Related papers: BacSoft: A Tool to Archive Data on Bacteria
In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
Bacterial quorum sensing can be engineered with a view to the design of biotechnological applications based on their intrinsic role as a means of communication. We propose the creation of a positive feedback loop that will promote the…
Open source bioinformatics tools running under MS Windows are rare to find, and those running under Windows HPC cluster are almost non-existing. This is despite the fact that the Windows is the most popular operating system used among life…
Background: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main…
Deoxyribonucleic Acid (DNA), with its high density and long durability, is a promising storage medium for long-term archival storage and has attracted much attention. Several studies have verified the feasibility of using DNA for archival…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
DNA-mediated computing is a novel technology that seeks to capitalize on the enormous informational capacity of DNA and has tremendous computational ability to compete with the current silicon-mediated computing, due to massive parallelism…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
We study the amount of reliable information that can be stored in a DNA-based storage system composed of short DNA molecules. In this regime, Shomorony and Heckel (2022) put forward a conjecture on the scaling of the number of information…
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the…
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that…
The volumes and complexity of data that companies need to handle are increasing at an accelerating rate. In order to compete effectively and ensure their commercial sustainability, it is becoming crucial for them to achieve robust…
Realization of universal computing units for nanorobots is highly promising in creating new and wide arrays of applications, particularly in the realm of distributed computation. However, such realization is also a challenging problem due…
We report a user-friendly software environment for battery data science. It is designed to streamline data management, data cleaning, and data analysis to help bridge the gap between the domain expertise of most battery scientists and the…
This paper presents a generic web-based database interface implemented in Prolog. We discuss the advantages of the implementation platform and demonstrate the system's applicability in providing access to integrated biochemical data. Our…
With advances in nano- and biotechnology, bacteria are receiving increasing attention in scientific research as a potential substrate for Internet of Bio-Nano Things (IoBNT), which involve networking and communication through nanoscale and…
In this paper we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where a data set is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
With the rapid advancement of brain-computer interface (BCI) technology, the volume of physiological data generated in related research and applications has grown significantly. Data is a critical resource in BCI research and a key factor…