openBIS is a framework for managing biological data and information. It has gained a lot of interest from many sides as it is very versatile in its deployment and use. What it does really well is keeping track of the large amounts of instrument data generated by the various platforms, for example in mass spectrometry, deep sequencing or screening. For each platform the system can be extended by a set of plugins to meet the needs of the individual laboratory, project or community. We have developed plugins for proteomics, metabolomics, lipidomics, deep sequencing, hts/hcs and more are coming.
If you are interested to test openBIS or to set up your own instance, here are the steps to be taken.
- Discussion with SyBIT about your needs. To schedule such a discussion, just send a mail to us. Describe your need and what you would use the system for. The agenda is
- Foreseen usage of the system: Raw file management, result data management, data publication, or a combination of them?
- Type of data: Screening, Mass Spec, Deep Sequencing, etc.
- Where is the data you want to manage: What data needs to be 'imported', managed?
- What kind of queries do you need, what are the most common 10 questions you ask about the data?
- We set up an instance of openBIS at your institution or wherever it is convenient for you to register your data in the system. We expect you to provide the server with operating system, PostgreSQL database and Java installed and ready for usage. The minimal system requirements are:
- Linux 64bit (e.g. CentOS 5)
- 2 cores, 8GB RAM, 1GB local fast harddisk (for database), 80GB harddisk (for datastore)
- Java Runtime Environment 1.6, PostgreSQL 9.0 database
- We download and install openBIS together with you, optimally you do this yourself (the instructions should be easy, if they are not, let us know how we can improve them)
- We configure and customize the system with you. Optimally this interaction goes through your local SyBIT contact. There should also be a person in your lab who will be responsible for the system as such and who is our main point of contact at your end. Our local SyBIT person and your person will work closely together.
- We load the first data and iterate with you in 2-week cycles about your additional needs. This continues for up to 3 months, depending on the complexity of your environment.