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a {color:[[ColorPalette::PrimaryMid]];}
a:hover {background-color:[[ColorPalette::PrimaryMid]]; color:[[ColorPalette::Background]];}
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h4 {font-size:1em;}
h5 {font-size:.9em;}
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a {text-decoration:none;}
dt {font-weight:bold;}
ol {list-style-type:decimal;}
ol ol {list-style-type:lower-alpha;}
ol ol ol {list-style-type:lower-roman;}
ol ol ol ol {list-style-type:decimal;}
ol ol ol ol ol {list-style-type:lower-alpha;}
ol ol ol ol ol ol {list-style-type:lower-roman;}
ol ol ol ol ol ol ol {list-style-type:decimal;}
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#contentWrapper .chkOptionInput {border:0;}
.externalLink {text-decoration:underline;}
.indent {margin-left:3em;}
.outdent {margin-left:3em; text-indent:-3em;}
code.escaped {white-space:nowrap;}
.tiddlyLinkExisting {font-weight:bold;}
.tiddlyLinkNonExisting {font-style:italic;}
/* the 'a' is required for IE, otherwise it renders the whole tiddler in bold */
a.tiddlyLinkNonExisting.shadow {font-weight:bold;}
#mainMenu .tiddlyLinkExisting,
#mainMenu .tiddlyLinkNonExisting,
#sidebarTabs .tiddlyLinkNonExisting {font-weight:normal; font-style:normal;}
#sidebarTabs .tiddlyLinkExisting {font-weight:bold; font-style:normal;}
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.header a:hover {background:transparent;}
.headerShadow {position:relative; padding:4.5em 0 1em 1em; left:-1px; top:-1px;}
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.siteSubtitle {font-size:1.2em;}
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.tabset {padding:1em 0 0 0.5em;}
.tab {margin:0 0 0 0.25em; padding:2px;}
.tabContents {padding:0.5em;}
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.tabContents li.listLink { margin-left:.75em;}
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.footer li {display:inline;}
.annotation {padding:0.5em; margin:0.5em;}
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.viewer {line-height:1.4em; padding-top:0.5em;}
.viewer .button {margin:0 0.25em; padding:0 0.25em;}
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.zoomer div {padding:1em;}
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#backstageArea {display:none; position:relative; overflow: hidden; z-index:150; padding:0.3em 0.5em;}
#backstageToolbar {position:relative;}
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/***
StyleSheet for use when a translation requires any css style changes.
This StyleSheet can be used directly by languages such as Chinese, Japanese and Korean which need larger font sizes.
***/
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body {font-size:0.8em;}
#sidebarOptions {font-size:1.05em;}
#sidebarOptions a {font-style:normal;}
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@media print {
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#displayArea {margin: 1em 1em 0em;}
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}
/*}}}*/
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<div class='headerShadow'>
<span class='siteTitle' refresh='content' tiddler='SiteTitle'></span>
<span class='siteSubtitle' refresh='content' tiddler='SiteSubtitle'></span>
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<div class='headerForeground'>
<span class='siteTitle' refresh='content' tiddler='SiteTitle'></span>
<span class='siteSubtitle' refresh='content' tiddler='SiteSubtitle'></span>
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<div id='mainMenu' refresh='content' tiddler='MainMenu'></div>
<div id='sidebar'>
<div id='sidebarOptions' refresh='content' tiddler='SideBarOptions'></div>
<div id='sidebarTabs' refresh='content' force='true' tiddler='SideBarTabs'></div>
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<div id='displayArea'>
<div id='messageArea'></div>
<div id='tiddlerDisplay'></div>
</div>
