Wednesday, September 23, 2020

Genome Sequencing and IT model for DNA damage repair at the same time

Sincerly I was fighting for this since 2012 An idea is hauting me since 2012 : " a genome sequencing solution and at the same time an IT model for DNA damage repair based on an open source Java framework which is Spring Batch + DNA algorithm of pattern recognition.

In fact I am not an expert but the Architecture sequence diagram describing how Spring Batch function and the dependency between Spring Batch Core and item reader, item Processor and item Writer had led me to think that we can use Spring batch as a genome sequencing framework for all the Human DNA genome and it could be a model for DNA damage repair like a genetic framework like Crispr Cas9.



Unfortunately I can't go further with my project idea here in Tunisia that's why I share it with you to forward it to appropriate authorities.

In fact I am not an expert but I did a template of that project. Maybe you find it useful, interesting and maybe you know someone who can continue development. 


Summary

Spring Batch+an algorithm of DNA pattern recognition to fight covid19, diseases and/or to figure out , vaccines,medicines etc


Description

Description

A Java IT Model for DNA damage repair and Genome sequencing solution

Author: Wadï Mami

15/06/2020

email: didipostman77@gmail.com

Abstract

Here I share with you my IT model for DNA damage repair and Genome Sequencing Solution. It can be used for Nano robots, to fight covid19 or any other disease, or to figure out a genetic framework like Crispr cas9 or vaccine design or medicines.

The Model

Since 2012 I tried a theory an IT model for DNA damage repair and genome sequencing solution based on an open source framework java which is Spring Batch + an algorithm of DNA pattern recognition.I did a template project to more explain

You will find a fully présentation of it following this link https://github.com/didipostman/GenomeSequencing

You just have to read the readme file and explore the source code I used a template code of * @author bruce.liu(mailto:jxta.liu@gmail.com) Very special thanks to him. The source code template is in Github under MIT license.

I thaugt even to go further to read all the human DNA by using spring batch-integration -Grid Gain.

http://aloiscochard.blogspot.com/2010/04/spring-batch-integration-module-for.html


I think only one instance of Spring Batch + an algorithm of DNA pattern recognition may be the solution to create a virus, a drugs or genetic framework like Crispr Cas 9 based on that architecture

It could help against covid 19 as we know RNA responsible of it.

As I told you before it is only the concept a simple sample, an idea in my point of view worth to be considered a hard work remains to be done

I cant go further with it may be someone find it useful and continue.

The model itself and all is only in the idea's stage, more development is needed. Unfortunately I can't go further with it. The idea is haunting me since 2012
maybe you find it useful, interesting and continue dev.

Conclusion

The model can be embeded in nano Robots and you can cure illnesses and viruses you know RNA / DNA like covid 19.

I used Karp Rabin in my template you can opt for another
algorithm. especially that Karp Rabin is not advised for long
patterns and also that in my Karp Rabin template in one line it
report only the first pattern if there is one and do not deal with others
sequences which can correspond to the pattern sought in the same line.

But the advantages of Karp Rabin is the passage from Monte-Carlo to Las Vegas

in my template I used two files: input for the ItemReader, and
output for the ItemWriter.

You can use a Database instead of these so-called files.

you can assign the value 150 for the commit-interval since at
below 10 we are faced with performance problems and above
200 the same.
and throttle-limit to 5 or 6
values advised by the authors of Spring Batch in Action:

Arnaud Cogoluègnes
Thierry Templier
Gary Gregory
Olivier Bazoud

Thank you

Best Regards

--


Minds, like parachutes, function best when open. ,,,

                      (o o)

/ --------oOO--(_)--OOo--------------------\

| Wadï Mami

| e-mail :didipostman77@gmail.com

| Github : didipostman
| \----------------------------------------/

|

|                           |

\---------------/ \------------------------/


Monday, June 22, 2020

To fight Covid19 / Cancer and others

Summary

Spring Batch+an algorithm of DNA pattern recognition to fight covid19, diseases and/or to figure out , vaccines,medicines etc


Description

Description

A Java IT Model for DNA damage repair and Genome sequencing solution

 

Author: Wadï Mami

15/06/2020

email: didipostman77@gmail.com

Abstract

 

Here I share with you my IT model for DNA damage repair and Genome Sequencing Solution. It can be used for Nano robots, to fight covid19 or any other disease, or to figure out a genetic framework like Crispr cas9 or vaccine design or medicines.

 

 

The Model

 

Since 2012 I tried a theory an IT model for DNA damage repair and genome sequencing solution based on an open source framework java which is Spring Batch + an algorithm of DNA pattern recognition.I did a template project to more explain

 

You will find a fully présentation of it following this link https://github.com/didipostman/GenomeSequencing

 

You just have to read the readme file and explore the source code I used a template code of * @author bruce.liu(mailto:jxta.liu@gmail.com) Very special thanks to him. The source code template is in Github under MIT license.

