We recommend deploying HiBrowser locally so that you can access your data privatly or data in your LAN.

https://hic.bioaimed.com

Although the instance we host at https://hic.bioaimed.com is an end-user application, you need to realize that your data will be flowing on the Interet [except for visualizing your local file]

Besides, multi-omics data, especially Hi-C data, is often very large. Therefor, in our host instace, the case may spend few minutes to fetching data.

Start the Browser standalone

Download the source code from our github repo.

1、backend

Requirements

python=3.8
numpy
django=4.1
django-cors-headers=3.13.0
requests=2.28.1

We recommend using conda to create a virtual environment.

Install conda firstly.

Enter the backend
conda create --name <your_name> --file requirements.txt
conda activate <your_name>
Modify /HicBrowser/setting.py, Change to your IP address or domain name

ALLOWED_HOSTS = ["192.168.31.196"]

python manage.py runserver 0.0.0.0:<your_port>

2、frontend

[For Developer]

Recommended using Visual Studio Code + Live Server

[For User]

Install nginx.

Enter /frontend
Copy all files to the root directory of your nginx

## How to find the root directory
# Linux
cat /usr/local/nginx/conf/nginx.conf

# Windows
## In your downloaded compressed file

Modify /js/setting.js, change to your backend address

export const api_url = '<your_ip>:<your_port>/api';

Start your nginx

# Linux
cd usr/local/nginx/sbin
./nginx

# Windows 
start  nginx.exe

visit http://<you_ip>

3、docs

Enter /docs
Open index.html with your browser[eg. Google Chrome]

4、docs in pdf

see usermanual.pdf in repo.

Example page

Three cases are available for users to view.

$\color{#FF3030}{Note}$ .hic file is generally very large(~20G), the example pages will be blocked while loading. Please be patient.

<your ip>/?example=100010
<your ip>/?example=100020
<your ip>/?example=100030
################################################ an instance we host
https://hic.bioaimed.com/browser/?example=100010
https://hic.bioaimed.com/browser/?example=100020
https://hic.bioaimed.com/browser/?example=100030

Data used in Supplementary:

The data used in the supplementary figures is listed below.

GM12878 Cell Line: https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1201682a-a223-482d-913d-3c3972b8eb65/4DNFIIRIHBR2.hic

mES Cell Line: https://cdn.bioaimed.com/mouse/mouse.hic

ChIP-seq Data: GEO accession code GSE36028

K562 and KBM-7 Cell Lines: https://data.4dnucleome.org/publications/cf0e49aa-173c-49d1-a7c7-22acbc83c064/

test data

Here are some test data we provide.It can be visualized in HiBrowser(your locally deployed or we host instance) by using URL. But it will be slow due to the network congestion.

You can download it from our data hub. [Total 110.35 GB]

### Hi-C file
#### human
1. https://cdn.bioaimed.com/human/4DNFI1E6NJQJ.hic
2. https://cdn.bioaimed.com/human/4DNFICSTCJQZ.hic
3. https://cdn.bioaimed.com/GSE126199/GSE126199_0.hic
4. https://cdn.bioaimed.com/GSE126199/GSE126199_4.hic
5. https://cdn.bioaimed.com/human/human.hic


#### mouse
6. https://cdn.bioaimed.com/mouse/mouse.hic

### hg19
1. https://cdn.bioaimed.com/human/Homo_sapiens_assembly19.fasta
2. https://cdn.bioaimed.com/human/Homo_sapiens_assembly19.fasta.fai
3. https://cdn.bioaimed.com/human/human_cytoBandIdeo.txt
4. https://cdn.bioaimed.com/human/human_refGene.txt.gz

### mm10
1. https://cdn.bioaimed.com/mouse/Mus_musculus.GRCm39.dna.primary_assembly.fa
2. https://cdn.bioaimed.com/mouse/Mus_musculus.GRCm39.dna.primary_assembly.fa.fai
3. https://cdn.bioaimed.com/mouse/mouse_refGene.txt.gz
4. https://cdn.bioaimed.com/mouse/mouse_cytoBand.txt

### human 3D structure
1. https://cdn.bioaimed.com/human/human_domain.txt
2. https://cdn.bioaimed.com/human/human_loop.txt
3. https://cdn.bioaimed.com/human/MCF10a_domin.txt
4. https://cdn.bioaimed.com/human/MCF10a_ab.bedGraph
5. https://cdn.bioaimed.com/human/MCF7_domin.txt
6. https://cdn.bioaimed.com/human/MCF7_ab.bedGraph


### mouse 3D structure
1. https://cdn.bioaimed.com/mouse/mouse_domain.txt
2. https://cdn.bioaimed.com/mouse/mouse_loop.txt


### track file

1. https://cdn.bioaimed.com/track/annotation/Homo_sapiens.GRCh38.94.chr.gff3.gz
2. https://cdn.bioaimed.com/track/annotation/Homo_sapiens.GRCh38.94.chr.gff3.gz.tbi
--
1. https://cdn.bioaimed.com/track/auto/case1.bed.gz
2. https://cdn.bioaimed.com/track/auto/case1.bed.gz.tbi
--
1. https://cdn.bioaimed.com/track/gwas/gwas_sample.gwas
--
1. https://cdn.bioaimed.com/track/seg/GBM-TP.seg.gz
--
1. https://cdn.bioaimed.com/track/variant/nstd186.GRCh38.variant_call.vcf.gz
2. https://cdn.bioaimed.com/track/variant/nstd186.GRCh38.variant_call.vcf.gz.tbi


### ATAC-seq
1. https://cdn.bioaimed.com/GSE126199/ATAC_0_telo.bw
2. https://cdn.bioaimed.com/GSE126199/ATAC_4_telo.bw


### RNA
1. https://cdn.bioaimed.com/GSE126199/RNA_0_telo.bw
2. https://cdn.bioaimed.com/GSE126199/RNA_4_telo.bw

### other
1. https://cdn.bioaimed.com/track/bw/GSM3609942_JWH107-CutRun-35-minus-IAA-CTCF.bam.bw
2. https://cdn.bioaimed.com/track/bw/GSM3609943_JWH108-CutRun-35-plus48-IAA-CTCF.bam.bw
3. https://cdn.bioaimed.com/track/bw/GSM3609944_JWH110-CutRun-42-minus-IAA-CTCF.bam.bw
4. https://cdn.bioaimed.com/track/bw/GSM3609945_JWH111-CutRun-42-plus48-IAA-CTCF.bam.bw

##### CTCF no IAA
1. https://cdn.bioaimed.com/track/bw/GSM4636526_ATAC-SEM-CTCF-AID_no_IAA-Rep42.free.bw
2. https://cdn.bioaimed.com/track/bw/GSM4636525_ATAC-SEM-CTCF-AID_no_IAA-Rep35.free.bw
3. https://cdn.bioaimed.com/track/bw/GSM4636524_ATAC-SEM-CTCF-AID_no_IAA-Rep27.free.bigwig

##### CTCF with IAA
1. https://cdn.bioaimed.com/track/bw/GSM4636529_ATAC-SEM-CTCF-AID_with_IAA-Rep42.free.bw
2. https://cdn.bioaimed.com/track/bw/GSM4636528_ATAC-SEM-CTCF-AID_with_IAA-Rep35.free.bw
3. https://cdn.bioaimed.com/track/bw/GSM4636527_ATAC-SEM-CTCF-AID_with_IAA-Rep27.free.bigwig

lyotvincent/HiBrowser