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<!--{{{-->
<div class='toolbar' macro='toolbar [[ToolbarCommands::ViewToolbar]]'></div>
<div class='title' macro='view title'></div>
<div class='subtitle'><span macro='view modifier link'></span>, <span macro='view modified date'></span> (<span macro='message views.wikified.createdPrompt'></span> <span macro='view created date'></span>)</div>
<div class='tagging' macro='tagging'></div>
<div class='tagged' macro='tags'></div>
<div class='viewer' macro='view text wikified'></div>
<div class='tagClear'></div>
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<div class='toolbar' macro='toolbar [[ToolbarCommands::EditToolbar]]'></div>
<div class='title' macro='view title'></div>
<div class='editor' macro='edit title'></div>
<div macro='annotations'></div>
<div class='editor' macro='edit text'></div>
<div class='editor' macro='edit tags'></div><div class='editorFooter'><span macro='message views.editor.tagPrompt'></span><span macro='tagChooser excludeLists'></span></div>
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To get started with this blank [[TiddlyWiki]], you'll need to modify the following tiddlers: * [[SiteTitle]] & [[SiteSubtitle]]: The title and subtitle of the site, as shown above (after saving, they will also appear in the browser title bar) * [[MainMenu]]: The menu (usually on the left) * [[DefaultTiddlers]]: Contains the names of the tiddlers that you want to appear when the TiddlyWiki is opened You'll also need to enter your username for signing your edits: <<option txtUserName>>
These [[InterfaceOptions]] for customising [[TiddlyWiki]] are saved in your browser Your username for signing your edits. Write it as a [[WikiWord]] (eg [[JoeBloggs]]) <<option txtUserName>> <<option chkSaveBackups>> [[SaveBackups]] <<option chkAutoSave>> [[AutoSave]] <<option chkRegExpSearch>> [[RegExpSearch]] <<option chkCaseSensitiveSearch>> [[CaseSensitiveSearch]] <<option chkAnimate>> [[EnableAnimations]] ---- Also see [[AdvancedOptions]]
<<importTiddlers>>
!CALL FOR PAPERS: 4th Workshop on using Emerging Parallel Architectures (WEPA 2012) http://www.staff.uni-mainz.de/schmi033/ !!held in conjunction with the [[International Conference on Computational Science (ICCS 2012)|http://www.iccs-meeting.org/]], Omaha, Nebraska, June 2 – 4, 2012 The computing landscape has undergone significant transformation with the emergence of more powerful processing elements such as ~GPUs, ~FPGAs, multi-cores, etc. On the multi-core front, Moore’s Law has transcended beyond the single processor boundary with the prediction that the number of cores will double every 18 months. Going forward, the primary method of gaining processor performance will be through parallelism. Multi-core technology has visibly penetrated the global market. Accordingly to the latest Top500 lists the HPC landscape has evolved from supercomputer systems into large clusters of dual or quad-core processors. Furthermore, ~GPUs, ~FPGAs and multi-cores have been shown to be formidable computing alternatives, where certain classes of applications witness more than one order of magnitude improvement over their GPP counterpart. Therefore, future computational science centers will employ resources such as FPGA and GPU architectures to serve as co-processors to offload appropriate compute-intensive portions of applications from the servers. This workshop provides a forum for exploring the capabilities of emerging parallel architectures to accelerate computational science applications. Papers are being sought on a wide variety of topics related to the field of using emerging parallel architectures for computational science including but not limited to: *Application studies on emerging architectures such as ~GPUs, ~FPGAs and Intel MIC *Parallel algorithms and methodologies on emerging architectures *Languages, models, tools, and compilation techniques for emerging architectures *Hybrid