tag:blogger.com,1999:blog-4503292949532760618.post1329088792741269181..comments2024-03-28T07:23:23.408-07:00Comments on DSHR's Blog: Dr. Pangloss and Data in DNADavid.http://www.blogger.com/profile/14498131502038331594noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-4503292949532760618.post-87476343589885002552018-01-25T13:18:50.858-08:002018-01-25T13:18:50.858-08:00Whatever you think about DNA as a storage medium, ...Whatever you think about DNA as a storage medium, you have to be <a href="https://motherboard.vice.com/en_us/article/7xe3dx/dna-storage-bitcoin-mystery-puzzle" rel="nofollow">impressed with its PR</a>:<br /><br />"A three-year old Bitcoin mystery came to an end last week after Sander Wuyts, a 26-year old Belgian PhD student at the University of Antwerp, cracked a code that revealed the key to one bitcoin inside a strand of synthetic DNA.<br /><br />The key—chemicals arranged to represent a string of text—was placed in the DNA as part of the <a href="https://www.ebi.ac.uk/research/goldman/dna-storage" rel="nofollow">DNA Storage Bitcoin Challenge</a>. The challenge began in 2015 after Nick Goldman, a researcher at the European Bioinformatics Institute, gave a presentation on using DNA to store information at the World Economic Forum’s annual meeting in Davos, Switzerland. During this presentation, Goldman distributed tubes of DNA in which he had encoded the key to a digital wallet containing one bitcoin. "<br /><br />But note:<br /><br />"You have to take into account that the process of reading out the data takes a couple of days instead of milliseconds compared to data saved on a hard drive,"David.https://www.blogger.com/profile/14498131502038331594noreply@blogger.comtag:blogger.com,1999:blog-4503292949532760618.post-44877999313560553922017-10-28T13:17:16.325-07:002017-10-28T13:17:16.325-07:00The paper describing data encoded in synthetic mon...The paper describing data encoded in synthetic monomers is <a href="https://dx.doi.org/10.1038/s41467-017-01104-3" rel="nofollow">here</a>. The <a href="http://www2.cnrs.fr/en/2977.htm" rel="nofollow">CNRS press release states</a>:<br /><br />"The team of chemists managed to synthesize polymers that can store up to eight bytes. Thus, they were able to record the word 'Sequence' in ASCII code, which assigns a unique byte to each letter and punctuation mark. By successfully decoding this word using mass spectrometry, they set a new record for the length of a molecule that may be read using this technique. Although manual analysis of the digital data does take a few hours, it should be possible to reduce the time needed to a few milliseconds by developing software to perform this task."David.https://www.blogger.com/profile/14498131502038331594noreply@blogger.comtag:blogger.com,1999:blog-4503292949532760618.post-58197059368732665192017-10-19T19:33:07.189-07:002017-10-19T19:33:07.189-07:00Chris Mellor at The Register reports on data stora...Chris Mellor at <i>The Register</i> reports on <a href="https://www.theregister.co.uk/2017/10/18/storing_data_in_monomers_read_through_mass_spectroscopy/" rel="nofollow">data storage in synthetic monomers</a>:<br /><br />"The basic storage element is a synthetic monomer, a molecule, which groups with others to form a chain called a polymer. In DNA the monomers are nucleotides and these are natural. The synthesised monomers here were designed to be sequenced (analysed) using moderate resolution mass spectroscopy (MS).<br /><br />Data is "written" using an automated monomer-polymer production method, assembled, or rather synthesized by automated phosphoramidite chemistry, into readable digital sequences - poly(phosphodiester)s chains."David.https://www.blogger.com/profile/14498131502038331594noreply@blogger.comtag:blogger.com,1999:blog-4503292949532760618.post-30090935543889288152017-08-10T09:16:06.348-07:002017-08-10T09:16:06.348-07:00The University of Washington team write:
"Th...The <a href="http://dnasec.cs.washington.edu/dnasec.pdf" rel="nofollow">University of Washington team write</a>:<br /><br />"The rapid improvement in DNA sequencing has sparked a big data revolution in genomic sciences, which has in turn led to a proliferation of bioinformatics tools. To date, these tools have encountered little adversarial pressure. This paper evaluates the robustness of such tools if (or when) adversarial attacks manifest. We demonstrate, for the first time, the synthesis of DNA which — when sequenced and processed — gives an attacker arbitrary remote code execution."David.https://www.blogger.com/profile/14498131502038331594noreply@blogger.comtag:blogger.com,1999:blog-4503292949532760618.post-41557358684412381782017-06-19T14:45:19.548-07:002017-06-19T14:45:19.548-07:00Digital-to-biological converter for on-demand prod...<a href="https://doi.org/10.1038/nbt.3859" rel="nofollow"><i>Digital-to-biological converter for on-demand production of biologics</i></a> by Kent S. Boles <i>et al</i> describes a combination of off-the-shelf hardware and software that can synthesize DNA sequences, among other things. The abstract is:<br /><br />"Manufacturing processes for biological molecules in the research laboratory have failed to keep pace with the rapid advances in automization and parellelization. We report the development of a digital-to-biological converter for fully automated, versatile and demand-based production of functional biologics starting from DNA sequence information. Specifically, DNA templates, RNA molecules, proteins and viral particles were produced in an automated fashion from digitally transmitted DNA sequences without human intervention."<br /><br />Eliminating human intervention will reduce costs, but not by the 6+ orders of magnitude needed to make DNA a viable storage medium.David.https://www.blogger.com/profile/14498131502038331594noreply@blogger.comtag:blogger.com,1999:blog-4503292949532760618.post-84867318825932346022017-04-25T07:02:36.573-07:002017-04-25T07:02:36.573-07:00The Microsoft/UW team continue their work with a s...The Microsoft/UW team continue their work with a <a href="https://boingboing.net/2017/04/24/sikh-coders-excellent-protes.html" rel="nofollow">second 10M-strand deal with Twist Bioscience</a>.David.https://www.blogger.com/profile/14498131502038331594noreply@blogger.comtag:blogger.com,1999:blog-4503292949532760618.post-88226616577627534742017-03-29T01:09:17.859-07:002017-03-29T01:09:17.859-07:00DNA isn't just capable of storing data, but al...DNA isn't just capable of storing data, but also of <a href="https://doi.org/10.1038/nbt.3805" rel="nofollow">processing data</a>. In <a href="https://doi.org/10.1038/nbt.3805" rel="nofollow"><i>Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells</i></a> Weinberg <i>et al</i> present:<br /><br />"a robust, general, scalable system, called 'Boolean logic and arithmetic through DNA excision' (BLADE), to engineer genetic circuits with multiple inputs and outputs in mammalian cells with minimal optimization."David.https://www.blogger.com/profile/14498131502038331594noreply@blogger.com