Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure.

Background: The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and significant computational challenges. As the cost of next-generation sequencing (NGS) has decreased, the amount of genomic data has surged globally. However, the cost and complexity of the computational resources required continue to be substantial barriers to leveraging big data.

KoNA: Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data.

During the last decade, the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges, including access to human data, as well as transfer, storage, and sharing of enormous amounts of data. To promote data-driven biological research, the Korean government announced that all biological data generated from government-funded research projects should be deposited at the Korea BioData Station (K-BDS), which consists of multiple databases for individual data types. Here, we introduce the Korean Nucleotide Archive (KoNA), a repository of nucleotide sequence data.

Introduction of the Korea BioData Station (K-BDS) for sharing biological data.

A wave of new technologies has created opportunities for the cost-effective generation of high-throughput profiles of biological systems, foreshadowing a "data-driven science" era. The large variety of data available from biological research is also a rich resource that can be used for innovative endeavors. However, we are facing considerable challenges in big data deposition, integration, and translation due to the complexity of biological data and its production at unprecedented exponential rates.

The impact of surface treatment in 3-dimensional printed implants for early osseointegration: a comparison study of three different surfaces.

3D printing technology has been gradually applied to various areas. In the present study, 3D-printed implants were fabricated with direct metal laser sintering technique for a dental single root with titanium. The 3D implants were allocated into following groups: not treated (3D-None), sandblasted with a large grit and acid-etched (3D-SLA), and target-ion-induced plasma-sputtered surface (3D-TIPS).

Comparison of 3D-Printed Dental Implants with Threaded Implants for Osseointegration: An Experimental Pilot Study.

This study aimed to compare bone healing and implant stability for three types of dental implants: a threaded implant, a three-dimensional (3D)-printed implant without spikes, and a 3D-printed implant with spikes. In four beagle dogs, left and right mandibular premolars (2nd, 3rd, and 4th) and 1st molars were removed. Twelve weeks later, three types of titanium implants (threaded implant, 3D-printed implant without spikes, and 3D-printed implant with spikes) were randomly inserted into the edentulous ridges of each dog.

Prometheus, an omics portal for interkingdom comparative genomic analyses.

Functional analyses of genes are crucial for unveiling biological responses, genetic engineering, and developing new medicines. However, functional analyses have largely been restricted to model organisms, representing a major hurdle for functional studies and industrial applications. To resolve this, comparative genome analyses can be used to provide clues to gene functions as well as their evolutionary history.

Bioinformatics services for analyzing massive genomic datasets.

The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines.

Closha: bioinformatics workflow system for the analysis of massive sequencing data.

Background: While next-generation sequencing (NGS) costs have fallen in recent years, the cost and complexity of computation remain substantial obstacles to the use of NGS in bio-medical care and genomic research. The rapidly increasing amounts of data available from the new high-throughput methods have made data processing infeasible without automated pipelines. The integration of data and analytic resources into workflow systems provides a solution to the problem by simplifying the task of data analysis.

Genome analysis of Hibiscus syriacus provides insights of polyploidization and indeterminate flowering in woody plants.

Hibiscus syriacus (L.) (rose of Sharon) is one of the most widespread garden shrubs in the world. We report a draft of the H.

A scaffold analysis tool using mate-pair information in genome sequencing.

We have developed a Windows-based program, ConPath, as a scaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find the longest acyclic graphs.