computer systems consisting of a combination of ~GPUs, ~FPGAs, etc. *Use of emerging architectures in clusters, grids and supercomputers !!Submission Guidelines: Authors are invited to submit manuscripts reporting original, unpublished research and recent developments. All accepted oral papers will be printed in the conference proceedings published by Elsevier Science in the open-access Procedia Computer Science series (on-line and CD). The submitted paper must be camera-ready and formatted according to the rules of [[Procedia Computer Science|http://www.elsevier.com/wps/find/journaldescription.cws_home/719435/description]] (for [[Latex formatting|http://www.iccs-meeting.org/iccs2012/procedia/ecrc-procs.zip]]; [[MSword|http://www.iccs-meeting.org/iccs2012/procedia/ProcediaComputerScience_template.dot]]). Submission implies the willingness of at least one of the authors to register and present the paper. Pdf and source versions of your paper must be submitted electronically through the [[ICCS 2012 paper submission system|http://www.iccs-meeting.org/iccs2012/papers/upload.php]]. Please, note that papers must not exceed ten pages in length, when typeset using the Procedia format. !!Important Dates: *Full paper submission: January 09, 2012 *Acceptance notification: February 09, 2012 *Camera ready papers: March 01, 2012 *Early registration opens: February 15, 2012 *Early registration ends: April 15, 2012 !!Workshop Co-Chairs: *Bertil Schmidt, Johannes Gutenberg University Mainz, Germany, bertil.schmidt@uni-mainz.de, http://www.staff.uni-mainz.de/schmi033/ *Douglas Maskell, Nanyang Technological University, Singapore, asdouglas@ntu.edu.sg !!Program Committee: *Deming Chen (UIUC, USA) *Robert Strzodka (MPI Informatik, Germany) *Dan Negrut (University of Wisconsin, USA) *Jan Philipp Weiss (KIT, Germany) *Thomas Steinke (ZIB Berlin, Germany) *Dominik Goeddeke (Uni Dortmund, Germany) *Andreas Kloeckner (NYU, USA) *Yongchao Liu (JGU Mainz, Germany) *Andre Brinkmann (JGU Mainz, Germany) *Stefan Kramer (JGU Mainz, Germany) *Bingsheng He (NTU, Singapore) *Rick Goh (IHPC, Singapore) *Alexander Heineke (TU Munich, Germany) *Josef Weidendorfer (TU Munich, Germany) *Lars Wienbrandt (Uni Kiel, Germany) *John Paul Walters (USC, USA) *Scott Emrich (Uni Notre Dame, USA) *Witold Rudnicki (Uni Warsaw, Poland) *Arpith Jacob (Washington Uni in St Louis, USA) *Mathieu Giraud (INRIA, France) *Rob Farber (PNNL, USA) *Stan Scott (Queens Uni Belfast, UK) *Chris Clarke (Uni Bath, UK) *Manfred Schimmler (University of Kiel, Germany) *Simon See (NVIDIA, Singapore) *Neil Bergmann (University of Queensland, Australia) *Alexandros Stamatakis (HITS, Germany) *Dominique Lavenier (IRISA, France) *Jaroslaw Zola (Iowa State Uni, USA) *Ananth Kalyanaraman (Washington State Uni, USA) *Gerrit Voss (Fraunhofer, Singapore) *Weiguo Liu (Fraunhofer, Singapore)
|!Address|Staudingerweg 9, 55128 Mainz, Germany| |!Office|05-233| |!Phone|+49-6131-39-22923| |!Fax|+49-6131-39-23534| |!Email|bertil.schmidt @ uni-mainz.de|
[[News]]
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[[News]] [[Publications]] [[Resume]] [[Software]] [[Teaching]] [[Contact]] <html> <img src="http://www.staff.uni-mainz.de/schmi033/CRC.jpg" width="100" align="left"> </html> <html> <img src="http://www.staff.uni-mainz.de/schmi033/Book1.jpg" width="100" align="left"> </html> <html> <img src="http://www.staff.uni-mainz.de/schmi033/GPUgems.jpg" width="100" align="left"> </html>
