An advanced & powerful three-tier solution
CLC Science Server is an advanced three-tier solution offering secure, powerful, and flexible bioinformatics computing on a server located centrally in your organization.
The three main components are
- Server software running on all major platforms (Windows, Mac OS X, and Linux)
- Data backend: Your file system, your existing database(s) (you can integrate it by using our API), or CLC Bioinformatics Database (Microsoft SQL Server 2003 & 2008, Oracle, mySQL, PostgreSQL, or H2), or any combination of the three
- Client software: Any CLC Workbench, any Web browser, and any custom developed clients can access the server concurrently
Among others, CLC Science Server provides you
- A powerful and modern three-tier server architecture
- Flexible options of executing centralized services
- Easy integration with other applications and services
- Powerful data integration and the possibility for database communication
- Secure access control framework and central action logging
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Deploy your own Scientific Software Services
CLC Science Server Platform makes it possible to deploy your own scientific software services in a centralized 3 tier software architecture, with full support of your existing IT infrastructure. Examples could be existing tools from the open source and commercial communities.
One of the biggest strengths of the platform is that you can also deploy tools, you have developed in-house, with either our API/SDK or integration layer to existing external applications.
Design and execute your own scientific workflows
Another big benefit is that with the Command Line Tools of CLC Science Server, it is possible to define your own workflows. This is done in terms of scripts that interact with CLC Command Line Tools.
Integrate CLC Science Server Platform into existing solutions
With the Service Oriented Architecture and the Command Line Tools, it is possible to integrate the platform into existing solutions and workflows, which ensures homogeny in your scientific software architecture throughout your organization.
Improve your scientific informatics infrastructure
With CLC Science Server, you will benefit from seamless data-sharing between your users. As highlights it is worth mentioning:
- Strong data encryption between clients and server with SSL
- Privilege control, that will help controlling and managing your bioinformatics data through an advanced permission system, based on user groups
- LDAP and Microsoft Active Directory support for your user account management
- Integrate and deploy existing bioinformatics tools and binaries from 3rd parties, with our External Application Integration support
- Creation BLAST databases and run BLAST jobs on the server against either databases on the server file system or temporary “on-the-fly” databases
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
CLC Science Server comes with three client options
Common for all clients to CLC Science Server is that they are built on our service oriented SOAP web-services. This gives a full choice on the client-side of the system, including option to design your own client.
CLC Main Workbench
CLC Main Workbench is the premium client for our Science Server. It gives the user full control of all bioinformatics analyses on the Science Server in terms of service-invocation and monitoring.
Furthermore it is possible to seamlessly view your results even with limited network-load, due to our advanced handling of genome sized sequences on the server-side. CLC Main Workbench contains also a variety of bioinformatics features, that any user will be able to run locally on his desktop computer.
Since the general communication with CLC Science Server is done through our SOAP-API, it is possible to use this to develop your own custom clients. Examples of this could be scripts or access from other applications.
Thin client – web browser
The thin client access to the Science Server is a powerful administration interface to the solution.
It is possible to do more user-oriented things like browsing data, upload/download data, access/edit meta-data on data and do data-queries.
CLC Server Command Line Tools
With a toolbox of Command Line Tools for the server, the advanced user can incorporate server-access in scripts, integrations etc.
Furthermore it is possible to inspect and invoke all services and upload/download any data in virtually any format.
Right from the start CLC Science Server has been designed for advanced customization. This fact makes it one of the most flexible bioinformatics platforms in the world.
The key-point is that the customer has the vision, CLC bio has the platform, and the combination of these drives a successful solution implementation. There are several approaches and options for customization to choose from.
CLC Science Server comes with an advanced API, that makes it possible to design/develop/deploy your own bioinformatics analyses directly on the system and making them available to the user through any of the platform’s client options.
Examples of relevant plugins could be deployment of proprietary algorithms or integration with existing IT-infrastructure.
Integration of External Applications
With the built-in support for External Command Line Applications, it is possible to deploy External Applications seamless into CLC Science Server without doing any programming. The result is bioinformatics analysis that is available for the end-user, with a graphical user-interface for service-invocation and viewing of results. The purpose of this is to make a platform for bioinformaticians, so they can concentrate on the creative side of their job, and thereby create more value for your organization.
Furthermore this has great advantages to biologists and bio-medical experts, since advanced tools and services can be available to them, with a nice user-friendly user-interface in terms of CLC Main Workbench. The simple goal is to enhance productivity in all parts of your organization.
CLC Science Server offers 3 very flexible solutions to manage your bioinformatics data.
The File System
When using this option you never have to worry about local data, different versions of data or disappearing data.
The simplest way to manage your data on the server-side is to attach a File System to the CLC Science Server. This serves as a central data store that is accessible and manageable from anywhere in your organization.
It is also possible to make use of advanced data-mining features to find exactly the data you need for your project.
CLC Bioinformatics Database
For maximum flexibility, security and scalability you can choose to use CLC Bioinformatics Database as Data Management system for the solution with all the same advantages of central storage as using a central File System.
CLC Bioinformatics Database in combination with CLC Science Server make your Data Management Layer highly scalable, by using the built-in tools of your favorite Database Management System (DBMS). Comes with built-in support for the most popular DBMS like Oracle, MySQL, MS SQL Server and PostgreSQL.
The solution has very flexible built-in tools for restricting access to different user-groups within your organization.
Custom Database Schemas
Using our APIs for Data Management you can integrate your own custom Database Schemas in the solution. We have several customers who can present great success with this.
The integration efforts are usually done by the customer, by CLC bio or as a combination.
If you have more interest in this, we suggest you have a look at our pages regarding CLC Development Kit or CLC Consulting Solutions.
Sequence data management.
Mikael Flensborg, Director of Enterprise Solutions & Worldwide Developer Relations at CLC bio elaborating on sequence data management.
Job Node Support
With the built-in Job Node Support of CLC Science Server, it is possible to attach an array of real or virtualized computers to the solution.
This array of computers will serve as the core execution points of your bioinformatic services based on queue prioritization. It is possible to configure each Job Node to only being execution-point to certain types of tasks.
With our next major update of CLC Science Server there will be support for DRMAs (Distributed Resource Management Application).
In the first version of the DRMA support there will be support for Oracle Grid Engine, and later we will address other DRMAs. The advantages of using a DRMA instead of the built-in Job Node support is that the job-queue policies are more advanced.