPIs are supported. Using a number of model organisms, we demonstrate the trade-off between data quality and quantity, and the benefit of higher data quality on PPI prediction precision and recall. A web interface and REST web service are available at http://bioinf.sce.carleton.ca/POSITOME/.

The production of anti-Zika virus (ZIKV) therapeutics has become increasingly important as the propagation of the devastating virus continues largely unchecked. Notably, a causal relationship between ZIKV infection and neurodevelopmental abnormalities has been widely reported, yet a specific mechanism underlying impaired neurological development has not been identified. Here, we report on the design of several synthetic competitive inhibitory peptides against key pathogenic ZIKV proteins through the prediction of protein-protein interactions (PPIs). Often, PPIs between host and viral proteins are crucial for infection and pathogenesis, making them attractive targets for therapeutics. Using two complementary sequence-based PPI prediction tools, we first produced a comprehensive map of predicted human-ZIKV PPIs (involving 209 human protein candidates). We then designed several peptides intended to disrupt the corresponding host-pathogen interactions thereby acting as anti-ZIKV therapeutics. The data generated in this study constitute a foundational resource to aid in the multi-disciplinary effort to combat ZIKV infection, including the design of additional synthetic proteins.

Big data analytic technologies such as Hadoop and Spark run on compute clusters that are managed by resource managers such as YARN. YARN manages resources available to individual applications, thereby affecting job performance. Manual tuning of YARN tuning parameters can result in sub-optimal and brittle performance. Parameters that are optimal for one job may not be well suited to another. In this paper we present KERMIT, the first on-line automatic tuning system for YARN. KERMIT optimizes in real-time YARN memory and CPU allocations to individual YARN containers by analysing container response-time performance. Unlike previous automatic tuning methods for specific systems such as Spark or Hadoop, this is the first study that focuses on the more general case of on-line, real-time tuning of YARN container density and how this affects performance of applications running on YARN. KERMIT employs the same tuning code to automatically tune any system that uses YARN, including both Spark and Hadoop. The effectiveness of our technique was evaluated for Hadoop and Spark jobs using the Terasort, TPCx-HS, and SMB benchmarks. KERMIT was able to achieve an efficiency of more than 92% of the best possible tuning configuration (exhaustive search of the parameter space) and up to 30% faster than basic manual tuning.

Selim Akl has been a ground breaking pioneer in the field of parallel sorting algorithms. His ‘Parallel Sorting Algorithms’ book [12], published in 1985, has been a standard text for researchers and students. Here we discuss recent advances in parallel sorting methods for many-core GPUs. We demonstrate that parallel deterministic sample sort for GPUs (GPU Bucket Sort) is not only considerably faster than the best comparison-based sorting algorithm for GPUs (Thrust Merge) but also as fast as randomized sample sort for GPUs (GPU Sample Sort). However, deterministic sample sort has the advantage that bucket sizes are guaranteed and therefore its running time does not have the input data dependent fluctuations that can occur for randomized sample sort.

This paper presents VelocityOLAP (VOLAP), a distributed real-time OLAP system for high velocity data. VOLAP makes use of dimension hierarchies, is highly scalable, and exploits both multi-core and multi-processor parallelism. In contrast to other high performance OLAP systems such as SAP HANA or IBM Netezza that rely on vertical scaling or special purpose hardware, VOLAP supports cost-efficient horizontal scaling on commodity hardware or modest cloud instances. Experiments on 20 Amazon EC2 nodes with TPC-DS data show that VOLAP is capable of bulk ingesting data at over 400 thousand items per second, and processing streams of interspersed insertions and aggregate queries at a rate of approximately 50 thousand insertions and 20 thousand aggregate queries per second with a database of 1 billion items. VOLAP is designed to support applications that perform large aggregate queries, and provides similar high performance for aggregations ranging from a few items to nearly the entire database.

E10 is a new maturity locus in soybean and FT4 is the predicted/potential functional gene underlying the locus. Flowering and maturity time traits play crucial roles in economic soybean production. Early maturity is critical for north and west expansion of soybean in Canada. To date, 11 genes/loci have been identified which control time to flowering and maturity; however, the molecular bases of almost half of them are not yet clear. We have identified a new maturity locus called “E10” located at the end of chromosome Gm08. The gene symbol E10e10 has been approved by the Soybean Genetics Committee. The e10e10 genotype results in 5–10 days earlier maturity than E10E10. A set of presumed E10E10 and e10e10 genotypes was used to identify contrasting SSR and SNP haplotypes. These haplotypes, and their association with maturity, were maintained through five backcross generations. A functional genomics approach using a predicted protein–protein interaction (PPI) approach (Protein–protein Interaction Prediction Engine, PIPE) was used to investigate approximately 75 genes located in the genomic region that SSR and SNP analyses identified as the location of the E10 locus. The PPI analysis identified FT4 as the most likely candidate gene underlying the E10 locus. Sequence analysis of the two FT4 alleles identified three SNPs, in the 5′UTR, 3′UTR and fourth exon in the coding region, which result in differential mRNA structures. Allele-specific markers were developed for this locus and are available for soybean breeders to efficiently develop earlier maturing cultivars using molecular marker assisted breeding.

Engineered proteins are synthetic novel proteins (not found in nature) that are designed to fulfill a predetermined biological function. Such proteins can be used as molecular markers, inhibitory agents, or drugs. For example, a synthetic protein could bind to a critical protein of a pathogen, thereby inhibiting the function of the target protein and potentially reducing the impact of the pathogen. In this paper we present the In-Silico Protein Synthesizer (InSiPS), a massively parallel computational tool for the IBM Blue Gene/Q that is aimed at designing inhibitory proteins. More precisely, InSiPS designs proteins that are predicted to interact with a given target protein (and may inhibit the target's cellular functions) while leaving non-target proteins unaffected (to minimize side-effects). As proof-of-concepts, two InSiPS designed proteins have been synthesized in the lab and their inhibitory properties have been experimentally verified through wet-lab experimentation.