malDB is an open-source peptide mass fingerprinting web application that allows the user to create their own peptide database tables to search against. Since malDB is built as a web application, you can use it as either:
- A web server that you access locally on your computer (via 127.0.0.1:8000)
- A web server running on a networked machine (access via <IP_ADDRESS>:8000)
malDB provides the following features:
- Uploading, digesting and storage of any proteome(s) in .fasta format
- Definition of custom mass modifications
- Searching through database tables using experimental mass lists to determine protein identity
- Multi-layer perceptron for predicting a protein's fingerprint based on primary sequence alone
- Additional useful mass spectrometry tools
Installing malDB involves deploying a Laravel application on a machine that can serve as a webserver. You can run malDB on your own computer but it is recommended that you use a networked machine with a high performance CPU and at least 16GB of RAM.
- Download Python (with data science libraries) if you have not already, and ensure the python binary is in your PATH. malDB has numpy and pandas as dependencies.
- Download PHP and add the root folder to your PATH so that the php binary is accessible.
- Download Composer and install it. Make sure it is added to your PATH. Restart any terminals after installing Composer.
- Download MySQL and install MySQL server and MySQL workbench.
- In the PHP folder, open php.ini and uncomment the following lines by removing the semicolon:
;extension=pdo_mysql => extension=pdo_mysql
;extension=fileinfo => extension=fileinfo
Note that if you don't have a php.ini file, you should rename the supplied php.ini.recommended or php.ini.development or php.ini.production to php.ini.
- Open the MySQL workbench, and add a schema to your MySQL database called 'maldb'.
- Clone this repository.
- In the repository root, rename
.env.exampleto.env. Now, open it up and set the appropriate environment variables to connect to the MySQL database (note that this file may be hidden in your filesystem, you may need to show hidden files to see it):
DB_CONNECTION=mysql
DB_HOST=127.0.0.1
DB_PORT=3306
DB_DATABASE=maldb
DB_USERNAME=myAdminUserName
DB_PASSWORD=myPassword
-
In a terminal, migrate to the root of the repository folder.
-
Run
composer install --ignore-platform-reqs(installs PHP dependencies) -
Run
npm install(installs javascript dependencies) -
Run
php artisan key:generate(generates a key in .env file) -
Run
php artisan migrate(creates the database tables) -
Run
php artisan storage:link(generates symlink to storage directory) -
In your MySQL
my.inifile, setmax_allowed_packet=128M. Otherwise, jobs digesting large proteomes will crash.
If you are on a Windows machine, you can simply run maldb.bat from the project root. This will run a batch script that excecutes the necessary commands to launch the WAN server and start a job queue. Otherwise, you can run:
php artisan serve(starts a local development server)- In a separate console window, run
php artisan queue:work --timeout=0to start the job queue.
You should now be able to access malDB in a web browser via http://127.0.0.1:8000/
- To run the server over LAN or WAN, use
php artisan serve --host 0.0.0.0 --port 8000(or any port of your choosing). Alternatively, you can choose to run this on an Apache or Nginx server. - The timeout argument specifies how long a queue job should run for before automatically failing. Large proteomes/search space can take a long time on slow machines, so a timeout time of 0 is recommended so these jobs can run overnight.
- Multiple queues can run concurrently by simply running multiple
php artisan queue:work --timeout=0commands in separate terminal windows. See Laravel documentation - Tutorials on how to use malDB, and how to perform peptide mass fingerprinting are built into the application under the 'Learn' page.
