TimeLogic

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,{{cite web |url=http://www.genomeweb.com/reagent-firm-active-motif-acquires-timelogic |title=Reagent Firm Active Motif Acquires TimeLogic |author=GenomeWeb staff reporter |date=26 August 2003 |work=GenomeWeb |accessdate=20 September 2011}} 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.{{cite web| title=TimeLogic's latest FPGA technology to be coupled with Geneious Server | date=January 18, 2011 |url=http://www.geneious.com/default,1341,timelogics_latest_fpga_technology_to_be_coupled_with_geneious_server.sm?section=geneious&pageid=1118 |accessdate=20 November 2011 }}

In 2011, TimeLogic formed a partnership with Bielefeld University's Center for Biotechnology (CeBiTec) to jointly develop accelerated computational tools.{{cite web |title=Active Motif and the CeBiTec Form Partnership to Jointly Develop Computational Tools for TimeLogic Corporation's FPGA-Based Hardware Accelerated Bioinformatics Platform |date=November 14, 2011 |url=http://www.cebitec.uni-bielefeld.de/content/view/246/1/ |accessdate=1 December 2011 |url-status=dead |archiveurl=https://web.archive.org/web/20120214162857/http://www.cebitec.uni-bielefeld.de/content/view/246/1/ |archivedate=14 February 2012 }}

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 [https://web.archive.org/web/20220515200835/http://www.timelogic.com/papers-citing-timelogic-products 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.{{Cite journal

| last7 = Collado-Vides | first9 = C. K. | first8 = J. D. | first7 = J.

| last10 = Mayhew

| title = The Complete Genome Sequence of Escherichia coli K-12 | first17 = Y.

| last17 = Shao | first16 = B.

| last16 = Mau | first15 = D. J.

| last15 = Rose | first14 = M. A.

| last14 = Goeden | first13 = H. A.

| last13 = Kirkpatrick | first12 = N. W.

| last12 = Davis | first11 = J.

| journal = Science

| last11 = Gregor

| doi = 10.1126/science.277.5331.1453 | first10 = G. F.

| pmid = 9278503

| year = 1997

| pages = 1453–1462

| volume = 277

| issue = 5331 | first6 = M. | first2 = G.

| last9 = Rode | first3 = C. A.

| last2 = Plunkett g

| last4 = Perna | first1 = F. R.

| last6 = Riley

| last5 = Burland

| last1 = Blattner

| last8 = Glasner | first5 = V. | first4 = N. T.

| last3 = Bloch

| doi-access = free

}}{{Cite journal |last1=Blattner |first1=F. R. |last2=Plunkett |first2=G. |last3=Bloch |first3=C. A. |last4=Perna |first4=N. T. |last5=Burland |first5=V. |last6=Riley |first6=M. |last7=Collado-Vides |first7=J. |last8=Glasner |first8=J. D. |last9=Rode |first9=C. K. |last10=Mayhew |first10=G. F. |last11=Gregor |first11=J. |last12=Davis |first12=N. W. |last13=Kirkpatrick |first13=H. A. |last14=Goeden |first14=M. A. |last15=Rose |first15=D. J. |date=1997-09-05 |title=The complete genome sequence of Escherichia coli K-12 |url=https://pubmed.ncbi.nlm.nih.gov/9278503/ |journal=Science |volume=277 |issue=5331 |pages=1453–1462 |doi=10.1126/science.277.5331.1453 |issn=0036-8075 |pmid=9278503}}{{Cite web |title=1997: E. coli Genome Sequenced |url=https://www.genome.gov/25520386/online-education-kit-1997-e-coli-genome-sequenced |access-date=2025-01-17 |website=www.genome.gov |language=en}}

In 2002, the rice genome, the first completely sequenced crop,{{cite news | last=Gillis | first=Justing | title=Rice Genome Fully Mapped | date=August 11, 2005 | work=washingtonpost.com | url=https://www.washingtonpost.com/wp-dyn/content/article/2005/08/10/AR2005081001054.html?referrer=email }} was annotated using DeCypher FrameSearch "to detect and guide the correction of frameshifts caused by indels."{{Cite journal

| last1 = Goff | first1 = S. A.

| last2 = Ricke | first2 = D.

| last3 = Lan | first3 = T. H.

| last4 = Presting | first4 = G.

| last5 = Wang | first5 = R.

| last6 = Dunn | first6 = M.

| last7 = Glazebrook | first7 = J.

| last8 = Sessions | first8 = A.

| last9 = Oeller | first9 = P.

| last10 = Varma | first10 = H.

| last11 = Hadley | first11 = D.

| last12 = Hutchison | first12 = D.

| last13 = Martin | first13 = C.

| last14 = Katagiri | first14 = F.

| last15 = Lange | first15 = B. M.

| last16 = Moughamer | first16 = T.

| last17 = Xia | first17 = Y.

| last18 = Budworth | first18 = P.

| last19 = Zhong | first19 = J.

| last20 = Miguel | first20 = T.

| last21 = Paszkowski | first21 = U.

| last22 = Zhang | first22 = S.

| last23 = Colbert | first23 = M.

| last24 = Sun | first24 = W. L.

| last25 = Chen | first25 = L.

| last26 = Cooper | first26 = B.

