CLC Bioinformatics Database
CLC Bioinformatics Database is a smart and efficient solution for managing centralized bioinformatics data in a 3-tier client/server architecture. The server contains one or more databases, and the clients are CLC Workbenches or could even be your existing applications.
The base components of the solution
- A database management system of choice; Microsoft SQL Server, Oracle, PostgreSQL, or MySQL.
- CLC Workbenches (clients) for interacting with the database.
- Thin client for administrating purposes. – Upload and download of data.
- CLC Database Middleware to ensure scalability and performance.
The most important benefits
- Seamless sequence data management
- Powerful data mining
- Flexible acccess control system and privilege management
- Custom metadata management
- Advanced data support
- Cross platform support on the client side (Windows, Mac OS X, and Linux)
- Mature API for customization and integration
The CLC Bioinformatics Database includes the following features:
- Web Client Access
- CLC Workbench Access
- LDAP/Active Directory Support
- Database API
- Multi Session Support (250 concurrent sessions)
See the latest improvements of CLC Bioinformatics Database
Upload and Download
Uploading and downloading data in nearly any format – including all major high-throughput sequencing formats – is one of the most important functionalities of any database.
With the CLC approach of importing data to the database, it has never been easier – in the Workbench you simply drag a folder of data of almost any format directly from your desktop to a database “folder”. And that’s it. Exporting data in almost any format is just as easy.
Multiple interfacing for uploading and downloading data
Another option is to use a web browser to upload and download data from any location, whether or not there is a Workbench installed on the computer.
Other more automated import/export actions can be performed using either the CLC Workbenches or other applications being integrated with the database using our Application Programming Interface (API).
Any kind of data may be stored in CLC Bioinformatics Database. It has native application support for the following data formats.
Supported data formats
- Phylip Alignments (.phy)
- Macromolecular Crystallographic Info File (.cif)
- Clustal Alignment (.aln)
- Embl (.emb)
- FASTA (.fsa)
- Vector NTI (.ma4, .pa4, oa4)
- Gene Construction Kit File (.gcc)
- Blast Db (.phr, .pal, .nhr, .nal)
- GCG Sequence (.gcg)
- GenBank (.gbk)
- Lasergene sequence (.pro, .seq)
- GCG Alignment (.msf)
- Newick (.nwk, .newick)
- Protein Data Bank (.pdb)
- PIR (.pir)
- CLC (.clc)
- Staden Sequence (.sdn)
- DNA Strider files (.str)
- SwissProt (.swp)
- Plain Text (.txt)
- Trace files (.abi, .ab1, .scf, .phd)
- Zip files (.zip)
- CT File
Flexible access control and privilege management
The database solution includes traditional support for access permissions. Each user has a unique username and password. Basically, users can have “no access”, “read access”, and/or “write access” to specified areas of data.
Access rights and permission settings
The access rights are defined on the on the folder level of the data structure. Different access rights can be given to each folder, resulting in a very flexible data security architecture.
From an administrative point of view this is very important since it gives even more control of the data and who can edit it. The access privilege model is based on users, user-groups, and privileges attached to the “directories” in the database.
The directory of users can either be CLC Authentication Directory (running in the same DB instance as the Bioinformatics Database) or an LDAP or Microsoft Active Directory.
Customization and Integration
Integrating custom database schemes can be done by implementing a plugin in the CLC Database Middleware.
Customizations are either developed by the customer, by CLC bio, or by a team of CLC bio / customer employees.
The SOAP API
CLC Bioinformatics Database Middleware enables an Application Programming Interface (SOAP API) that makes it one of the most flexible database solutions in the market. It enables the following features that can all be implemented outside a CLC Workbench:
- Import/export of data to/from the database by creating your own client scripts or applications.
- Access and modification of any data structure and data content in the database
- Powerful data mining
- Migration of data from existing databases to CLC Bioinformatics Database
- Integration of third party technologies/tools with the database
- Metadata management
The CLC Workbenches also comes with an API (the Software Developer Kit). This ensures the option of full integration of the CLC Workbenches with existing databases.
These features can be used “command line”/scripting or directly from a program, or script making it possible to carry out batch operations and to integrate the database with almost any other system.
Example: CLC Database Integration Point and custom Integration Point (marked with red.)