Recurrence risk prediction of acute coronary syndrome per patient as a personalized ACS recurrence risk: a retrospective study.

Acute coronary syndrome (ACS) has been one of the most important issues in global public health. The high recurrence risk of patients with coronary heart disease (CHD) has led to the importance of post-discharge care and secondary prevention of CHD. Previous studies provided binary results of ACS recurrence risk; however, studies providing the recurrence risk of an individual patient are rare. In this study, we conducted a model which provides the recurrence risk probability for each patient, along with the binary result, with two datasets from the Korea Health Insurance Review and Assessment Service and Chungbuk National University Hospital. The total data of 6,535 patients who had been diagnosed with ACS were used to build a machine learning model by using logistic regression. Data including age, gender, procedure codes, procedure reason, prescription drug codes, and condition codes were used as the model predictors. The model performance showed 0.893, 0.894, 0.851, 0.869, and 0.921 for accuracy, precision, recall, F1-score, and AUC, respectively. Our model provides the ACS recurrence probability of each patient as a personalized ACS recurrence risk, which may help motivate the patient to reduce their own ACS recurrence risk. The model also shows that acute transmural myocardial infarction of an unspecified site, and other sites and acute transmural myocardial infarction of an unspecified site contributed most significantly to ACS recurrence with an odds ratio of 97.908 as a procedure reason code and with an odds ratio of 58.215 as a condition code, respectively.

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.

High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology-a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in JAVA and is freely available at http://clustomcloud.kopri.re.kr.

PyroTrimmer: a software with GUI for pre-processing 454 amplicon sequences.

The ultimate goal of metagenome research projects is to understand the ecological roles and physiological functions of the microbial communities in a given natural environment. The 454 pyrosequencing platform produces the longest reads among the most widely used next generation sequencing platforms. Since the relatively longer reads of the 454 platform provide more information for identification of microbial sequences, this platform is dedicated to microbial community and population studies. In order to accurately perform the downstream analysis of the 454 multiplex datasets, it is necessary to remove artificially designed sequences located at either ends of individual reads and to correct low-quality sequences. We have developed a program called PyroTrimmer that removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in other programs as well, PyroTrimmer has novelty in terms of the following features: i) more sensitive primer detection using Levenstein distance and global pairwise alignment, ii) the first stand-alone software with a graphic user interface, and iii) various options for trimming and filtering out the low-quality sequence reads. PyroTrimmer, written in JAVA, is compatible with multiple operating systems and can be downloaded free at http://pyrotrimmer.kobic.re.kr.

WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model.

SUMMARY: WEbcoli is a WEb application for in silico designing, analyzing and engineering Escherichia coli metabolism. It is devised and implemented using advanced web technologies, thereby leading to enhanced usability and dynamic web accessibility. As a main feature, the WEbcoli system provides a user-friendly rich web interface, allowing users to virtually design and synthesize mutant strains derived from the genome-scale wild-type E.coli model and to customize pathways of interest through a graph editor. In addition, constraints-based flux analysis can be conducted for quantifying metabolic fluxes and charactering the physiological and metabolic states under various genetic and/or environmental conditions. AVAILABILITY: WEbcoli is freely accessible at http://webcoli.org. CONTACT: cheld@nus.edu.sg.