and software founded 1981 headquarters carlsbad ca usa area served worldwide products decypher tera blast decyphersw decypherhmm genedetective pipeworks parent active motif inc. website timelogic timelogic is the bioinformatics division of active motif inc. the company is headquartered in carlsbad california . timelogic develops fpga accelerated tools for biological sequence comparison in the field of high performance bioinformatics and biocomputing . contents 1 history 2 selected scientific contributions 3 products 4 see also 5 references history edit 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 1 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 . 2 in 2011 timelogic formed a partnership with bielefeld university s center for biotechnology cebitec to jointly develop accelerated computational tools . 3 selected scientific contributions edit 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 . 4 in 2002 the rice genome the first completely sequenced crop 5 was annotated using decypher framesearch to detect and guide the correction of frameshifts caused by indels . 6 in 2004 a high throughput genomic approach to the study of horizontal gene transfer in plant parasitic nematodes 7 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 . 8 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 . 9 also in 2007 a physical map of the soybean pathogen fusarium virguliforme was developed using exonic fragments identified with decypher genedetective . 10 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 . 11 products edit 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 12 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 edit list of bioinformatics companies references edit genomeweb staff reporter 26 august 2003 . reagent firm active motif acquires timelogic . genomeweb . retrieved 20 september 2011 . timelogic s latest fpga technology to be coupled with geneious server . january 18 2011 . retrieved 20 november 2011 . active motif and the cebitec form partnership to jointly develop computational tools for timelogic corporation s fpga based hardware accelerated bioinformatics platform . november 14 2011 . retrieved 1 december 2011 . blattner f. r. ; plunkett g g. ; bloch c. a. ; perna n. t. ; burland v. ; riley m. ; collado vides j. ; glasner j. d. ; rode c. k. ; mayhew g. f. ; gregor j. ; davis n. w. ; kirkpatrick h. a. ; goeden m. a. ; rose d. j. ; mau b. ; shao y. 1997 . the complete genome sequence of escherichia coli k 12 . science . 277 5331 1453 1462 . doi 10.1126 science .277.5331.1453 . pmid 9278503 . gillis justing august 11 2005 . rice genome fully mapped . washingtonpost.com . goff s. a. ; ricke d. ; lan t. h. ; presting g. ; wang r. ; dunn m. ; glazebrook j. ; sessions a. ; oeller p. ; varma h. ; hadley d. ; hutchison d. ; martin c. ; katagiri f. ; lange b. m. ; moughamer t. ; xia y. ; budworth p. ; zhong j. ; miguel t. ; paszkowski u. ; zhang s. ; colbert m. ; sun w. l. ; chen l. ; cooper b. ; park s. ; wood t. c. ; mao l. ; quail p. 2002 . a draft sequence of the rice genome oryza sativa l. ssp . japonica . science . 296 5565 92 100 . doi 10.1126 science .1068275 . pmid 11935018 . scholl e. h. ; thorne j. l. ; mccarter j. p. ; bird d. m. 2003 . horizontally transferred genes in plant parasitic nematodes a high throughput genomic approach . genome biology . 4 6 r39 . doi 10.1186 gb 2003 4 6 r39 . pmc 193618 . pmid 12801413 . yooseph s. ; sutton g. ; rusch d. b. ; halpern a. l. ; williamson s. j. ; remington k. ; eisen j. a. ; heidelberg k. b. ; manning g. ; li w. ; jaroszewski l. ; cieplak p. ; miller c. s. ; li h. ; mashiyama s. t. ; joachimiak m. p. ; van belle c. ; chandonia j. m. ; soergel d. a. ; zhai y. ; natarajan k. ; lee s. ; raphael b. j. ; bafna v. ; friedman r. ; brenner s. e. ; godzik a. ; eisenberg d. ; dixon j. e. ; taylor s. s. 2007 . the sorcerer ii global ocean sampling expedition expanding the universe of protein families . plos biology . 5 3 e16 . doi 10.1371 journal.pbio .0050016 . pmc 1821046 . pmid 17355171 . venter j. craig october 18 2007 . a life decoded my genome my life . new york new york viking adult . isbn 0 670 06358 4 . oclc 165048736 . shultz j. l. ; ali s. ; ballard l. ; lightfoot d. a. 2007 . development of a physical map of the soybean pathogen fusarium virguliforme based on synteny with fusarium graminearum genomic dna . bmc genomics . 8 262 . doi 10.1186 1471 2164 8 262 . pmc 1978504 . pmid 17683537 . zhan b. ; fadista j. ; thomsen b. ; hedegaard j. ; panitz f. ; bendixen c. 2011 . global assessment of genomic variation in cattle by genome resequencing and high throughput genotyping . bmc genomics . 12 557 . doi 10.1186 1471 2164 12 557 . pmc 3248099 . pmid 22082336 . birney e. ; clamp m. ; durbin r. 2004 . genewise and genomewise . genome research . 14 5 988 995 . doi 10.1101 gr .1865504 . pmc 479130 . pmid 15123596 . retrieved from https en.wikipedia.org w index.php title timelogic & oldid 678228786 categories bioinformaticsbioinformatics softwarecomputational sciencecompanies based in carlsbad california navigation menu personal tools not logged intalkcontributionscreate accountlog in namespaces article talk variants views read edit view history more search navigation main pagecontentsfeatured contentcurrent eventsrandom articledonate to wikipediawikipedia store interaction helpabout wikipediacommunity portalrecent changescontact page tools what links hererelated changesupload filespecial pagespermanent linkpage informationwikidata itemcite this page print export create a bookdownload as pdfprintable version languages add links this page was last modified on 28 august 2015 at 03 09 . text is available under the creative commons attribution sharealike license ; 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