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Abstract MotivationAs nanopore technology reaches ever higher throughput and accuracy, it becomes an increasingly viable candidate for reading out DNA data storage. Nanopore sequencing offers considerable flexibility by allowing long reads, real-time signal analysis, and the ability to read both DNA and RNA. We need flexible and efficient designs that match nanopore’s capabilities, but relatively few designs have been explored and many have significant inefficiency in read density, error rate, or compute time. To address these problems, we designed a new single-read per-strand decoder that achieves low byte error rates, offers high throughput, scales to long reads, and works well for both DNA and RNA molecules. We achieve these results through a novel soft decoding algorithm that can be effectively parallelized on a GPU. Our faster decoder allows us to study a wider range of system designs. ResultsWe demonstrate our approach on HEDGES, a state-of-the-art DNA-constrained convolutional code. We implement one hard decoder that runs serially and two soft decoders that run on GPUs. Our evaluation for each decoder is applied to the same population of nanopore reads collected from a synthesized library of strands. These same strands are synthesized with a T7 promoter to enable RNA transcription and decoding. Our results show that the hard decoder has a byte error rate over 25%, while the prior state of the art soft decoder can achieve error rates of 2.25%. However, that design also suffers a low throughput of 183 s/read. Our new Alignment Matrix Trellis soft decoder improves throughput by 257× with the trade-off of a higher byte error rate of 3.52% compared to the state of the art. Furthermore, we use the faster speed of our algorithm to explore more design options. We show that read densities of 0.33 bits/base can be achieved, which is 4× larger than prior MSA-based decoders. We also compare RNA to DNA, and find that RNA has 85% as many error-free reads when compared to DNA. Availability and implementationSource code for our soft decoder and data used to generate figures is available publicly in the Github repository https://github.com/dna-storage/hedges-soft-decoder (10.5281/zenodo.11454877). All raw FAST5/FASTQ data are available at 10.5281/zenodo.11985454 and 10.5281/zenodo.12014515. 

There are a set of primordial features and functions expected of any modern information system: a substrate stably carrying data; the ability to repeatedly write, read, erase, reload, and compute on specific data from that substrate; and the overall ability to execute such functions in a seamless and programmable manner. For nascent molecular information technologies, proof of principle realization of this set of primordial capabilities would advance the vision for their continued development. Here, we present a DNA-based store and compute engine that captures these primordial capabilities. This system comprises multiple image files encoded into DNA and adsorbed onto ~50 um diameter, highly porous, hierarchically branched, colloidal substrate particles comprised of naturally abundant cellulose acetate. Their surface areas are over 200 cm2/mg with binding capacities of over 1012 DNA oligos/mg, 10 terabytes/mg, or 104 terabytes/cm3. This “dendricolloid” stably holds DNA files better than bare DNA with an extrapolated ability to be repeatedly lyophilized and rehydrated over 170 times compared to 60 times, respectively. Accelerated aging studies project half-lives of ~6000 and 2 million years at 4 ˚C and -18 ˚C, respectively. The data can also be erased and replaced, and non-destructive file access is achieved through transcribing from distinct synthetic promoters. The resultant RNA molecules can be directly read via nanopore sequencing and can also be enzymatically computed to solve simplified 3x3 chess and sudoku problems. Our study establishes a feasible route for utilizing the high information density and parallel computational advantages of nucleic acids. 

Persistent memory presents a great opportunity for crash-consistent computing in large-scale computing systems. The ability to recover data upon power outage or crash events can significantly improve the availability of large-scale systems, while improving the performance of persistent data applications (e.g., database applications). However, persistent memory suffers from high write latency and requires specific programming model (e.g., Intel’s PMDK) to guarantee crash consistency, which results in long latency to persist data. To mitigate these problems, recent standards advocate for sufficient back-up power that can flush the whole cache hierarchy to the persistent memory upon detection of an outage, i.e., extending the persistence domain to include the cache hierarchy. In the secure NVM with extended persistent domain(EPD), in addition to flushing the cache hierarchy, extra actions need to be taken to protect the flushed cache data. These extra actions of secure operation could cause significant burden on energy costs and battery size. We demonstrate that naive implementations could lead to significantly expanding the required power holdup budget (e.g., 10.3x more operations than EPD system without secure memory support). The significant overhead is caused by memory accesses of secure metadata. In this paper, we present Horus, a novel EPD-aware secure memory implementation. Horus reduces the overhead during draining period of EPD system by reducing memory accesses of secure metadata. Experiment result shows that Horus reduces the draining time by 5x, compared with the naive baseline design. 

Abstract MotivationDNA-based data storage is a quickly growing field that hopes to harness the massive theoretical information density of DNA molecules to produce a competitive next-generation storage medium suitable for archival data. In recent years, many DNA-based storage system designs have been proposed. Given that no common infrastructure exists for simulating these storage systems, comparing many different designs along with many different error models is increasingly difficult. To address this challenge, we introduce FrameD, a simulation infrastructure for DNA storage systems that leverages the underlying modularity of DNA storage system designs to provide a framework to express different designs while being able to reuse common components. ResultsWe demonstrate the utility of FrameD and the need for a common simulation platform using a case study. Our case study compares designs that utilize strand copies differently, some that align strand copies using multiple sequence alignment algorithms and others that do not. We found that the choice to include multiple sequence alignment in the pipeline is dependent on the error rate and the type of errors being injected and is not always beneficial. In addition to supporting a wide range of designs, FrameD provides the user with transparent parallelism to deal with a large number of reads from sequencing and the need for many fault injection iterations. We believe that FrameD fills a void in the tools publicly available to the DNA storage community by providing a modular and extensible framework with support for massive parallelism. As a result, it will help accelerate the design process of future DNA-based storage systems. Availability and implementationThe source code for FrameD along with the data generated during the demonstration of FrameD is available in a public Github repository at https://github.com/dna-storage/framed, (https://dx.doi.org/10.5281/zenodo.7757762). 