 

I thaugt even to go further to read all the human DNA by using spring batch-integration -Grid Gain.

http://aloiscochard.blogspot.com/2010/04/spring-batch-integration-module-for.html


I think only one instance of Spring Batch + an algorithm of DNA pattern recognition may be the solution to create a virus, a drugs or genetic framework like Crispr Cas 9 based on that architecture

It could help against covid 19 as we know RNA responsible of it.

As I told you before it is only the concept a simple sample, an idea in my point of view worth to be considered a hard work remains to be done

I cant go further with it may be someone find it useful and continue.

The model itself and all is only in the idea's stage, more development is needed. Unfortunately I can't go further with it. The idea is haunting me since 2012
maybe you find it useful, interesting and continue dev.

Conclusion

The model can be embeded in nano Robots and you can cure illnesses and viruses you know RNA / DNA like covid 19.

I used Karp Rabin in my template you can opt for another
algorithm. especially that Karp Rabin is not advised for long
patterns and also that in my Karp Rabin template in one line it
report only the first pattern if there is one and do not deal with others
sequences which can correspond to the pattern sought in the same line.

But the advantages of Karp Rabin is the passage from Monte-Carlo to Las Vegas

in my template I used two files: input for the ItemReader, and
output for the ItemWriter.

You can use a Database instead of these so-called files.

you can assign the value 150 for the commit-interval since at
below 10 we are faced with performance problems and above
200 the same.
and throttle-limit to 5 or 6
values advised by the authors of Spring Batch in Action:

Arnaud Cogoluègnes
Thierry Templier
Gary Gregory
Olivier Bazoud

Monday, June 15, 2020

Sunday, May 3, 2020

Java Nano robots covid19

My Java IT model Spring Batch + algorithm pattern récognition Can be embeded (nano robots) so you Can create tools of détections for viruses liké covid19 and you Can eradicate them and also you Can cure many other illnesses

HTTPS://www.github.com/didipostman/GenomeSequencing

Wednesday, May 8, 2019

Crispr Cas9 Like Framework

A concept theory to cure illnesses like Cancer Diabete HIV etc + génome sequencing a framework like Apache Spark

I am from Africa Tunisia I spent 7 years since 2012 to dig for a solution to cure illnesses like Cancer Diabete HIV alzheimer etc Brief all the illnesses that we know DNA pattern responsible of them I think Spring Batch + Karp Rabin ( or other algorithm of pattern recognition)  could help curing such kind of illnesses a team of Spring batch architects and bioinformaticians need to be mounted to reverse Engineering Spring Batch genetically to have a genetic framework like Crisprcas9 or a virus or drugs based on that architecture that's why I share with you my IT model for Dna damage repair it was in Github under MIT License the account was unfortunately deleted it is only the theory concept may be some one find it interesting and useful and continue the development of that project

What I mean is to obtain a genetic framework like Crispr cas9 framework based on Spring Batch Architecture In fact English is not my first language it is a theory the code of Spring Batch is in Github the question is how from java open source framework code like Spring Batch + Karp Rabin algorithm or any other pattern recognition algorithm  can we use it as a model to obtain a genetic framework like Crispr cas9 framework



The picture above describes How Spring Batch can be an IT model. ItemReader reads a DNA FlatFile then return Item. A Karp Rabin Class algorithm is called inside DNAsequenceProcessor class that implements ItemProcessor to process and return transformed item ( 0 for clean, 1 for item containing malicious DNA pattern )

Item writer write transformed items ( patching the malicious sequences in parallel simultaneously )

I think Spring Batch + Karp Rabin is the solution ( in theory )  it remains to create the genetic model based on that solution or a virus and why not create drugs based on that architecture.

As I told you before it is only the concept a simple sample an idea in my point of view worth to be considered a hard work remains to be done

I cant go further with it may be someone find it useful and continue

WE can too develop a génome sequencing solution based on using many PC nodes each node with many Java jar Spring Batch jobs with Grid Gain task handler for each jar all thé jobs orchestred by Spring integration
So Spring Integration + Spring Batch + Grid Gain = Apache Spark like framework

Références : Spring Batch in Action
                       Pro Spring Batch
                       Spring par la pratique
                       Pro Spring Batch intégration

NB : instead of a Flat File we can use databases ( Oracle, etc...)


--

Minds, like parachutes, function best when open. ,,,

                      (o o)

/ --------oOO--(_)--OOo--------------------\

| Wadï Mami

| e-mail :wmami@steg.com.tn

| Github : didipostman
| \----------------------------------------/

|

|                           |

\---------------/ \------------------------/