computer science

TimeLogic

TimeLogic is a computer science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand TimeLogic rather than just read about it. In short: TimeLogic was the bioinformatics division of Active Motif, Inc. The company is headquartered in Carlsbad, California.

Key takeaways

TimeLogic belongs to computer science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect TimeLogic to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of TimeLogic from memory before moving on to harder problems.

Reference excerpt

TimeLogic was the bioinformatics division of Active Motif, Inc. The company is headquartered in Carlsbad, California. TimeLogic developed FPGA-accelerated tools for biological sequence comparison in the field of high performance bioinformatics and biocomputing.

History TimeLogic was founded in 1981 by James W. (Jim) Lindelien and developed one of the first commercial hardware-accelerated tools for bioinformatics, an FPGA-accelerated version of the Smith-Waterman algorithm. TimeLogic's DeCypher systems have expanded to provide accelerated implementations of the ubiquitous bioinformatics algorithms BLAST, Smith-Waterman, and HMMER using field programmable gate array (FPGA) technology. In 2003, TimeLogic was acquired by Active Motif, a biotechnology reagent company started by Invitrogen co-founder Joseph Fernandez. In 2008, TimeLogic formed a partnership with Biomatters to integrate Geneious Pro with the accelerated algorithms on DeCypher systems. In 2011, TimeLogic formed a partnership with Bielefeld University's Center for Biotechnology (CeBiTec) to jointly develop accelerated computational tools.

Selected scientific contributions Accelerated bioinformatics algorithms have played an important role in high throughput genomics, and DeCypher systems have been widely published as an enabling technology for genomic discovery in over 180 peer-reviewed scientific research articles, including the selected milestones below: In 1997, the annotation of the first complete sequence of the E. coli K12 genome used DeCypher Smith-Waterman to determine the function of new translated sequences. In 2002, the rice genome, the first completely sequenced crop, was annotated using DeCypher FrameSearch "to detect and guide the correction of frameshifts caused by indels." In 2004, a high throughput genomic approach to the study of horizontal gene transfer in plant-parasitic nematodes was conducted using DeCypher Tera-BLAST, Timelogic's implementation of the BLAST algorithm. In 2007, HMM profiling of metagenomics sequences generated by the Sorcerer II Global Ocean Sampling Expedition (GOS) were performed using DeCypherHMM to discover 1700 new protein families and matches to 6000 sequences previously categorized in scientific literature as ORFans. Dr. Craig Venter credited TimeLogic in his biography, noting that the DeCypher system performed "an order of magnitude or two more than had been achieved before. The final computation took two weeks but would have run for well more than a century on a standard computer." Also in 2007, a physical map of the soybean pathogen Fusarium virguliforme was developed using exonic fragments identified with DeCypher GeneDetective. In 2011, a global assessment of the genomic variation in cattle was conducted using DeCypher Tera-BLAST "to accurately detect chromosomal positions of the SNP sites."

Products DeCypher Server is a high performance server with the DeCypher Similarity Search Engine FPGA-based accelerator that can be reprogrammed on the fly to run all of TimeLogic's accelerated search algorithms. Tera-BLAST is an accelerated BLAST algorithm implementation, which includes Tera-BLASTN, Tera-BLASTP, Tera-BLASTX, Tera-TBLASTN, and Tera-TBLASTX. Tera-BLAST also includes Tera-Probe, a proprietary algorithm for probe design. DeCypher Smith-Waterman is an accelerated Smith-Waterman algorithm implementation, which also includes FrameSearch. DeCypherHMM is an accelerated HMMER algorithm implementation, which also includes HFST, a frameshift tolerant HMM search. GeneDetective is an accelerated implementation similar to Ewan Birney's GeneWise for discovery of genes, intron, exons, and splice sites in eukaryotic genomes. PipeWorks is a drag-and-drop graphical interface for the design of accelerated bioinformatics pipelines.

See also List of bioinformatics companies

References

Worked examples

Example 1 — a first encounter with TimeLogic

Start with the simplest possible case. Write down what TimeLogic claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In computer science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to TimeLogic before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about TimeLogic ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of TimeLogic

In research: TimeLogic appears in computer science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses TimeLogic in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: TimeLogic is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics companies, Companies based in Carlsbad, California, Computational science, so understanding it makes those chapters shorter.
In everyday life: Look for TimeLogic outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study TimeLogic in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what TimeLogic means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain TimeLogic out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is TimeLogic in simple terms?

TimeLogic was the bioinformatics division of Active Motif, Inc. The company is headquartered in Carlsbad, California.

Why does TimeLogic matter?

Because it connects several computer science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study TimeLogic?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on TimeLogic.