| last27 = Park | first27 = S.

| last28 = Wood | first28 = T. C.

| last29 = Mao | first29 = L.

| last30 = Quail | first30 = P.

| title = A Draft Sequence of the Rice Genome (Oryza sativa L. Ssp. Japonica)

| doi = 10.1126/science.1068275

| journal = Science

| volume = 296

| issue = 5565

| pages = 92–100

| year = 2002

| pmid = 11935018

| pmc =

| bibcode = 2002Sci...296...92G

| s2cid = 2960202

}}

In 2004, a high throughput genomic approach to the study of horizontal gene transfer in plant-parasitic nematodes{{Cite journal

| last1 = Scholl | first1 = E. H.

| last2 = Thorne | first2 = J. L.

| last3 = McCarter | first3 = J. P.

| last4 = Bird | first4 = D. M.

| title = Horizontally transferred genes in plant-parasitic nematodes: A high-throughput genomic approach

| journal = Genome Biology

| volume = 4

| issue = 6

| pages = R39

| year = 2003

| doi = 10.1186/gb-2003-4-6-r39

| pmid = 12801413

| pmc =193618

| doi-access = free

}} was conducted using DeCypher Tera-BLAST, Timelogic's implementation of the BLAST algorithm.{{Cite news |date=November 1, 2010 |title=MULTBLAST: A web application for multiple BLAST searches |work=pmc.ncbi.nlm.nih.gov|pmc=3040504 }}

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.{{Cite journal

| last1 = Yooseph | first1 = S.

| last2 = Sutton | first2 = G.

| last3 = Rusch | first3 = D. B.

| last4 = Halpern | first4 = A. L.

| last5 = Williamson | first5 = S. J.

| last6 = Remington | first6 = K.

| last7 = Eisen | first7 = J. A.

| last8 = Heidelberg | first8 = K. B.

| last9 = Manning | first9 = G.

| last10 = Li

| doi = 10.1371/journal.pbio.0050016 | first10 = W.

| last11 = Jaroszewski | first11 = L.

| last12 = Cieplak | first12 = P.

| last13 = Miller | first13 = C. S.

| last14 = Li | first14 = H.

| last15 = Mashiyama | first15 = S. T.

| last16 = Joachimiak | first16 = M. P.

| last17 = Van Belle | first17 = C.

| last18 = Chandonia | first18 = J. M.

| last19 = Soergel | first19 = D. A.

| last20 = Zhai | first20 = Y.

| last21 = Natarajan | first21 = K.

| last22 = Lee | first22 = S.

| last23 = Raphael | first23 = B. J.

| last24 = Bafna | first24 = V.

| last25 = Friedman | first25 = R.

| last26 = Brenner | first26 = S. E.

| last27 = Godzik | first27 = A.

| last28 = Eisenberg | first28 = D.

| last29 = Dixon | first29 = J. E.

| last30 = Taylor | first30 = S. S.

| title = The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

| journal = PLOS Biology

| volume = 5

| issue = 3

| pages = e16

| year = 2007

| pmid = 17355171

| pmc =1821046

| doi-access = free

}} 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."{{Cite book |title=A Life Decoded: My Genome: My Life |author=Venter, J. Craig |isbn=978-0-670-06358-1 |oclc=165048736 |date=October 18, 2007 |publisher=Viking Adult |location=New York, New York |url-access=registration |url=https://archive.org/details/lifedecodedmygen00vent }}

Also in 2007, a physical map of the soybean pathogen Fusarium virguliforme was developed using exonic fragments identified with DeCypher GeneDetective.{{Cite journal

| last1 = Shultz | first1 = J. L.

| last2 = Ali | first2 = S.

| last3 = Ballard | first3 = L.

| last4 = Lightfoot | first4 = D. A.

| title = Development of a physical map of the soybean pathogen Fusarium virguliforme based on synteny with Fusarium graminearum genomic DNA

| doi = 10.1186/1471-2164-8-262

| journal = BMC Genomics

| volume = 8

| pages = 262

| year = 2007

| issue = 1

| pmid = 17683537

| pmc =1978504

| doi-access = free

}}

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."{{Cite journal

| last1 = Zhan | first1 = B.

| last2 = Fadista | first2 = J.

| last3 = Thomsen | first3 = B.

| last4 = Hedegaard | first4 = J.

| last5 = Panitz | first5 = F.

| last6 = Bendixen | first6 = C.

| doi = 10.1186/1471-2164-12-557

| title = Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

| journal = BMC Genomics

| volume = 12

| pages = 557

| year = 2011

| issue = 1

| pmid = 22082336

| pmc = 3248099

| doi-access = free

}}

• 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{{Cite journal

| last1 = Birney | first1 = E.

| authorlink1 = Ewan Birney

| last2 = Clamp | first2 = M.

| last3 = Durbin | first3 = R.

| authorlink3 = Richard M. Durbin

| doi = 10.1101/gr.1865504

| title = GeneWise and Genomewise

| journal = Genome Research

| volume = 14

| issue = 5

| pages = 988–995

| year = 2004

| pmid = 15123596

| pmc =479130

}} 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.

• List of bioinformatics companies

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Category:Bioinformatics companies

Category:Computational science

Category:Companies based in Carlsbad, California