BASE

Introduction

BASE is the web-based tool for biobrick evaluation, helping researchers build new devices and systems.

• The BASE web server is designed to provide a ranking to all existing biobricks and help users design their new devices.
• Firstly, users can use the search function to find biobricks according to the score given by BASE and choose one they need.
• Then users can make their own devices by using construction function. After construction, users can upload the device to BASE, and improve the device via the compare function.
• At last, users may apply the upload function to submit the device to the iGEM Registry and/or BASE database.

Requirement

Our web pages are developed by jQuery and Amaze UI.

We use Perl as back-end and MySQL as the database.

Usage

You can visit BASE to use our software.

Home

A brief introduction of our project.

Search

You can type the keywords you want to search into the input field. Of course, our back-end supports multi-keywords. What you have to do is just separating the words by '*'.

• For example, Terminator*RBS
• You can choose either part or device type.
• The button Advanced will lead to making some advanced choices. Now you can change the weight of each dimension so that the back-end algorithm will pay more attention on the one with higher weight. In addition, modifying the number of rows which will be shown is permitted.
• The results will be demonstrated as a table. Of course you will be informed of how many rows there are. There are four colors, blue implies high score and red implies the lower one. You can click the Brick_id to redirect to the iGem official website so that you can get more information. The details of the score will be shown if you click Score of a specific row.
• Remember to click the help button if you want more instructions.

Device Design

You can design your own bio-brick in this part of our software.

Construct

In this part, you can drag the left icons to the blank and input functions you would like to realize. Our back-end algorithm will tell you which brick you should choose.

• You can add no more than 32 bricks.
• The order of bricks is important.
• Click Next-Compare to evaluation your device.
• Help button is always useful.

Evaluate

According to the brick id and functions, the back-end will automatically evaluate your device, tell you the score and the optimal one of each brick.

• The text fields will be automatically filled with the brick id and functions in Contruct part if you click the Next-Evaluate button.
• You can add and delete as many rows as you want.
• Click Upload button to upload your device after evaluation.

Upload

This is the last part of our design. After completing the required information of your device, you can upload it to our database and iGem official database soon.

• Some text fields will be automatically filled with what you input in the former parts.

File Structure

base_v6

Including four .txt files and one .sql file. They are the source file of the database.

front-end

The source files of our website.

• Device Design: source files of device design function, including three .pl files which will be changed when installing.
• Assets: The UI framework.
• help: help documents
• home: source files of homepage.
• icon: icons of website.
• iconpng: icons of website.
• search: source files of search function, including one .pl file which will be changed when installing.
• mainCSS.css: .css file.
• mainJS.js: .js file.

BASE (Biobrick Auxiliary Selection Explorer)

An instruction of our project.

Draft of science and Technology Museum poster

An instruction of our project.

README.md

A document for users.

Install

You can just visit our website without any installation. But you are permitted to boot up a copy of your web server.

What you need is Apache, MySQL, Perl, PHP and this project.

Apache

MacOS

Apache is installed and you don't have to download it from the Internet. Just open the terminal and input $ sudo apachectl start command.

Windows

We recommend you to download XAMPP(Apache+MySQL+PHP+PERL) to configure the environment.

Notice that win xp and win 2003 are not supported.

• Open the control panel, find module Apache and click start.
• Click Explorer button to the root directory of XAMPP. Move the project file into htdocs directory.
• Now, you can enjoy the service of apache.

Linux

We recommend you to download XAMPP(Apache+MySQL+PHP+PERL) to configure the environment.

• Open the control panel, find tab Manage Servers, start the Apache Web Server.
• Back to tab Welcome, click Open Application Folder to the root directory of XAMPP. Move the project file into htdocs directory.
• Now, you can enjoy the service of apache.

MySQL

MacOS

MySQL is not included in the original operating system. You can download it from MySQL Download. But it is not fast for most users in China. MySQL SOHU Mirror will be a better choice.

• Launch: You can easily control the status of MySQL in perference after installation.
• Move to the root directory of the project. Enter directory base_v6.
• Login: Open terminal, type in $ mysql -u root -p. At first the password is empty. You can change it by $ sudo /usr/local/mysql/bin/mysqladmin -u root password yourpassword command.
• Remember to change your password in Perl source file. We will remind you later.
• Then type in MySQL> create database base; to create base database.
• Type in MySQL> use base; to use base.
• Type in MySQL> source base_v6.sql; to update data in the database.
• After that, all the data is stored in the database named base.

Windows

XAMPP will do most of the works. We suppose that you have installed the XAMPP.

• Open the control panel, find module MySQL and click start.
• Click Shell button on the right of the panel.
• Move to the root directory of the project. Enter directory base_v6.
• Type in # mysql -u root -p. At first the password is empty, so click Enter on the keyboard again to use MySQL. Of course, you can change your password by type in # mysqladmin -u root -p password yourpassword.
• Type in MySQL> create database base; to create base database.
• Type in MySQL> use base; to use base.
• Type in MySQL> source base_v6.sql; to update data in the database.

Linux

XAMPP will do most of the works. We suppose that you have installed the XAMPP.

• Open the control panel, click tab Manage Server and start MySQL Database.
• Open terminal, move to the root directory of the project. Enter directory base_v6.
• Type in $ ../../../bin/mysql -u root -p to connect to MySQL. At first the password is empty, so click Enter on the keyboard again to use MySQL. Of course, you can change your password by type in $ ../../../bin/mysqladimin -u root -p password yourpassword.
• Type in MySQL> create database base; to create base database.
• Type in MySQL> use base; to use base.
• Type in MySQL> source base_v6.sql; to update data in the database.

Perl

MacOS

Perl is automatically installed in MacOS.

• Type in perl xxx.pl arguments... to run the xxx.pl.
• You should install DBI and DBD to use MySQL in Perl scripts.
• Open terminal, move to the root directory, type in $ perl makefile.pl
• Type in $ make test
• Type in $ make
• Type in $ make install or $ sudo make install if it isn't the root user.
• After installation of these two plugins, you can use MySQL in Perl scripts.

Windows

XAMPP will do most of the works. We suppose that you have installed the XAMPP.

• Click Shell button on the right of the panel.
• Type in perl xxx.pl arguments... to run the xxx.pl.
• If the system tells you that your computer lacks libmysql.dll_, you should just download one from the Internet and drag it to C:\Windows\system32.

Linux

XAMPP will do most of the works. We suppose that you have installed the XAMPP.

• Back to tab Welcome, click Open Application Folder to the root directory of XAMPP.
• Move to bin directory, find perl file and move to /usr/bin and replace the original file. This means that once we type in perl xxx.pl arguments... in the terminal, we will use the Perl interpreter included in XAMPP instead of the original one.

PHP

MacOS

PHP is automatically installed in MacOS.

• Type in $ sudo open -e /etc/apache2/httpd.conf in terminal.
• Find #LoadModule php5_module in this file and remove the #.
• Restart apache server. $ sudo apachectl restart
• Then put the directory of our project into /Library/WebServer/Documents.
• Open your browser, visit http://localhost/iGem2015_SJTU_Software/search/search.html to use our website.

Windows

XAMPP will do all the works. You don't need to do anything.

Linux

XAMPP will do all the works. You don't need to do anything.

Project

Find my $password = ""; in all the .pl file. Change it to my $password = "xxx"; where xxx is your password of username root in MySQL.