TimeLogic<sup>®</sup> Technology

DeCypher Software

System Software and User Interfaces

Our DeCypher® systems include all of the software necessary to perform hardware accelerated searches as well as various administrative utilities that make the life of the system administrator much easier.

DeCypher® Clustering

Our DeCypher® software also includes functionality that allows for the assembly of large, multi server-node systems. In these cases, job queuing and distribution capabilities are managed by the DeCypher® software and the end-users subsequently communicate exclusively with the head node. As new search jobs are submitted to the queue, the DeCypher® software submits those jobs to individual nodes, ensuring that all nodes are kept busy. Additional DeCypher® functionality includes the ability to set each DeCypher® node with a preference rating for specific algorithms. In a mixed environment with variations in accelerator card density per server, this would allow the largest, most computationally intensive jobs to be sent to the server with the most FPGA accelerator hardware. Having a multi-node system allows for the processing of multiple search jobs simultaneously whereas adding additional FPGA accelerator cards to the servers in your multi-node system ensures that individual jobs are processed more quickly. 

DeCypher® User Interfaces

Our DeCypher® software includes two principal mechanisms for accepting and processing requests; a command-line interface (CLI) tool and a web-based interface that you access via a web browser. Both provide the functionality necessary to build new DeCypher® databases and execute job searches. Advanced users will find the CLI provides great flexibility and the opportunity to integrate your DeCypher® system into any existing analysis pipelines. The CLI application is also included with your DeCypher® software so that additional machines can be configured for remote use with the DeCypher® server. The CLI client software does not need to run on the same type of system as the DeCypher® server.

Web Interface

DeCypher® includes a web interface based on the industry standard Apache web server. Accessible by Mac, PC and Unix, users will have direct interactive access to DeCypher® for all their similarity search needs, with results returned by email or directly back to your favorite web browser.


Search results can be delivered via email notification or graphically via the browser. NCBI HTML and text results formats are available to simplify integration with your existing pipelines. The web interface utilizes the Apache web server and convenient cascading stylesheets (CSS) for easy integration with your institution's look and feel.

Job results can be sent to your browser, your email, or by file I/O as:
  • Graphical Alignments with biologically relevant alignment details, including % identity, gapping, frame shifts, mismatches, and multiple domains.
  • HTML Hypertext with links to annotation servers.
  • Tab- and Comma- Record Sets, ideal for further manipulation by Perl and MS-Excel, as it outputs only the fields you select.
  • ASCII plain text.

The web interface, with the Core Admin Module, provides management of users, groups, databases, and jobs, all in a remotely-accessible easy to use package.

Command-line Interface

Advanced bioinformatics pipeline programmers will appreciate the complete sockets-driven command-line package included at no extra charge with DeCypher®. If you prefer to develop applications solely on client-side, this package makes the underlying network connection to DeCypher® completely transparent. Perl, shell and C applications programming are a breeze. Full ANSI C source codes are provided for the client-side CLI programs. Current users who would like this package absolutely free need only contact our Support Team.