!Group website now online The website of my research group is now online: [[Parallel and Distributed Architectures|http://hpc.informatik.uni-mainz.de/]] !CUSHAW short read aligner published in Bioinformatics CUSHAW has evolved into a software package designed for next-generation sequencing read alignment. This is the first version of the package, which only provides support for ungapped read alignment. It is a CUDA compatible short read aligner to large genomes based on the ~Burrows-Wheeler transform (BWT) and is programmed in CUDA C++ parallel programming language. Performance evaluation, using simulated as well as real short read datasets, reveals that CUSHAW running on one or two ~GPUs achieves significant speedups in terms of execution time, while yielding comparable or even better alignment quality for paired-end alignments, compared to three popular ~BWT-based aligners: Bowtie, BWA and ~SOAP2. This aligner does not support for gapped alignments. !!![[Download|http://cushaw.sourceforge.net/]] !!!Y. Liu, __B. Schmidt__, D. Maskell: //[[CUSHAW: a CUDA compatible short read aligner to large genomes based on the ~Burrows-Wheeler transform|http://bioinformatics.oxfordjournals.org/content/early/2012/05/09/bioinformatics.bts276.abstract]]//, ''Bioinformatics'', doi:10.1093/bioinformatics/bts276, 2012 !CALL FOR PAPERS: 4th Workshop on using Emerging Parallel Architectures (WEPA 2012) http://www.staff.uni-mainz.de/schmi033/ !!held in conjunction with the [[International Conference on Computational Science (ICCS 2012)|http://www.iccs-meeting.org/]], Omaha, Nebraska, June 4 – 6, 2012 The computing landscape has undergone significant transformation with the emergence of more powerful processing elements such as ~GPUs, ~FPGAs, multi-cores, etc. On the multi-core front, Moore’s Law has transcended beyond the single processor boundary with the prediction that the number of cores will double every 18 months. Going forward, the primary method of gaining processor performance will be through parallelism. Multi-core technology has visibly penetrated the global market. Accordingly to the latest Top500 lists the HPC landscape has evolved from supercomputer systems into large clusters of dual or quad-core processors. Furthermore, ~GPUs, ~FPGAs and multi-cores have been shown to be formidable computing alternatives, where certain classes of applications witness more than one order of magnitude improvement over their GPP counterpart. Therefore, future computational science centers will employ resources such as FPGA and GPU architectures to serve as co-processors to offload appropriate compute-intensive portions of applications from the servers. This workshop provides a forum for exploring the capabilities of emerging parallel architectures to accelerate computational science applications. Papers are being sought on a wide variety of topics related to the field of using emerging parallel architectures for computational science including but not limited to: *Application studies on emerging architectures such as ~GPUs, ~FPGAs and Intel MIC *Parallel algorithms and methodologies on emerging architectures *Languages, models, tools, and compilation techniques for emerging architectures *Hybrid computer systems consisting of a combination of ~GPUs, ~FPGAs, etc. *Use of emerging architectures in clusters, grids and supercomputers !!Submission Guidelines: Authors are invited to submit manuscripts reporting original, unpublished research and recent developments. All accepted oral papers will be printed in the conference proceedings published by Elsevier Science in the open-access Procedia Computer Science series (on-line and CD). The submitted paper must be camera-ready and formatted according to the rules of [[Procedia Computer Science|http://www.elsevier.com/wps/find/journaldescription.cws_home/719435/description]] (for [[Latex formatting|http://www.iccs-meeting.org/iccs2012/procedia/ecrc-procs.zip]]; [[MSword|http://www.iccs-meeting.org/iccs2012/procedia/ProcediaComputerScience_template.dot]]). Submission implies the willingness of at least one of the authors to register and present the paper. PostScript and source versions of your paper must be submitted electronically through the [[ICCS 2012 paper submission system|http://www.iccs-meeting.org/iccs2012/papers/upload.php]]. Please, note that papers must not exceed ten pages in length, when typeset using the Procedia