Dna-storalator: a computational simulator for DNA data storage
Background DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium and thus presents an extremely dense and durable storage device. However, the unique nature of the errors in DNA, which include in...
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| Published in | BMC bioinformatics Vol. 26; no. 1; pp. 204 - 17 |
|---|---|
| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
BioMed Central
04.08.2025
BioMed Central Ltd Springer Nature B.V BMC |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1471-2105 1471-2105 |
| DOI | 10.1186/s12859-025-06222-0 |
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| Abstract | Background
DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium and thus presents an extremely dense and durable storage device. However, the unique nature of the errors in DNA, which include insertion, deletion, and substitution errors, requires the development of new algorithmic and coding solutions for these storage systems.
Results
The DNA-Storalator is a cross-platform software tool that simulates in a simplified digital point of view biological and computational processes involved in the process of storing data in DNA molecules. The simulator receives an input file with the designed DNA strands that store digital data and emulates the different biological and algorithmical components of DNA-based storage system. The biological component includes simulation of the synthesis, PCR, and sequencing stages which are expensive and complicated and therefore are not widely accessible to the community. These processes amplify the data and generate noisy copies of each DNA strand, where the errors are insertions, deletions, long-deletions, and substitutions. The DNA-Storalator injects errors to the data based on the error rates, as they vary between different synthesis and sequencing technologies. The rates are based on comprehensive analysis of data from previous experiments but can also be customized. Additionally, the tool can analyze new datasets and characterize their error rates to build new error models for future usage in the simulator. The DNA-Storalator also enables control of the amplification process and the distribution of the number of copies per designed strand. The coding and algorithmic components are: 1. Clustering algorithms which partition all output noisy strands into groups according to the designed strand they originated from; 2. State-of-the-art reconstruction algorithms that are invoked on each cluster to output a close/exact estimation of the designed strand; 3. Integration with external error-correcting codes and other encoding and decoding techniques.
Conclusions
The suggested computational DNA storage simulator grants researchers from all fields an accessible complete simulator to examine new biological technologies, coding techniques, and algorithms for current and future DNA storage systems.
Keywords
: DNA data storage, DNA storage simulator, reconstruction algorithms, clustering algorithms, DNA sequencing errors, DNA synthesis errors, DNA-based data storage |
|---|---|
| AbstractList | Abstract Background DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium and thus presents an extremely dense and durable storage device. However, the unique nature of the errors in DNA, which include insertion, deletion, and substitution errors, requires the development of new algorithmic and coding solutions for these storage systems. Results The DNA-Storalator is a cross-platform software tool that simulates in a simplified digital point of view biological and computational processes involved in the process of storing data in DNA molecules. The simulator receives an input file with the designed DNA strands that store digital data and emulates the different biological and algorithmical components of DNA-based storage system. The biological component includes simulation of the synthesis, PCR, and sequencing stages which are expensive and complicated and therefore are not widely accessible to the community. These processes amplify the data and generate noisy copies of each DNA strand, where the errors are insertions, deletions, long-deletions, and substitutions. The DNA-Storalator injects errors to the data based on the error rates, as they vary between different synthesis and sequencing technologies. The rates are based on comprehensive analysis of data from previous experiments but can also be customized. Additionally, the tool can analyze new datasets and characterize their error rates to build new error models for future usage in the simulator. The DNA-Storalator also enables control of the amplification process and the distribution of the number of copies per designed strand. The coding and algorithmic components are: 1. Clustering algorithms which partition all output noisy strands into groups according to the designed strand they originated from; 2. State-of-the-art reconstruction algorithms that are invoked on each cluster to output a close/exact estimation of the designed strand; 3. Integration with external error-correcting codes and other encoding and decoding techniques. Conclusions The suggested computational DNA storage simulator grants researchers from all fields an accessible complete simulator to examine new biological technologies, coding techniques, and algorithms for current and future DNA storage systems. Keywords: DNA data storage, DNA storage simulator, reconstruction algorithms, clustering algorithms, DNA sequencing errors, DNA synthesis errors, DNA-based data storage DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium and thus presents an extremely dense and durable storage device. However, the unique nature of the errors in DNA, which include insertion, deletion, and substitution errors, requires the development of new algorithmic and coding solutions for these storage