User Manual
Contents
1. 0 Disclaimer This values are just an approximation the actual www guptalab org dnacloud values may vary Report bugs at dnacloud gupta Figure 3 Estimate of Memory required for encoding the file to DNA DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org Pt 2 g a DNA CLOUD 4 File Preferences Help Generate File from DNA String Please Write DNA String Decode Reset Generate File from already encoded files Estimate properties File Selected C Users Win8_Jenovo Desktop encodeok y Choose File Select a DNA File from your Fie System Enter salt concentration mM 1 Lenght Of DNA String approx 300325 Enter cost for a base 1 Number of DNA Chunks approx 12010 T e Veasciea He File Selected C Users Win8_lenovo Desktop encodeok jpg dna Details for the DNA GC Content in DNA String 50 0671487603 Total Cost of DNA String 290400 0 Min Melting Point A C nuceotide 4 30196581197 Max Melting Point A C nudeotide 4 21435897436 DNA CLOUD A 2013 Generated using DNA CLOUD Version 1 0 www guptalab org dnacloud Report bugs at dnacloud gupta Disclaimer This values are just an approximation and the actual values may vai 1 50 AM 7 27 2013 Pf a Figure 4 Estimate of Memory required for encoding the file to DNA 4 Export This will help the user to export the file generated to different formats DNA2. File Selected C Users Win8_lenovo Desktop encodeok Mobile Number 9069599059 Lenght Of DNA String approx 300325 Email Address pinky gmail com Number of DNA Chunks approx 12010 File Name Eg a mkv dna encode jog dna Select dna File Decode selected File U te taneh paconensa spg Am IEAA poke DNA CLOUD Disclaimer Please note that this details will be used to identify user of the DNA strings by Bio Companies hence these are mandatory to be filled Version 1 0 www guptalab org dnacioud Sess Gana aaia Close Report bugs at dnacloud gup a HS j Figure 6 User details and barcode generated 8 Help Menu Help menu which is tells about the software and developers There are four options in the Help Menu 1 User Manual 2 Product Demo 3 Product Feedback 4 About Us e First option will open default User Manual document in user s default PDF reader software e Second option product demo will open the homepage of DNA Cloud where the demo is available e Third option will open the feedback form where you can give feedback for the softwate DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org 11 Finally about option recognize the contributors in this project There is a dialog box that opens which contains information like logo of the software version of the software name of the software License of the software Credits button and URL of the
3. These values are approximated File size in bytes Size of DNA string Free Memory Required DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org 7 To generate DNA chunks To generate DNA strings Amount of DNA Required Biochemical Properties This will estimate the biochemical properties of the DNA sequence used to store the data Select dna file from the system which contains the DNA sequences to estimate the properties This will take salt concentration mM and cost per base as an input Calculate option will estimate the GC content of DNA melting temperature of the DNA and total cost to store the file in DNA as shown in Figure 4 All the values are approximated Save option can be used to save estimated information B DNA CLOUD File Preferences Help Generate File from DNA String Please Write DNA String Decode Reset Generate File from already encoded files Estimate the numbers File Selected C Users Win8_lenovo Desktop encodeok l Choose File Selecta File from your File System Lenght Of DNA String approx 300325 File Size bytes 1405172 Size of DNA String 7728446 Number of DNA Chunks approx 12010 Free Memory Required To genrate DNA String 8MB To generate DNA Chunks 36 MB Select dna File Decode selected File Amount of DNA Required 1 405172e 14 gms File Selected C Users Win8_lenovo Desktop encodeok jpg dna DNA CLOUD Version 1
4. Laboratory of Natural Information Processing DA IICT Gandhinagar DNA Cloud 2 0 User Manual DNA CLOUD DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org DNA Cloud 2 0 User Manual 2015 Manish K Gupta Laboratory of Natural Information Processing DA IICT Gandhinagar Gujarat 382007 http www guptalab org dnacloud The software described in this book is furnished under an open source license agreement and may be used only in accordance with the terms of the agreement Any selling or distribution of the program or its parts original or modified is prohibited without a written permission from Manish K Gupta Documentation version 2 0 This file was last modified on Jan 27 2015 Credits amp Team Principle Investigator Manish K Gupta PhD Graduate Mentor Dixita Limbachiya Developers Vijay Dhameliya Madhav Khakhar Software Logo Foram Joshi Acknowledgments We would like to thank Thorsten Weimann and Anand B Pillai whose open source libraries python barcode and pytxt2pdf respectively have been used in the softwate DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org Table of contents General Information Page No 1 Introduction 3 2 Overview 3 Product Scope 4 Product Perspective System Summary 4 Getting Started 4 5 User Details 6 Encode 7 Decode 5 8 Estimator 6 9 Export 8 10 Help 9 Support and Feedback 10