As interest in DNA-based information storage grows, the costs of synthesis have been identified as a key bottleneck. A potential direction is to tune synthesis for data. Data strands tend to be composed of a small set of recurring code word sequences, and they contain longer sequences of repeated data. To exploit these properties, we propose a new framework called DINOS. DINOS consists of three key parts: (i) The first is a hierarchical strand assembly algorithm, inspired by gene assembly techniques that can assemble arbitrary data strands from a small set of primitive blocks. (ii) The assembly algorithm relies on our novel formulation for how to construct primitive blocks, spanning a variety of useful configurations from a set of code words and overhangs. Each primitive block is a code word flanked by a pair of overhangs that are created by a cyclic pairing process that keeps the number of primitive blocks small. Using these primitive blocks, any data strand of arbitrary length can be assembled, theoretically. We show a minimal system for a binary code with as few as six primitive blocks, and we generalize our processes to support an arbitrary set of overhangs and code words. (iii) We exploit our hierarchical assembly approach to identify redundant sequences and coalesce the reactions that create them to make assembly more efficient. We evaluate DINOS and describe its key characteristics. For example, the number of reactions needed to make a strand can be reduced by increasing the number of overhangs or the number of code words, but increasing the number of overhangs offers a small advantage over increasing code words while requiring substantially fewer primitive blocks. However, density is improved more by increasing the number of code words. We also find that a simple redundancy coalescing technique is able to reduce reactions by 90.6% and 41.2% on average for decompressed and compressed data, respectively, even when the smallest data fragments being assembled are 16 bits. With a simple padding heuristic that finds even more redundancy, we can further decrease reactions for the same operating point up to 91.1% and 59% for decompressed and compressed data, respectively, on average. Our approach offers greater density by up to 80% over a prior general purpose gene assembly technique. Finally, in an analysis of synthesis costs in which we make 1 GB volume using de novo synthesis versus making only the primitive blocks with de novo synthesis and otherwise assembling using DINOS, we estimate DINOS as 10 5 × cheaper than de novo synthesis. 

The performance of persistent applications is severely hurt by current secure processor architectures. Persistent applications use long-latency flush instructions and memory fences to make sure that writes to persistent data reach the persistency domain in a way that is crash consistent. Recently introduced features like Intel's Asynchronous DRAM Refresh (ADR) make the on-chip Write Pending Queue (WPQ) part of the persistency domain and help reduce the penalty of persisting data since data only needs to reach the on-chip WPQ to be considered persistent. However, when persistent applications run on secure processors, for the sake of securing memory many cycles are added to the critical path of their write operations before they ever reach the persistent WPQ, preventing them from fully exploiting the performance advantages of the persistent WPQ. Our goal in this work is to make it feasible for secure persistent applications to benefit more from the on-chip persistency domain. We propose Dolos, an architecture that prioritizes persisting data without sacrificing security in order to gain a significant performance boost for persistent applications. Dolos achieves this goal by an additional minor security unit, Mi-SU, that utilizes a much faster secure process that protects only the WPQ. Thus, the secure operation latency in the critical path of persist operations is reduced and hence persistent transactions can complete earlier. Dolos retains a conventional major security unit for protecting memory that occurs off the critical path after inserting secured data into the WPQ. To evaluate our design, we implemented our architecture in the GEM5 simulator and analyzed the performance of 6 benchmarks from the WHISPER suite. Dolos improves their performance by 1.66x on average. 

Non-volatile memory (NVM) is poised to augment or replace DRAM as main memory. With the right abstraction and support, non-volatile main memory (NVMM) can provide an alternative to the storage system to host long-lasting persistent data. However, keeping persistent data in memory requires programs to be written such that data is crash consistent (i.e. it can be recovered after failure). Critical to supporting crash recovery is the guarantee of ordering of when stores become durable with respect to program order. Strict persistency, which requires persist order to coincide with program order of stores, is simple and intuitive but generally thought to be too slow. More relaxed persistency models are available but demand higher programming complexity, e.g. they require the programmer to insert persist barriers correctly in their program. We identify the source of strict persistency inefficiency as the gap between the point of visibility (PoV) which is the cache, and the point of persistency (PoP) which is the memory. In this paper, we propose a new approach to close the PoV/PoP gap which we refer to as Battery-Backed Buffer (BBB). The key idea of BBB is to provide a battery-backed persist buffer (bbPB) in each core next to the L1 data cache (L1D). A store value is allocated in the bbPB as it is written to cache, becoming part of the persistence domain. If a crash occurs, battery ensures bbPB can be fully drained to NVMM. BBB simplifies persistent programming as the programmer does not need to insert persist barriers or flushes. Furthermore, our BBB design achieves nearly identical results to eADR in terms of performance and number of NVMM writes, while requiring two orders of magnitude smaller energy and time to drain. 

Abstract Data storage in DNA is a rapidly evolving technology that could be a transformative solution for the rising energy, materials, and space needs of modern information storage. Given that the information medium is DNA itself, its stability under different storage and processing conditions will fundamentally impact and constrain design considerations and data system capabilities. Here we analyze the storage conditions, molecular mechanisms, and stabilization strategies influencing DNA stability and pose specific design configurations and scenarios for future systems that best leverage the considerable advantages of DNA storage.