Mambo-MS is Metabolomics Australia's (MA) central library of metabolites. It aimed to assist in the interpretation of hyphenated mass spectrometry (gas chromatography-mass spectrometry/liquid chromatography mass spectrometry) metabolomics experiments."
Mambo-MS consists of three major components:
User Management System
The User management system consists of managing different user groups such as System Administrator, Node Representative, MA Lab Staff and Clients, each of who posses different privileges in accessing the database.
Store of metabolite records
The metabolite records that are stored in Mambo-MS consists of:
- NIST database that is made up of more than 250,000 records (local only to MA);
- GC-MS records that are generated at MA Nodes; and
- LC-MS records generated at MA Nodes.
Search and visualisation of metabolite records
The search component of Mambo-MS is made up of keyword based search and mass spectrum based search.
This project is led by Metabolomics Australia Bioinformatics group, and is a collaboration with the Australian Bioinformatics Facility located at the Centre for Comparative Genomics.
The Mambo-MS server is a Django application which uses the Apache web server and PostgreSQL.
Mambo-MS is distributed as RPM, tested on Centos 6.x (x86_64). To satisfy dependencies, Epel and REMI repos need to be enabled:
sudo rpm -Uvh http://repo.ccgapps.com.au/repo/ccg/centos/6/os/noarch/CentOS/RPMS/ccg-release-6-2.noarch.rpm sudo rpm -Uvh http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm sudo rpm -Uvh http://rpms.famillecollet.com/enterprise/remi-release-6.rpm
The database and python database driver aren't dependencies of the Mambo-MS RPM, so have to be installed manually:
sudo yum install postgresql-server python-psycopg2 postgresql-plpython
Addtionally, Mambo-MS requires a higher version of matplotlib than
is available in Centos 6.x. It can be installed using the pip
python package installer:
sudo yum install freetype-devel libpng-devel python-pip sudo pip install --upgrade numpy==1.6.2 sudo pip install --upgrade matplotlib==1.2.1
Install the Mambo-MS RPM, replacing X.X.X with the desired version:
sudo yum install mamboms-X.X.X
If starting from a fresh CentOS install, you will need to configure PostgreSQL:
service postgresql initdb service postgresql start chkconfig postgresql on
To enable password authentication in PostgreSQL, you need to edit
/var/lib/pgsql/data/pg_hba.conf. As described in the
documentation, add the following line to pg_hba.conf:
# TYPE DATABASE USER CIDR-ADDRESS METHOD host all all 127.0.0.1/32 md5
Then restart postgresql.
The database is created in the normal way for Django/PostgreSQL, but a stored procedure file must be installed:
sudo su postgres createuser -e -DRS -P mamboms createdb -e -O mamboms mamboms psql < /usr/local/webapps/mamboms/lib/django_mamboms-*.egg/mamboms/mambomsapp/migrations/spectra_search_storedproc.sql exit
The default database, username, password are all set to mamboms. These settings can be changed, see (:ref:`django-settings`).
Run Django syncdb and South migrate:
sudo mamboms syncdb --noinput sudo mamboms migrate
The preconfigured user will have e-mail address [email protected]
with password admin. Once you have set up your own users, the
[email protected] user can be deleted.
The Mambo-MS RPM installs an example Apache config file at
/etc/httpd/conf.d/mamboms.ccg. This config is designed to work out
of the box with an otherwise unconfigured CentOS Apache
installation. All that is needed is to rename mamboms.ccg to
mamboms.conf so that Apache will pick it up.
If you have already made changes to the default Apache configuration,
you may need to tweak mamboms.conf so that the existing setup is
not broken. It may be necessary to consult the Apache and
mod_wsgi documentation for this.
By default, the storage for uploaded files is located at
/var/lib/mamboms/scratch.
There should be ample disk space on this filesystem and some data redundancy would be desirable. If this is not the case, then you could mount a suitable file system at this path. If the data repository needs to be at another location, its path can be configured in the settings file.
The default settings for Mambo-MS are installed at
/usr/local/webapps/mamboms/defaultsettings/mamboms.py. In case any
settings need to be overridden, this can be done by creating an
optional appsettings file. To set up the appsettings file, do:
mkdir -p /etc/ccgapps/appsettings
touch /etc/ccgapps/appsettings/{__init__,mamboms}.py
The Python variable declarations in
/etc/ccgapps/appsettings/mamboms.py will override the defaults,
which can be seen in settings.py.
Mambo-MS does not yet ship with a SELinux policy. For Mambo-MS to function correctly on a CentOS server, SELinux must be disabled.
The CentOS wiki contains instructions on how to disable SELinux.
New versions of Mambo-MS are made available in the CCG yum repository.
Warning
Some versions will require "database migrations" to update the database. While every care is taken to ensure smooth upgrades, we still advise to make a backup of the database before upgrading. This can be done with a command such as:
su - postgres -c "pg_dump mamboms | gzip > /tmp/mamboms-$(date +%Y%m%d).sql.gz"
Install the Mambo-MS RPM, replacing X.X.X with the desired version:
sudo yum install mamboms-X.X.X
Run Django syncdb and South migrate:
sudo mamboms syncdb --noinput sudo mamboms migrate
After changing the configuration or upgrading, start/restart the web server with:
service httpd restart
Mambo-MS is available at https://your-web-host/mamboms/. A login page should be visible at this URL. The default login details are:
| Username | [email protected] |
| Password | admin |
The Mambo-MS code is hosted at BitBucket.
https://bitbucket.org/ccgmurdoch/mambo-ms
Any bugs or questions can be raised on the issue tracker:
https://ccgmurdoch.atlassian.net/browse/MAM
The Mambo-MS project was originally hosted at Google Code but is no longer.
- MA Informatics Group Leader
- Prof. Malcolm McConville
- Computer Scientist
- Dr. Saravanan Dayalan
- System Administrator
- Thu Nguyen
- Project Director
- Prof. Matthew Bellgard
- Project Leader
- Adam Hunter
- Software Developers
- Brad Power, Tamas Szabo, Maciej Radochonski, Nick Takayama
- System Administrator
- David Schibeci