systems. The DNA-Storalator is a cross-platform software tool that simulates in a simplified digital point of view biological and computational processes involved in the process of storing data in DNA molecules. The simulator receives an input file with the designed DNA strands that store digital data and emulates the different biological and algorithmical components of DNA-based storage system. The biological component includes simulation of the synthesis, PCR, and sequencing stages which are expensive and complicated and therefore are not widely accessible to the community. These processes amplify the data and generate noisy copies of each DNA strand, where the errors are insertions, deletions, long-deletions, and substitutions. The DNA-Storalator injects errors to the data based on the error rates, as they vary between different synthesis and sequencing technologies. The rates are based on comprehensive analysis of data from previous experiments but can also be customized. Additionally, the tool can analyze new datasets and characterize their error rates to build new error models for future usage in the simulator. The DNA-Storalator also enables control of the amplification process and the distribution of the number of copies per designed strand. The coding and algorithmic components are: 1. Clustering algorithms which partition all output noisy strands into groups according to the designed strand they originated from; 2. State-of-the-art reconstruction algorithms that are invoked on each cluster to output a close/exact estimation of the designed strand; 3. Integration with external error-correcting codes and other encoding and decoding techniques. The suggested computational DNA storage simulator grants researchers from all fields an accessible complete simulator to examine new biological technologies, coding techniques, and algorithms for current and future DNA storage systems. Background DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium and thus presents an extremely dense and durable storage device. However, the unique nature of the errors in DNA, which include insertion, deletion, and substitution errors, requires the development of new algorithmic and coding solutions for these storage systems. Results The DNA-Storalator is a cross-platform software tool that simulates in a simplified digital point of view biological and computational processes involved in the process of storing data in DNA molecules. The simulator receives an input file with the designed DNA strands that store digital data and emulates the different biological and algorithmical components of DNA-based storage system. The biological component includes simulation of the synthesis, PCR, and sequencing stages which are expensive and complicated and therefore are not widely accessible to the community. These processes amplify the data and generate noisy copies of each DNA strand, where the errors are insertions, deletions, long-deletions, and substitutions. The DNA-Storalator injects errors to the data based on the error rates, as they vary between different synthesis and sequencing technologies. The rates are based on comprehensive analysis of data from previous experiments but can also be customized. Additionally, the tool can analyze new datasets and characterize their error rates to build new error models for future usage in the simulator. The DNA-Storalator also enables control of the amplification process and the distribution of the number of copies per designed strand. The coding and algorithmic components are: 1. Clustering algorithms which partition all output noisy strands into groups according to the designed strand they originated from; 2. State-of-the-art reconstruction algorithms that are invoked on each cluster to output a close/exact estimation of the designed strand; 3. Integration with external error-correcting codes and other encoding and decoding techniques. Conclusions The suggested computational DNA storage simulator grants researchers from all fields an accessible complete simulator to examine new biological technologies, coding techniques, and algorithms for current and future DNA storage systems. Keywords : DNA data storage, DNA storage simulator, reconstruction algorithms, clustering algorithms, DNA sequencing errors, DNA synthesis errors, DNA-based data storage BackgroundDNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium and thus presents an extremely dense and durable storage device. However, the unique nature of the errors in DNA, which include insertion, deletion, and substitution errors, requires the development of new algorithmic and coding solutions for these storage systems.ResultsThe DNA-Storalator is a cross-platform software tool that simulates in a simplified digital point of view biological and computational processes involved in the process of storing data in DNA molecules. The simulator receives an input file with the designed DNA strands that store digital data and emulates the different biological and algorithmical components of DNA-based storage system. The biological component includes simulation of the synthesis, PCR, and sequencing stages which are expensive and complicated and therefore are not widely accessible to the community. These processes amplify the data and generate noisy copies of each DNA strand, where the errors are insertions, deletions, long-deletions, and substitutions. The DNA-Storalator injects errors to the data based on the error rates, as they vary between different synthesis and sequencing technologies. The rates are based on comprehensive analysis of data from previous experiments but can also be customized. Additionally, the tool can analyze new datasets and characterize their error rates to build new error models for future usage in the simulator. The DNA-Storalator also enables control of the amplification process and the distribution of the number