5. References 10 DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org General Information 1 Introduction The world data increase two fold every year To store this huge data is burning issue Since time immemorial mankind has wanted to shate and use information for later use First it was through the caveman paintings and symbols Then we invented the alphabets ideograms numbers and other symbols Using these books were written and stored for future generations in palm leaves papyrus sheets or paper The invention of printing brought the Gutenberg revolution making multiple copies easily and spreading education to millions of people Printed books occupy space Libraries and archives are bursting at the seams Enter the computer age and digitization using the binary code of combining zeros and ones 0 1 for alphabets and other such symbols and reading them using the on off electrical signals which has made electronic storage possible cutting down the size and space for hard copies Integrated circuits processors and related electronic wizardry have shrunk the size of computers and storage devices from room size to finger nail size But the storage and maintenance on this energy craving devices is burdensome With the idea of using the natural hard drive DNA as storage device Goldman 2013 e al 1 and Church 2012 e al 2 had stored file of size one Peta Bytes on 1 gram of DNA Inspired from the
6. ants compress data he can choose lossless compression Once the user selects the file to be encoded the list of information for the encoded file will be displayed as below Length of DNA stting No of DNA oligonucleotides chunks Length of each DNA oligonucleotide File size in bytes To save the encoded file user can save the file with specific name on specific location by using Encode your File button It will generate the file with extension dna that has DNA string for the file selected RESET button can clear the selected file and select new file by this option It is like clear button Lec I E o Fie Preferences Help Follow Us DNA ENCODER Encode data file into DNA String Select any data fle audio video doc etc from your computer Detalls approx Fie Selected D dec2014 naturalcomputingDec201 4 Supple_Golaycode dnastoragecapacitycalculation decoder png Lenght Of DNA Sting 728931 Number of DNA Chunks 23154 Length of each DNA Chunk 117 File Size Bytes 132533 Golay Encoding wi Encode you File Reset file Selected No Compeession DNA CLOUD Version 1 0 Visit us at www guptalab org dnacioud Contact us at dnacloud guptatab org C 2013 Gupta Lab ww guptalab org dnacloud ar ao On 29 01 2015 Figure 1 File to DNA Encode 2 Decode This option is available under the file menu which will retrieve the data stored in DNA DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Vis
7. g Started Once you have successfully installed the software open DNA Cloud by double clicking on the icon available on your desktop screen a window with three menu options on the menu bar will appear The dialogue box will appear with two buttons If user wants to convert the data to DNA string click on File to DNA button If user wants to retrieve the data stored in DNA select DNA to File options Software has following main sections File menu includes following option Encode File to DNA Decode DNA to File Estimator Export Generated Barcode Export DNA Synthesizer file Import DNA Sequencer file Export dna to PDF Clear temp files NS NN NN NNR Exit Preferences menu includes following option Password protection Change password User Details 1 Encode This option is available under the File menu which will convert any type of data to DNA strings When the user clicks on this option the screen in as shown in figure 1 appears User has to select the file to be converted into DNA string by clicking on Choose File button In DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org DNA Cloud 2 0 there is additional feature for select the type of data encoding technique and compression technique User can select Golay code type of encoding for compress and efficient data encoding Also user can select the type of compression There is option for lossy and lossless compression If user w
8. itus athttp www guptalab org 6 When the user clicks on this option the screen in as shown in Figure 2 appears User can enter the DNA string from which data is to be retrieved in the text box against Please write DNA string option Select dna file option Once the file to be decoded is selected click on Decode Selected file option To save the decoded file give the name and save the file at specific location This will generate the original file that was encoded in DNA RESET button can clear the selected file and select new file by this option It is like clear button DNA4 CLOUD File Preferences Help Follow Us DNA DECODER Generate data file from already encoded DNA files Fie Selected E eg encoded_dixita_ png dnac Length of DNA String approx 580550 Number of DNA Chunks approx gt 23219 Select dnac File GolayDecodng Decode selected File Try DNA String just for fun Please Write DNA Sting Decode Reset DNA CLOUD Version 1 0 Visit us at www guptalab org dnacioud Contact us at dnacloud guptatab org C 2013 Gupta Lab ww guptalab oig dnacloud 29 01 2015 a E Figure 2 DNA to File Decode 3 Estimator This will give various statistics for encoded file and biochemical properties of DNA of the decoded file Estimator has two main sections Memory Required User can select the file to be encoded from the system and the following values of the file are estimated as given in Figure 3