format. !!Important Dates: *Full paper submission: --January 09, 2012-- ''January 20, 2012 (Deadline extended)'' *Acceptance notification: --February 09, 2012-- February 20, 2012 *Camera ready papers: --March 01, 2012-- March 10, 2012 *Early registration opens: February 15, 2012 *Early registration ends: April 15, 2012 !!Workshop Co-Chairs: *Bertil Schmidt, Johannes Gutenberg University Mainz, Germany, bertil.schmidt@uni-mainz.de, http://www.staff.uni-mainz.de/schmi033/ *Douglas Maskell, Nanyang Technological University, Singapore, asdouglas@ntu.edu.sg !!Program Committee: *Deming Chen (UIUC, USA) *Robert Strzodka (MPI Informatik, Germany) *Dan Negrut (University of Wisconsin, USA) *Jan Philipp Weiss (KIT, Germany) *Thomas Steinke (ZIB Berlin, Germany) *Dominik Goeddeke (Uni Dortmund, Germany) *Andreas Kloeckner (NYU, USA) *Yongchao Liu (JGU Mainz, Germany) *Andre Brinkmann (JGU Mainz, Germany) *Stefan Kramer (JGU Mainz, Germany) *Bingsheng He (NTU, Singapore) *Rick Goh (IHPC, Singapore) *Alexander Heineke (TU Munich, Germany) *Josef Weidendorfer (TU Munich, Germany) *Lars Wienbrandt (Uni Kiel, Germany) *John Paul Walters (USC, USA) *Scott Emrich (Uni Notre Dame, USA) *Witold Rudnicki (Uni Warsaw, Poland) *Arpith Jacob (Washington Uni in St Louis, USA) *Mathieu Giraud (INRIA, France) *Rob Farber (PNNL, USA) *Stan Scott (Queens Uni Belfast, UK) *Chris Clarke (Uni Bath, UK) *Manfred Schimmler (University of Kiel, Germany) *Simon See (NVIDIA, Singapore) *Neil Bergmann (University of Queensland, Australia) *Alexandros Stamatakis (HITS, Germany) *Dominique Lavenier (IRISA, France) *Jaroslaw Zola (Iowa State Uni, USA) *Ananth Kalyanaraman (Washington State Uni, USA) *Gerrit Voss (Fraunhofer, Singapore) *Weiguo Liu (Fraunhofer, Singapore) !Papers !!![[PASHA|http://www.biomedcentral.com/1471-2105/12/354/abstract]] de-novo assembler for large genomes now published in BMC Bioinformatics. [[PASHA|http://www.biomedcentral.com/1471-2105/12/354/abstract]] is a parallelized short read assembler for large genomes using de Bruijn graphs. The proof-of-concept implementation takes advantange of hybrid computing systems comprising shared-memory multi-core ~CPUs and distributed-memory compute clusters to assemble human genomes efficiently. [[Download PASHA|http://sites.google.com/site/yongchaosoftware/pasha]] !Presentations !!!Keynote speaker at JOBIM 2012 I will be Keynote Speaker at the 13th edition of the yearly French conference on bioinformatics, JOBIM 2012, in Rennes !!!<html> <img src="http://www.staff.uni-mainz.de/schmi033/GTCAsia.jpg" width="300"> </html> Invited talk at GTC Asia 2011 I will be giving an invited talk at the [[GTC Asia 2011|http://www.gputechconf.cn/en/home.html]] conference in Beijing about Life Sciences and Bioinformatics. !!!<html> <img src="http://www.staff.uni-mainz.de/schmi033/gtc.jpg" width="120"> </html> Invited talk at GTC 2012 I will be giving an invited talk at the [[NVIDIA GTC 2012|http://www.gputechconf.com/page/home.html]] conference in San Jose about using //~GPUs for Bioinformatics//. !!!Presentation at PRIB 2011 I will be presenting our paper //~CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA// at the [[PRIB 2011|http://prib2011.org/]] conference in Delft. !!!<html> <img src="http://www.staff.uni-mainz.de/schmi033/europar.png" width="120"> </html> Two presentations at ~EuroPar 2011 I will be presenting our paper //Iterative Sparse ~Matrix-Vector Multiplication for Integer Factorization on ~GPUs// at the [[Euro-Par 2011|http://europar2011.bordeaux.inria.fr/ ]] conference in Bordeaux. In addition to that, I will give a ''invited talk'' at the [[UCHPC 2011|http://www.lrr.in.tum.de/~weidendo/uchpc11/]] workshop held in conjunction with ~Euro-Par. !!!Video of my presentation at IMA Workshop available online Video and Slides of my invited talk at the [[IMA Workshop on High Performance Computing and Emerging Architectures|http://www.ima.umn.edu/2010-2011/W1.10-14.11/]] in