of copies per designed strand. The coding and algorithmic components are: 1. Clustering algorithms which partition all output noisy strands into groups according to the designed strand they originated from; 2. State-of-the-art reconstruction algorithms that are invoked on each cluster to output a close/exact estimation of the designed strand; 3. Integration with external error-correcting codes and other encoding and decoding techniques.ConclusionsThe suggested computational DNA storage simulator grants researchers from all fields an accessible complete simulator to examine new biological technologies, coding techniques, and algorithms for current and future DNA storage systems.Keywords: DNA data storage, DNA storage simulator, reconstruction algorithms, clustering algorithms, DNA sequencing errors, DNA synthesis errors, DNA-based data storage DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium and thus presents an extremely dense and durable storage device. However, the unique nature of the errors in DNA, which include insertion, deletion, and substitution errors, requires the development of new algorithmic and coding solutions for these storage systems. The DNA-Storalator is a cross-platform software tool that simulates in a simplified digital point of view biological and computational processes involved in the process of storing data in DNA molecules. The simulator receives an input file with the designed DNA strands that store digital data and emulates the different biological and algorithmical components of DNA-based storage system. The biological component includes simulation of the synthesis, PCR, and sequencing stages which are expensive and complicated and therefore are not widely accessible to the community. These processes amplify the data and generate noisy copies of each DNA strand, where the errors are insertions, deletions, long-deletions, and substitutions. The DNA-Storalator injects errors to the data based on the error rates, as they vary between different synthesis and sequencing technologies. The rates are based on comprehensive analysis of data from previous experiments but can also be customized. Additionally, the tool can analyze new datasets and characterize their error rates to build new error models for future usage in the simulator. The DNA-Storalator also enables control of the amplification process and the distribution of the number of copies per designed strand. The coding and algorithmic components are: 1. Clustering algorithms which partition all output noisy strands into groups according to the designed strand they originated from; 2. State-of-the-art reconstruction algorithms that are invoked on each cluster to output a close/exact estimation of the designed strand; 3. Integration with external error-correcting codes and other encoding and decoding techniques. The suggested computational DNA storage simulator grants researchers from all fields an accessible complete simulator to examine new biological technologies, coding techniques, and algorithms for current and future DNA storage systems. Background DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium and thus presents an extremely dense and durable storage device. However, the unique nature of the errors in DNA, which include insertion, deletion, and substitution errors, requires the development of new algorithmic and coding solutions for these storage systems. Results The DNA-Storalator is a cross-platform software tool that simulates in a simplified digital point of view biological and computational processes involved in the process of storing data in DNA molecules. The simulator receives an input file with the designed DNA strands that store digital data and emulates the different biological and algorithmical components of DNA-based storage system. The biological component includes simulation of the synthesis, PCR, and sequencing stages which are expensive and complicated and therefore are not widely accessible to the community. These processes amplify the data and generate noisy copies of each DNA strand, where the errors are insertions, deletions, long-deletions, and substitutions. The DNA-Storalator injects errors to the data based on the error rates, as they vary between different synthesis and sequencing technologies. The rates are based on comprehensive analysis of data from previous experiments but can also be customized. Additionally, the tool can analyze new datasets and characterize their error rates to build new error models for future usage in the simulator. The DNA-Storalator also enables control of the amplification process and the distribution of the number of copies per designed strand. The coding and algorithmic components are: 1. Clustering algorithms which partition all output noisy strands into groups according to the designed strand they originated from; 2. State-of-the-art reconstruction algorithms that are invoked on each cluster to output a close/exact estimation of the designed strand; 3. Integration with external error-correcting codes and other encoding and decoding techniques. Conclusions The suggested computational DNA storage simulator grants researchers from all fields an accessible complete simulator to examine new biological technologies, coding techniques, and algorithms for current and future DNA storage systems. Keywords: DNA data storage, DNA storage simulator, reconstruction algorithms, clustering algorithms, DNA sequencing errors, DNA synthesis errors, DNA-based data storage DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium and thus presents an extremely dense and durable storage device. However, the unique nature of the errors in DNA, which include insertion, deletion, and substitution errors, requires the development of new algorithmic and coding solutions for these storage systems.BACKGROUNDDNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium and thus presents an extremely dense and durable storage device. However, the unique nature of the errors in DNA, which include insertion, deletion, and substitution errors, requires the development of new algorithmic and coding solutions for these storage systems.The DNA-Storalator is a cross-platform software tool that simulates in a simplified digital point of view biological and computational processes involved in the process of storing data in DNA molecules. The simulator receives an input file with the designed DNA strands that store digital data and emulates the different biological and algorithmical components of DNA-based storage system. The biological component includes simulation of the synthesis, PCR, and sequencing stages which are expensive and complicated and therefore are not widely accessible to the community. These processes amplify the data and generate noisy copies of each DNA strand, where the errors are insertions, deletions, long-deletions, and substitutions. The DNA-Storalator injects errors to the data based on the error rates, as they vary between different synthesis and sequencing technologies. The rates are based on comprehensive analysis of data from previous experiments but can also be customized. Additionally, the tool can analyze new datasets and characterize their error rates to build new error models for future usage in the simulator. The DNA-Storalator also enables control of the amplification process and the distribution of the number of copies per designed strand. The coding and algorithmic components are: 1. Clustering algorithms which partition all output noisy strands into groups according to the designed strand they originated from; 2. State-of-the-art reconstruction algorithms that are invoked on each cluster to output a close/exact estimation of the designed strand; 3. Integration with external error-correcting codes and other encoding and decoding techniques.RESULTSThe DNA-Storalator is a cross-platform software tool that simulates in a simplified digital point of view biological and computational processes involved in the process of storing data in DNA molecules. The simulator receives an input file with the designed DNA strands that store digital data and emulates the different biological and algorithmical components of DNA-based storage system. The biological component includes simulation of the synthesis, PCR, and sequencing stages which are expensive and complicated and therefore are not widely accessible to the community. These processes amplify the data and generate noisy copies of each DNA strand, where the errors are insertions, deletions, long-deletions, and substitutions. The DNA-Storalator injects errors to the data based on the error rates, as they vary between different synthesis and sequencing technologies. The rates are based on comprehensive analysis of data from previous experiments but can also be customized. Additionally, the tool can analyze new datasets and characterize their error rates to build new error models for future usage in the simulator. The DNA-Storalator also enables control of the amplification process and the distribution of the number of copies per designed strand. The coding and algorithmic components are: 1. Clustering algorithms which partition all output noisy strands into groups according to the designed strand they originated from; 2. State-of-the-art reconstruction algorithms that are invoked on each cluster to output a close/exact estimation of the designed strand; 3. Integration with external error-correcting codes and other encoding and decoding techniques.The suggested computational DNA storage simulator grants researchers from all fields an accessible complete simulator to examine new biological technologies, coding techniques, and algorithms for current and future DNA storage systems.CONCLUSIONSThe suggested computational DNA storage simulator grants researchers from all fields an accessible complete simulator to examine new biological technologies, coding techniques, and algorithms for current and future DNA storage systems. |
| ArticleNumber | 204 |
| Audience | Academic |
| Author | Sabary, Omer Yaakobi, Eitan Shabat, Dvir Ben Furman, Nili Chaykin, Gadi |
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| Keywords | reconstruction algorithms DNA sequencing errors DNA synthesis errors DNA-based data storage DNA storage simulator clustering algorithms DNA data storage |
| Language | English |
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DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a... DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium... Background DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a... BackgroundDNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a... Abstract Background DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules... |
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| SubjectTerms | Accessibility Algorithms Analysis Bioinformatics Biological activity Biomedical and Life Sciences Clustering Computational Biology - methods Computational Biology/Bioinformatics Computer Appl. in Life Sciences Computer applications Computer Simulation Data storage Decoding Deoxyribonucleic acid Design Digital data DNA DNA - chemistry DNA - genetics DNA biosynthesis DNA sequencing DNA synthesis Error correcting codes Error correction Error correction & detection Gene sequencing Information Storage and Retrieval - methods Life Sciences Microarrays Nucleotide sequencing Performance evaluation Polymerase chain reaction Probability Random variables Reconstruction Sequence Analysis, DNA - methods Simulation Software Storage systems Strands Synthesis Technology Technology application Testing |
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| Title | Dna-storalator: a computational simulator for DNA data storage |
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