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ABrowse - The Advanced Genome Browser

中文版

Introduction

ABrowse (Advanced Genome Browser) is a lightweight general-purpose Genome Browser framework that we developed to help biologists build an easy-to-use Genome Browser. ABrowse's visualization engine runs in the browser, providing a very good interactive experience for users. The framework currently supports data formats such as GTF, BedGraph, SAM (SAM format support is shown in the screenshot below RNASeq Mapping Sample Track), and a custom data format for storing transcript splice sites. The data is imported into the local mongoDB via the interface provided by ABrowse, and developers can add support for more data formats based on our API.

ABrowse supports multiple visualization methods of the same data format, and with our JavaScript API, developers can add even more visualization methods to the data format.

This software is browser-server architecture, the back end uses the Spring Boot framework, the front uses HTML5 + JavaScript. The directory src/main/resources/docs/ has more documentation.

Quick Start

Screenshot

Let's start with a screenshot. ABrowse Screenshot

Pre-request

  • openjdk 1.8.0 (later than 1.8.0, or oracle-jdk should work as well, but is not tested)
  • Apache Maven 3.6.1 (other versions should work, but is not tested)
  • MariaDB 10.0 (MySQL or some other version of MariaDB should work, but is not tested)
  • MongoDB 2.6.10 (other versions should work, but is not tested)
  • a browser that supports SVG and HTML5 (who doesn't? We recommend chrome or firefox or safari)

Create Database in MariaDB/MySQL

As a demo version, please do not change the following statement (If you want to use another password, please modify spring.datasource.password in file src/main/resources/application )

# create abrowse database
create database abrowse;

# create user abrowse，only allowed connection from localhost，the password is abs_passwd
grant all privileges on abrowse.* to 'abrowse'@'localhost' identified by 'abs_passwd';

# create user abrowse，only allowed connection from 127.0.0.1，the password is abs_passwd
grant all privileges on abrowse.* to 'abrowse'@'127.0.0.1' identified by 'abs_passwd';

# update privileges
flush privileges;

import the genome configure json files to mongodb

## import the global configuration
mongoimport -d abrowsedemo -c config_genome --file src/main/resources/docs/conf/global.abrowse.json --jsonArray

## import human genome configuration
mongoimport -d abrowsedemo -c config_genome --file src/main/resources/docs/conf/human.abrowse.json --jsonArray

Compile and Run

git clone https://github.com/klcola/abrowse.git
cd abrowse
# If it is the first compile, this step could take quite a few minutes to finish since
# maven will download many depended jar packages.
mvn clean install

java -jar target/abrowse-2.0-alpha.jar

If all goes well, open the browser and input 'http://127.0.0.1:8383' in the address bar, and you will see the abrowse index page in the web browser. You will see a blank canvas in the page because we does not import any data into the abrowse database yet.

Add Admin User Recorder

Now let's add admin user for abrowe. Please MAKE SURE you have finished the previous step, or the table in MariaDB/MySQL will not be created automatically.

use abrowse;
insert into role values (1, 'ROLE_ADMIN');
insert into role values (10000000, 'ROLE_USER');

# abrowse_demo 是密码，gly 是用户名，这两个都可以改成你自己的
insert into user values (1, 'abrowse_demo', 'gly');
insert into user_roles values (1, 1);

Import GTF Data

To click the '登录' button and then type the username gly, password abrowse_demo to login. After that, click the gear button left to the '退出gly' button, you will see the following page ABrowse 管理员界面截图

You may first delete the empty old track by entering the 'DELETE TRACK' page. Then go to ensembl web site to download gtf file.

wget ftp://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.gtf.gz
gzip -d Homo_sapiens.GRCh38.99.gtf.gz

Entering the 'LOAD GENCODE GTF DATA' page，and fill the blanks as the following picture. Please note that the TrackName SHOULD NOT has space character, the Track Display Name could have space character, the Track Description could have space character and could also be blank. And fill the absolute path of file Homo_sapiens.GRCh38.99.gtf and click the 'IMPORT' button. ABrowse 导入 GTF 文件界面截图

Finally, we get our first ABrowse running instance. ABrowse Demo 截图

To Developers

templates name rules: the / should be replaced by __

eg：

/admin/user_management/create_user

admin__user_management__create_user

thymeleaf variables' name rules： The iterator of Map should end with Entry，eg：

<select name="trackGroupName" id="trackGroupName" class="selectpicker">
    <option th:each="trackGroupEntry : ${configGenome.trackGroupMap}" th:value="${trackGroupEntry.value.name}"
            th:text="${trackGroupEntry.value.displayName}">
    </option>
</select>

git default case insensitive，to make git case sensitive：

git config core.ignorecase false

Multiple Language support

ABrowse supports multiple languages，please refer to src/resources/i18n/ for more information.

Contact

kongl@mail.cbi.pku.edu.cn

Disclaimer

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.