Minneapolis are available [[here|http://www.ima.umn.edu/2010-2011/W1.10-14.11/abstracts.html#10541]] !Other News !!![[Taipan|http://bioinformatics.oxfordjournals.org/content/25/17/2279.full]] evaluated as best de-novo assembler for Microorganisms by two independent comparisons Two recent comparisons in [[A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies|http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0017915]] and [[Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons|http://bioinformatics.oxfordjournals.org/content/27/2/153.full]] have both ranked [[Taipan|http://bioinformatics.oxfordjournals.org/content/25/17/2279.full]] as the best performing assembler for small genomes from single end short reads (length 36 to 75bps). !!!<html> <img src="http://www.staff.uni-mainz.de/schmi033/cmotif.gif" width="150" > </html> [[CUDA-MEME|http://sites.google.com/site/yongchaosoftware/mcuda-meme]] used in [[CompleteMOTIFs|http://cmotifs.tchlab.org/]] pipeline developed by Harvard Medical School. ~CompleteMOTIFs is a motif discovery platform to find motifs in their peak datasets from transcription factor (TF) binding experiments such as ~ChIP-seq and ~ChIP-chip.~CUDA-MEME is sued to speed up the computation process. More details are described in [[CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments|http://bioinformatics.oxfordjournals.org/content/27/5/715.full]]
![[Citations|http://scholar.google.com/citations?hl=en&user=fUxQceoAAAAJ]] (Google scholar)
!Books
#__B. Schmidt__: [[Bioinformatics: High Performance Parallel Computer Architectures, Taylor & Francis/CRC Press|http://www.crcpress.com/product/isbn/9781439814888 <a href="javascript:" cref="CitaviPicker9781439814888"><img style="border: 0px none;" src="data:image/png;base64,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" alt="Pick It!" title="Titel anhand dieser ISBN in Citavi-Projekt übernehmen"></a> ]], July 2010
!Proceedings
#S. Aluru, S. Bandyopadhyay, U. Catalyurek, D. Dubhashi, P. Jones, M. Parashar, __B. Schmidt__: Contemporary Computing: 4th International Conference (~IC3 2011), Springer, CCIS Series, 2011
#J. Rajapakse, __B. Schmidt__, G. Volkert, Proceedings of the 2nd IAPR Workshop on Pattern Recognition in Bioinformatics (PRIB 2007), Lecture Notes in Bioinformatics, Springer, LNCS Volume 4774, 2007
#F.K. Fuss, S. L. Chia, S.S. Venkatraman, S.M. Krishnan, __B. Schmidt__, Proceedings of the International Bioengineering Conference 2004 (IBEC 2004), Singapore 2004
!Book Chapters
#T.D. Nguyen, __B. Schmidt__, Z. Zheng, C.K. Kwoh://~Large-Scale Clustering of Short Reads for Metagenomics on ~GPUs//, in ''Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data'', Wiley, 2012, (to appear)
#L. Ligowski, W. Rudnicki, Y. Liu, __B. Schmidt__: //Accurate scanning of sequence databases with the ~Smith-Waterman algorithm//, in ''GPU Comuting Gems'', Emerald Edition, Morgan Kaufmann, 2011
#M. Giraud, __B. Schmidt__, S. Janot, J.S. Varre: //Many-core high-performance computing in Bioinformatics//, in ''Advances in Genomic Sequence Analysis and Pattern Discovery'', World Scientific, 2011
#__B. Schmidt__, C. Chen, W. Liu, W. Mitchell: //~PheGee@Home: A Grid-based Tool for Comprative Genomics//, in ''Handbook of Research on Compuational Grid Technologies for Life Science, Biomedicine and Healthcare'', IGI Global, 2009
#__B. Schmidt__, W. Liu, C. Chen: //Hierarchical Grid Computing for High Performance Bioinformatics//, in ''Grids for Bioinformatics and Computational Biology'', Wiley & Sons, 2007
#__B. Schmidt__, H. Schröder: //~Special-Purpose Computing for Biological Sequence Analysis//, in ''Parallel Computing in Bioinformatics and Computational Biology'', Wiley & Sons, New York, 2005
#__B. Schmidt__, M. Schimmler, H. Schröder: //~High-Speed Cryptography//, in ''Embedded Cryptographic Hardware: Methodologies & Architectures'', Nova Science Publishers, 2004
!Journals
