TimeLogic,
TimeLogic<sup>®</sup> Technology

Frequently Asked Questions

TimeLogic and DeCypher Information


Contents

General 

How is TimeLogic affiliated with Active Motif? 

The TimeLogic Corporation was purchased by Active Motif in 2003. TimeLogic® is a brand name for the DeCypher® product line.

What technology is used to accelerate your bioinformatics algorithms?

We have taken some very commonly used bioinformatics algorithms and optimized them to run on our proprietary FPGA accelerator cards (J-Series Similarity Search Engine).

How big can I go in building a DeCypher® system?

Since our technology scales well, we can easily add capacity to a DeCypher server by adding more FPGA cards. This allows for increased per job performance. Multiple servers can also be linked together to form a multi-node system, which allows for improved multi-job throughput.

As far as system size limits go, we have yet to reach that upper limit. We have customers with literally dozens of our FPGA cards incorporated into large, multi-node DeCypher® systems.

On these multi-node systems, our DeCypher® software automatically handles job distribution and queueing. End-user communication is via the Master node and the DeCypher® software handles the rest.

What does FPGA mean?

FPGA means field programmable gate array. More Information.

Which algorithms are accelerated?

The various types of BLAST (Tera-BLAST), several implementations of Smith-Waterman (DeCypherSW™), multiple variations of HMM and profile searches (DeCypherHMM™), and GeneDetective (for gene modeling) are supported. Our new NGS data mapping algorithm, VelociMapper, will be available in 2013.

What is the increase in performance using your system?

DeCypher® systems provide from 60X - 900X gain in performance based on the specific algorithm and the number of cards in a single server. For heuristic algorithms, performance is very data & parameter setting specific and rather than provide generic performance numbers, TimeLogic prefers to conduct performance benchmark tests for our prospective customers, using their own data and parameter settings preferences. Please contact us for your own custom benchmark tests.

What are the key differences between your DeCypher® Systems and those offered by other vendors for accelerated biocomputing?

Our enterprise DeCypher® systems are built-to-order appliances that arrive to our customer's site ready to go. With customer assistance, we configure our DeCypher systems so that our customers can hit the ground running. Additionally, TimeLogic has been providing application-specific support to our Bioinformatics customers for over 15 years and our experienced team can assist with optimizing job search parameters, something our competitors don't do.

Our DeCypher systems also come with a variety of utilities that improve the life of the DeCypher system administrator. For example, job queuing and job distribution capabilities are built into our DeCypher software as is the capability to provide information security and management to a large diverse group of end-users. These are features that our competitor systems don't include.

Finally, other vendors that provide hybrid compute systems (using either GPU and/or FPGA technology) sell a developmental platform that puts the onus on the customer to develop and support their own tools. Typically these other vendors tout the 'openness' of their platform but in reality, developing accelerated tools for specific hardware accelerators is a unique skill set that hasn't, at least traditionally, led to the development of many tools. Correspondingly, TimeLogic encourages our customers to let us work with you to develop custom tools. Our platform is also open to the introduction of new algorithms and we would happily assist you in that effort. We think this collaboration hastens the process and results in the development of better tools.

Can the system accept a single sequence query?

Yes. You can submit a search with a single query sequence, but you will see the most dramatic acceleration in performance when you submit hundreds to thousands of sequences.

Hardware

Can your FPGA cards be installed in my own server?

In order to ensure the high-quality that we demand for our DeCypher® systems, we thoroughly test the host-servers that we use. As long as your host-server is on our list of tested hardware, and it meets our minimum hardware specifications, it can be used in a DeCypher® system.

We currently support the following server:

Dell R720 (2U rackmount server)
CPUs: 2 Intel Xeon E5-2690 2.90 GHz (32 threads total)
RAM: 64 GB RAM
Other: gigabit ethernet
Operating System: 2x146GB storage (RAID1)
Storage: 6x300GB storage (RAID5)
Support: ProSupport from Dell - 7x24 HW/SW Tech Support, 3 year period

Required Operating Systems:
RedHat Enterprise v6.x
CentOS v6/x
Windows 2008

Our J-Series Similarity Search Engine FPGA cards require a PCIe slot (one per card). Installation of the FPGA card(s) and DeCypher® software require a trained TimeLogic specialist.

Can more than one SeqCruncher card be installed per server?

Yes. The above servers support 1 or 2 SeqCruncher cards for the Dell R720.

Can your FPGA cards and associated DeCypher® software be run in a Linux environment?

Yes. You can also install the card and run the software in a PC Windows or Linux environment.

Can I accelerate my own bioinformatics algorithm with your SeqCruncher card?

Our FPGA cards are designed to run only DeCypher® software algorithms. So technically the answer is No, but if you have a computational challenge that you'd like to address using our FPGA hardware, please contact us, we may be able to work together to create an accelerated algorithm that will run on our FPGA hardware.

Can I install the command line interface client on my laptop?

Yes.  The command line interface client can be installed on any remote machine running a Windows, Linux or Mac OS X environment.

Software

What is DeCypher®?

DeCypher® employs a comprehensive set of ultra-fast analysis tools that let you experiment with varied parameter settings—or completely different algorithms—to define the best possible sequence annotation protocol. DeCypher® features both a web interface & a command line client, enabling all users to execute powerful bioinformatics analyses.

How would I use DeCypher® to predict the function of a gene? 

DeCypher® enables you to quickly process comprehensive BLASTX searches of your gene sequences against a well-curated protein database of known proteins. To reinforce your conclusions, it is possible to compare your protein sequence with an annotated Hidden Markov Model database such as PFAM. A match to a specific protein family can imply similar function. DeCypher's HMM-Framesearch method is also available for automatic translation of your nucleic sequences and frameshift tolerant alignments while assigning protein family identification.

Can I use DeCypher® to rapidly identify exons and splice variants?

Yes. The GeneDetective™ algorithm allows you to map ESTs or amino acid sequences to genomic data to build sophisticated gene models. This system uses multiple sequence alignment methods to accurately describe exons and introns, and then it delivers a interactive graphical view of your gene model for exploration of splice variants. Since our accelerated Tera-Blast algorithm is used in this process, your jobs takes much less time than alternative methods require.

Can DeCypher® be used for protein structure modeling?

Yes. For homology modeling, DeCypher®'s BLAST and robust Smith-Waterman methods can be used to find sequences with known protein structure by comparison with protein structure data such as that found in the Protein Data Bank (PDB).

Can DeCypher® be used to identify distantly-related sequences?

Yes. DeCypherHMM™ enables you to build your own Hidden Markov Model database from a collection of similar proteins. This model can then be used to search for remote homologs through comparison with a large sequence database.

Database FTP Download Sites

The following list displays database sources of selected files for creating DeCypher® or CodeQuest® target databases.

Type Site Database Name Database
Description & Notes
Sequence NCBI nr NCBI non-redundant
protein database
nt NCBI non-redundant
nucleotide database
Uniprot swissprot Uniprot Swiss-Prot
protein database
trembl Uniprot trEMBL
protein database
HMM PFAM pfam-fs PFAM HMM library,
local alignment models
pfam-ls PFAM HMM library,
global alignment models
TIGRFAMs tigrfam TIGRFAMs HMM
library, standard
tigrfam-frag TIGRFAMs HMM
library, fragment-mode

 

Other Database Sources: