Related papers: BacSoft: A Tool to Archive Data on Bacteria
Biomolecular computers, along with quantum computers, may be a future alternative for traditional, silicon-based computers. Main advantages of biomolecular computers are massive parallel processing of data, expanded capacity of storing…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
Bacteriophages densely pack their long dsDNA genome inside a protein capsid. The conformation of the viral genome inside the capsid is consistent with a hexagonal liquid crystalline structure. Experiments have confirmed that the details of…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…
Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper…
Structural DNA nanotechnology has advanced to the extent that extremely complex structures can be designed. Much of this advancement has been due to the development of automated DNA design and simulation tools. Typically, the tools (e.g.…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
In open-source software development environments; textual, numerical and relationship-based data generated are of interest to researchers. Various data sets are available for this data, which is frequently used in areas such as software…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
The object of this article is to review the development of ultrahigh-density, nanoscale data storage, i.e., nanostorage. As a fundamentally new type of storage system, the recording mechanisms of nanostorage may be completely different to…
As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive…
Objective: Data clustering is a common exploration step in the omics era, notably in genomics and proteomics where many genes or proteins can bequantified from one or more experiments. Bayesian clustering is a powerful algorithm that can…
Temporal evolution of a clonal bacterial population is modelled taking into account reversible mutation and selection mechanisms. For the mutation model, an efficient algorithm is proposed to verify whether experimental data can be…
Database Management System (DBMS) is designed to help store and process large collections of data, and is incredibly flexible to perform various kinds of optimizations as long as it achieves serializability with a high-level interface…
This paper introduces a new concept. We intend to give life to a software agent. A software agent is a computer program that acts on a user's behalf. We put a DNA inside the agent. DNA is a simple text, a whole roadmap of a network of…