Coding for Optimized Writing Rate in DNA Storage

A method for encoding information in DNA sequences is described. The method is based on the precisionresolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis method. The suggested method optimizes the amount of information bits per synthesis time unit, namely, the writing rate. Additionally, the encoding scheme studied here takes into account the existence of multiple copies of the DNA sequence, which are independently distorted. Finally, quantizers for various run-length distributions are designed

Coding for Optimized Writing Rate in DNA Storage

A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis method. The suggested method optimizes the amount of information bits per synthesis time unit, namely, the writing rate. Additionally, the encoding scheme studied here takes into account the existence of multiple copies of the DNA sequence, which are independently distorted. Finally, quantizers for various run-length distributions are designed.Comment: To appear in ISIT 202

Coding for Optimized Writing Rate in DNA Storage

A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis method. The suggested method optimizes the amount of information bits per synthesis time unit, namely, the writing rate. Additionally, the encoding scheme studied here takes into account the existence of multiple copies of the DNA sequence, which are independently distorted. Finally, quantizers for various run-length distributions are designed

Identification of the Unknown Soldier and the Fight for the Right to Anonymity: The Human Genome Project and Implications of a National DNA Database

The focus of this writing is the use of DNA for identification purposes and the issues that arise when genetic traits and/or predisposition to physical or mental conditions are linked to the individual specifically, along with the implications of a national DNA database as a system of identification. It has become the general rule that it is not an unreasonable invasion of privacy to take DNA for the purpose of identifying criminal offenders through a DNA database. This writing will examine the potential for nonconsensual inclusion of nearly everyone into such a system, as well as the ramifications in the areas of employment and individual insurance coverage if access to genetic information is not controlled. Current legislative efforts will be explored in an attempt to advocate the best direction for future legislation of information that is too vitally useful to prohibit, yet too indiscriminately dangerous to leave vulnerable to all who may find it useful

Identification of the Unknown Soldier and the Fight for the Right to Anonymity: The Human Genome Project and Implications of a National DNA Database

The focus of this writing is the use of DNA for identification purposes and the issues that arise when genetic traits and/or predisposition to physical or mental conditions are linked to the individual specifically, along with the implications of a national DNA database as a system of identification. It has become the general rule that it is not an unreasonable invasion of privacy to take DNA for the purpose of identifying criminal offenders through a DNA database. This writing will examine the potential for nonconsensual inclusion of nearly everyone into such a system, as well as the ramifications in the areas of employment and individual insurance coverage if access to genetic information is not controlled. Current legislative efforts will be explored in an attempt to advocate the best direction for future legislation of information that is too vitally useful to prohibit, yet too indiscriminately dangerous to leave vulnerable to all who may find it useful

DNA multi-bit non-volatile memory and bit-shifting operations using addressable electrode arrays and electric field-induced hybridization.

DNA has been employed to either store digital information or to perform parallel molecular computing. Relatively unexplored is the ability to combine DNA-based memory and logical operations in a single platform. Here, we show a DNA tri-level cell non-volatile memory system capable of parallel random-access writing of memory and bit shifting operations. A microchip with an array of individually addressable electrodes was employed to enable random access of the memory cells using electric fields. Three segments on a DNA template molecule were used to encode three data bits. Rapid writing of data bits was enabled by electric field-induced hybridization of fluorescently labeled complementary probes and the data bits were read by fluorescence imaging. We demonstrated the rapid parallel writing and reading of 8 (23) combinations of 3-bit memory data and bit shifting operations by electric field-induced strand displacement. Our system may find potential applications in DNA-based memory and computations

Molecular access to multi-dimensionally encoded information

Polymer scientist have only recently realized that information storage on the molecular level is not only restricted to DNA-based systems. Similar encoding and decoding of data have been demonstrated on synthetic polymers that could overcome some of the drawbacks associated with DNA, such as the ability to make use of a larger monomer alphabet. This feature article describes some of the recent data storage strategies that were investigated, ranging from writing information on linear sequence-defined macromolecules up to layer-by-layer casted surfaces and QR codes. In addition, some strategies to increase storage density are elaborated and some trends regarding future perspectives on molecular data storage from the literature are critically evaluated. This work ends with highlighting the demand for new strategies setting up reliable solutions for future data management technologies

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations.

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results