PrimeGen

This repository contains code and tutorials for Multiplex PCR experiment from MGI-X.

1. Requirement

• docker >= 23.0.5
• docker-compose >= 2.17.3
• make >= 3.81
• nodejs >= 16.20.0
• npm >= 8.19.4
• yarn >= 1.22.19
• nginx >= 1.18.0 (Ubuntu)

The versions listed are all versions used during development. It may be okay to be lower than this version, but it has not been verified

2. primer design demo

2.1 design primer for protein mutation experiment

python /code/x-multiplex-pcr/seq_search/src/plasmid.py --fasta_path /data/protein_data/Luc.fa  --out_path /data/output/ --gene_name Luc

2.2 design primer for pathogen analysis experiment

python /code/x-multiplex-pcr/seq_search/src/MTB_primer_design.py --fasta_path /data/protein_data/MTB.fa --snp_path /data/protein_data/MTB_target_snp.csv  --out_path /data/output/ --gene_name MTB

2. deploy

2.1 nginx config

server {
        listen 4433;
        server_name 172.16.47.11;
		location / {
			proxy_pass http://127.0.0.1:3001/;
					proxy_connect_timeout 300s;
					proxy_send_timeout 300s;
					proxy_read_timeout 300s;
		}	

		location /search/ {
			proxy_pass http://127.0.0.1:8082/;
			proxy_connect_timeout 300s;
			proxy_send_timeout 300s;
			proxy_read_timeout 300s;
		}	
}

2.2. build

make build

2.3. start

sudo bash run.sh

if you want stop project, you can run:

sudo bash stop.sh

3. visit

web: http://localhost:4433

3.1 Login

Login account:

account: admin
password: admin

4.Conversation flow example

4.1 Experiment of Protein Mutation Analysis of Luciferase

user: I want to do a PCR experiment for luciferase protein mutation detection.

user: i have no gene name

user choose the gene he wants(I have submitted)

user upload plasmid-modified files (I have submitted)

user: yes ，start primer design ... user: all params use default value ... user: ok,yes

5.Fault detection of OT-2