Spring Batch + Karp Rabin = How Crispr Cas 9 Works
Is there a mathematical model or informatic one to describe how Crispr Cas9 works? I don't know.
I share with you my theoretical Model on How Crispr Cas 9 Works.
Spring Batch + Karp Rabin = How Crispr Cas 9 Works
Vulgarization Spring Batch + Karp Rabin = How Crispr Cas9 works
Author : Wadï Mami
Publication Date : 07/06/2021
Email : wmami@steg.com.tn
Wadï Mami Theory on explaining how Could Spring Batch + karp rabin explain how Crispr Cas9 Works.
CRISPR-Cas9
CRISPR-Cas9 was adapted from a naturally occurring genome editing system in bacteria. The bacteria capture snippets of DNA from invading viruses and use them to create DNA segments known as CRISPR arrays.The CRISPR arrays allow the bacteria to "remember" the viruses (or closely related ones). If the viruses attack again, the bacteria produce RNA segments from the CRISPR arrays to target the viruses' DNA. The bacteria then use Cas9 or a similar enzyme to cut the DNA apart, which disables the virus.
Spring Batch reads and process DNA sequentially until reaching commit-interval value then it writes transformed items (DNA) simultaneously.
ItemReader, handed to an ItemProcessor, and aggregated. Once the number of items read equals the commit intervalBelow is a code representation of the same concepts shown above:
List items = new Arraylist(); for(int i = 0; i < commitInterval; i++){ Object item = itemReader.read() Object processedItem = itemProcessor.process(item); items.add(processedItem); } itemWriter.write(items);
Spring Batch is the bacteria.
The bacteria capture snippets of DNA from invading viruses and use them to create DNA segments known as CRISPR
arrays
example private String dna_pattern = "AATTCC"; //snippets of DNA from invading viruses in
<=> Spring Batch read DNA file or DNA database , The DNA file or the DNA database are Viruses DNA.
SpringBatch read() --->ItemReader and ItemReader return item. <=> Spring Batch process() ----> ItemProcessor and
return transformed item = DNA segments known as CRISPR arrays Here I use DNA_sequenceProcessor class that
implements ItemProcessor and uses Karp Rabin (you can use other DNA pattern recognition algorithm)
The CRISPR arrays allow the bacteria to "remember" the viruses (or closely related ones). If the viruses attack again,
the bacteria produce RNA segments from the CRISPR arrays to target the viruses' DNA example private String
dna_pattern = "AATTCC"; in
The bacteria then use Cas9 or a similar enzyme to cut the DNA apart, which disables the virus.
<=> Spring batch write(transformed items) ----> ItemWriter ( cut Virus DNA ).
Conclusion
Spring Batch + Karp Rabin = how CRISPR Cas9 works is my IT theoretical model may be it could be interesting and useful for drugs discovery. The model is an idea that had been haunting me since 2012. I share it with you. I can’t go further with it, may be you find it useful interesting and continue developement. The model is under MIT License
https://github.com/didipostman/CrisprCas9
If the Theory model is wrong or unseful or uninteresting read below there is always something to win from this idea
Abstract :
Processing large volume of data has always been a major problem due to the increasing volume of the data. Batch processing can be applied in many use cases. Among them why not Pattern Matching for DNA Sequencing Data. In this article, I am going to demonstrate batch processing using one of the projects of Spring which is Spring Batch. Spring Batch provides functions for processing large volumes of data in batch jobs. In our case reading DNA file or database table and seeking for patterns I mean all the locations of the specified pattern inside a DNA sequence.
Spring batch to process huge data : Spring Batch is a lightweight, comprehensive batch framework designed to enable the development of robust batch applications vital for the daily operations of enterprise systems.
A step is an object that encapsulates a sequential phase of a job and holds all the necessary information to define and control processing. It delegates all the
information to a Job (job.xml) to carry out its task.
<step id="dnaSeqStep">
<tasklet transaction-manager="transactionManager">
<chunk reader="csvItemReader" writer="csvItemWriter"
processor="DNA_SequenceProcessor" commit-interval="2">
</chunk>
</tasklet>
</step>
Configuring ItemReader We will now define ItemReader for our model which will be used for
reading data from CSV file.
<bean:property name="resource"
value="classpath:ch02/data/DNA.csv"/>
<bean:property name="lineMapper">
<bean:bean
class="org.springframework.batch.item.file.mapping.DefaultLineMapper">
<bean:property name="lineTokenizer" ref="lineTokenizer"/>
<bean:property name="fieldSetMapper">
<bean:bean class="org.springframework.batch.item.file.mapping.BeanWrapperFieldSetMapper">
<bean:property name="prototypeBeanName" value="DNA_Sequence">
</bean:property>
</bean:bean>
</bean:property>
</bean:bean>
</bean:property>
</bean:bean>
<!-- lineTokenizer -->
<bean:bean id="lineTokenizer"
class="org.springframework.batch.item.file.transform.DelimitedLineTokenizer">
<bean:property name="delimiter" value=","/>
<bean:property name="names">
<bean:list>
<bean:value>dna</bean:value>
<bean:value>crissprArrays</bean:value>
</bean:list>
</bean:property>
</bean:bean>
**Configuring ItemProcessor
As you can see I use a DNASequence_Processor class that implements itemProcessor and use Karp Rabin Algorithm.
ItemWriter
Once the data is processed, the data needs to be stored in a file as per our requirement.
<bean:property name="resource" value="file:target/ch02/outputFile.csv"/>
<bean:property name="lineAggregator">
<bean:bean
class="org.springframework.batch.item.file.transform.DelimitedLineAggregator">
<bean:property name="delimiter" value="|"></bean:property>
<bean:property name="fieldExtractor">
<bean:bean
class="org.springframework.batch.item.file.transform.BeanWrapperFieldExtractor">
<bean:property name="names"
value="dna, seqDNA_Arrays">
</bean:property>
</bean:bean>
</bean:property>
</bean:bean>
</bean:property>
</bean:bean>
Conclusion
This article just scratched the surface of Spring Batch in general. The example used in this article is not production-ready code. You can define job configuration depending on your project requirements.
Here The Github repository for the project
github.com/didipostman/SBKarpRabin
DNA is a sequence of letters such as A, C, G, T. Searching for specific sequences is often difficult due to measurement errors, mutations or evolutionary alterations. Thus, similarity of two sequences using Levenshtein Distance is more useful than exact matches.
So instead of Karp Rabin we will use Levenshtein Distance or Jaro_Winkler_Similarity by using
Package org.apache.commons.text.similarity commons.apache.org/proper/commons-text/apid..
Nano Robots could be guided by
+ Karp Rabin (or Levenshtein Distance or JaroWinkler Similarity) it is just a suggestion I am not an expert a #nanotechnology #java #developer then you can cure diseses like #cancer #diabetes etc
The Ultimate definitive guide on how Spring batch could may explain how CRISPR Cas9Works read this link https://didipostmanprojects.blogspot.com/2023/01/the-definitive-explanation-on-how.html
-- Minds, like parachutes, function best when open. ,,,
(o o)
/ --------oOO--(_)--OOo--------------------\
| Wadï Mami didipostman
| Github : https://www.github.com/didipostman
| e-mail : wmami@steg.com.tn / didipostman77@gmail.com
| Twitter : @MamiWad3
| \----------------------------------------/
| |
| \---------------/ \------------------------/
The Ultimate definitive guide on how Spring batch could may explain how CRISPR Cas9Works read this link https://didipostmanprojects.blogspot.com/2023/01/the-definitive-explanation-on-how.html
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