[ensembl-dev] FW: FW: Inquiry Regarding Backend Code for Ensembl VEP Tool

[Syed Hossain]

I also just wanted to add that, the repositories and documentation I 
mentioned are for how Ensembl VEP works and would allow you to 
understand CLI version of the tool. There is no easy way to implement 
web application version of the tool using our codebase. I would advise 
to implement your own version of web application that runs Ensembl VEP 
in the background (the docker image would be handy in such case - 
https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#docker)

But if you want to learn more about the web implementation side you 
might want to look at the following repositories -
https://github.com/Ensembl/ensembl-webcode - main hub of Ensembl website 
codebase
https://github.com/Ensembl/public-plugins - has relevant code for the 
tools
Again, I would advise it would be easier to have your own implementation 
rather than going through these parts of the code.

Best regards,
Nakib

On 2024-06-18 13:53, Syed Hossain wrote:
> Hi,
> 
> Thanks for your query and your interest in VEP!
> 
> The repository you are looking for is the following -
> https://github.com/Ensembl/ensembl-vep
> 
> But keep in mind that, ensembl-vep depends on other Ensembl 
> repositories, like -
> https://github.com/Ensembl/ensembl
> https://github.com/Ensembl/ensembl-variation
> https://github.com/Ensembl/ensembl-io
> 
> 
> The other questions are kind of broad and is not sufficient to be 
> answered in an email. It is good idea to start with the documentation 
> first. I would recommend going through the following documentations -
> Ensembl VEP documentation - 
> https://www.ensembl.org/info/docs/tools/vep/index.html
> Variation API diagrams etc. - 
> https://www.ensembl.org/info/docs/api/variation/index.html
> Which and how variation data are stored/processed - 
> https://www.ensembl.org/info/genome/variation/index.html
> 
> They will give you the overall idea of how Ensembl VEP works. If you 
> have specific questions after that we will be happy to answer.
> 
> 
> Best regards,
> Nakib
> 
> On 2024-06-17 15:25, Siyang Feng wrote:
>> From: Siyang Feng <feng.siy at northeastern.edu>
>> Date: Monday, June 17, 2024 at 10:21 AM
>> To: dev at ensembl.org <dev at ensembl.org>
>> Subject: Inquiry Regarding Backend Code for Ensembl VEP Tool
>> 
>> Dear Ensembl Team,
>> 
>>  I hope this message finds you well. I’m Siyang Feng, a student
>> major in Computer Science.
>> 
>>  I am writing to inquire about the backend implementation of the
>> Variant Effect Predictor (VEP) tool available on your website,
>> specifically at the following URL:
>> https://useast.ensembl.org/Homo_sapiens/Tools/VEP.
>> 
>>  I’m interested in understanding the technical details and
>> architecture of the backend system that powers the VEP tool on your
>> website. We are particularly keen on the following aspects:
>> 
>>  	* The backend codebase or repository, if available.
>> 	* The process for handling and processing the user-submitted variant
>> data.
>> 	* The parameters used in the VEP tool and how they are managed and
>> utilized.
>> 	* Any documentation or resources that could help us integrate a
>> similar solution in our own backend system.
>> 
>>  I greatly appreciate the efforts of the Ensembl team in providing
>> such a valuable resource to the scientific community. Thank you for
>> your time and assistance.
>> 
>>  Siyang Feng
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