Related papers: BacSoft: A Tool to Archive Data on Bacteria
The rapid development of the DNA nanotechnology field has been facilitated by advances in CAD software. However, as more complex concepts arose, the lag between the needs and software capabilities appeared. Further derailed by manual…
Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…
Living in the age of the digital media explosion, the amount of data that is being stored increases dramatically. However, even if existing storage systems suggest efficiency in capacity, they are lacking in durability. Hard disks, flash,…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
DNA-based storage is an emerging storage technology that provides high information density and long duration. Due to the physical constraints in the reading and writing processes, error correction in DNA storage poses several interesting…
The sophisticated tools and techniques employed by Nature for purposeful storage of information stand in stark contrast to the primitive and relatively inefficient means used by man. We describe some impressive features of biological data…
A key goal of bioinformatics is to create database systems and software platforms capable of storing and analysing large sets of biological data. Hundreds of biological databases are now available and provide access to huge amount of…
Current biocomputing approaches predominantly rely on engineered circuits with fixed logic, offering limited stability and reliability under diverse environmental conditions. Here, we use the GRNN framework introduced in our previous work…
In this report, we present example data sets and collections for the BeSpaceD platform. BeSpaceD is a spatio-temporal modelling and reasoning software framework. We describe the content of a number of the data sets and how the data was…
Clustering techniques have been the key drivers of data mining, machine learning and pattern recognition for decades. One of the most popular clustering algorithms is DBSCAN due to its high accuracy and noise tolerance. Many superior…
This article describes our experience developing and maintaining automated tests for scientific applications. The main idea evolves around building on already existing tests by cloning and grafting. The idea is demonstrated on a minimal…
Deoxyribonucleic Acid (DNA) as a storage medium with high density and long-term preservation properties can satisfy the requirement of archival storage for rapidly increased digital volume. The read and write processes of DNA storage are…
Obtaining a relevant dataset is central to conducting empirical studies in software engineering. However, in the context of mining software repositories, the lack of appropriate tooling for large scale mining tasks hinders the creation of…
In this paper we will describe a new approach on the well-known suffix-array algorithm using Big Table Data Technology. We will demonstrate how it is possible to refactor a well-known algorithm coupled by taking advantage of an…
Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current…
Documentation is one of the most neglected activities in Software Engineering, although it is an important method of assuring quality and understanding. Bioinformatics software is generally written by researchers from fields other than…