9. software It will remove all the files generated by the software 6 Exit Exit will help to quit from the software 7 User details This option is available in preferences menu This is mandatory to make the data of the user stored in the DNA to avail only to the respective user For the data security user has to feed his details in the dialogue box as given below Once the user feeds the data as shown in Figure 6 the dialogue box to enter the password appear This help to user to retrieve his files converted to DNA safely If user does not feed the information the software will remind it again and dialogue box will appear again and again till the user enters the details Barcode for the user information is generated by which one can retrieve the data easily It includes the information like name of the user contact number email address Generate Barcode will generate barcode for the user details along with the filename stored Barcode can be exported to other image formats by using Export Generated Barcode option in File menu DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org 10 These barcode generated can be used by biotech companies to tag the DNA on which the particular file is to be stored u DNA CLOUD s File Preferences Help Generate File from DNA String Please Write DNA String Decode Reset Generate File from already encoded files Enter your details Full Name Dixita Limbachiya
10. software On pressing Credits it opens a PDF document for the credits Support and Feedback Users ate requested to contact team at the email dnacloud guptalab org for feedback and any other issues with the software Two platform specific installers Windows and Mac and Linux are available on the project home page along with source code with open soutce license agreement References 1 Goldman Nick et al Towards practical high capacity low maintenance information storage in synthesized DNA Nature 2013 2 Church George M Yuan Gao and Sriram Kosuri Next generation digital information storage in DNA Science 337 6102 2012 1628 1628 DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org 13
11. strings can be exported to file format that can be used as input for the synthesizer File can be exported to FASTQ file format that is required by the sequencer These options are available in File menu This will generate the feasible output of the DNA sttings that is to be used by respective machines To export the DNA file for the synthesizer to synthesize the DNA use Export DNA synthesizer File option To decode the file stored in DNA use Import DNA sequencer file option to get the DNA sequences to be decoded Above mentioned export options are under development it will be available in next version The dna file can be exported to PDF with all software output details in single PDF by using the option Export dna to PDF in the File menu as shown in Figure 5 DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org 9 File Preferences Help File to DNA DNA to File Estimator gt Export Generated Barcode Export DNA Synthesizer File Import DNA Sequencer File Export dna to pdf with Details Clear temp Files C Users Win8 _Jenovo pesktop encodeok jpg dna Bit 300325 Number of DNA Chunks approx 12010 Select dna File Decode selected File DNA CLOUD Version 1 0 www guptalab org dnacloud Report bugs at dnacloud guptalab org 1 53 AM 1 27 2013 f ao Figure 5 Export dna to PDF 5 Clear temp files This will clear all your history of the
12. work of Goldman we have developed the software DNA Cloud for encoding and decoding the file to DNA We have used the encoding and decoding method described by the Goldman in 1 We have made the encoding and decoding procedure memory efficient 2 Overview DNA Cloud has been primarily developed to facilitate the storage of data in DNA The software encourages the users to encode and decode the data It converts any type of data into DNA strings and enables it to store in DNA Also it helps to retrieve the data stored in DNA 3 Product Scope This software provides the user with e Encode the any type of data text image audio and video to DNA string e Decode the data stored in the DNA string e Estimator is used to estimate the total length of DNA string used to convert the data and also the cost for the storage and biochemical properties of DNA e Export the converted data to various feasible formats for different application DNA Cloud 2 0 User Manual Last updated on Jan 28 2015 Visitus athttp www guptalab org 4 Product Perspective This product s main aim is to make the process of making the computerization and computation of DNA storage user friendly System Summary Operating Systems Windows 7 Mac OS X Linux This software requires the system to have specifications similar to Processor of 2 4 GHz Core 2 Duo 100 MB Hard Disk 1GB Random Access Memory and Basic peripherals like keyboard mouse etc Gettin
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