#Y. Liu, __B. Schmidt__, D. Maskell: //[[CUSHAW: a CUDA compatible short read aligner to large genomes based on the ~Burrows-Wheeler transform|http://bioinformatics.oxfordjournals.org/content/early/2012/05/09/bioinformatics.bts276.abstract]]//, ''Bioinformatics'', doi:10.1093/bioinformatics/bts276, 2012 (IF: 4.877)
#__B. Schmidt__, H. Aribowo, H.V. Dang: //Iterative Sparse ~Matrix-Vector Multiplication for Accelerating the Block Wiedemann Algorithm over GF(2) on ~Multi-GPU Systems//, ''Concurrency and Computation: Practice and Experience'', 2012, (accepted) (IF: 0.907)
#Y. Chen, __B. Schmidt__, D. Maskell: //A Reconfigurable Accelerator for the Word Matching Stage of BLASTN//, ''IEEE Transactions on VLSI'', 2012, (accepted) (IF: 0.904)
#Y. Liu, __B. Schmidt__, D. Maskell: //Parallelized short read assembly of large genomes using de Bruijn graphs//, ''BMC Bioinformatics'' 12:354, 2011 (IF: 3.43) <html> <img src="http://www.staff.uni-mainz.de/schmi033/highlyaccessed.gif" > </html>
#W. Liu, __B. Schmidt__, W. ~Müller-Wittig: //~CUDA-BLASTP: Accelerating BLASTP on ~CUDA-enabled Graphics Hardware//, ''IEEE/ACM Transactions on Computational Biology and Bioinformatics'' 8(6):1678-1684, 2011 (IF: 2.246)
#H. Shi, __B. Schmidt__, W. Liu, W. ~Müller-Wittig: //Parallel Mutual Information Estimation for Inferring Gene Regulatory Networks on ~GPUs//, ''BMC Research Notes'' 4:189, 2011
#Y. Liu, __B. Schmidt__, D. Maskell: //~DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI//, ''BMC Bioinformatics'' 12:85, 2011 (IF: 3.43) <html> <img src="http://www.staff.uni-mainz.de/schmi033/highlyaccessed.gif" > </html>
#L. Kuttippurathu, M Hsing, Y. Liu, __B. Schmidt__, D. Maskell, K. Lee, A. He, W.T. Pu, S.W. Kong: //~CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments//, ''Bioinformatics'' 27(5):715-717, 2011 (IF: 4.926) <html> <img src="http://www.staff.uni-mainz.de/schmi033/cmotif.gif" width="120" > </html>
#Y. Liu, __B. Schmidt__, D. Maskell: //~MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities//, ''Bioinformatics'' 26(16):1958-1964, 2010 (IF: 4.926)
#A. Wirawan, C.K. Kwoh, __B. Schmidt__: //Multi Threaded Vectorized Distance Matrix Computation on the Cell/BE and x86/~SSE2 Architectures//, ''Bioinformatics'' 26(10): 1368-1369, 2010 (IF: 4.926)
#Y. Liu, __B. Schmidt__, D. Maskell://CUDASW++2.0: enhanced ~Smith-Waterman protein database search on ~CUDA-enabled ~GPUs based on SIMT and virtualized SIMD abstractions//, ''BMC Research Notes'' 3:93, 2010 <html> <img src="http://www.staff.uni-mainz.de/schmi033/highlyaccessed.gif" > </html>
#H. Shi, __B. Schmidt__, W. Liu, W. ~Müller-Wittig: //A Parallel Algorithm for Error Correction in ~High-Throughput ~Short-Read Data on ~CUDA-enabled Graphics Hardware//, ''Journal of Computational Biology'' 17(4):603-615, 2010 (IF: 1.563)
#Y. Liu, __B. Schmidt__, W. Liu, D. Maskell: //~CUDA-MEME: Accelerating Motif Discovery in Biological Sequences Using ~CUDA-enabled Graphics Processing Units//, ''Pattern Recognition Letters'' 31(14):2170 - 2177, 2010 (IF: 1.559)
#J. Schroder, H. Schroder, S. Puglisi, R. Sinha, __B. Schmidt__: //SHREC: A short-read error correction method//, ''Bioinformatics'' 25(17):2157-2163, 2009 (IF: 4.926)
#__B. Schmidt__, R. Sinha, B. ~Beresford-Smith, S. Puglisi: //A Fast Hybrid Short Read Fragment Assembly Algorithm//, ''Bioinformatics'' 25(17),2279-2280, 2009 (IF: 4.926) [[A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies|http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0017915]] and [[Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons|http://bioinformatics.oxfordjournals.org/content/27/2/153.full]] have both ranked this algorithm (Taipan) as the ''best performing assembler'' for small genomes
#T. Oliver, __B. Schmidt__, Y. Jacop, D. Maskell: //~High-Speed Biological Sequence Analysis with Hidden Markov Models on Reconfigurable Platforms//, ''IEEE Transactions on Information Technology in Biomedicine'' 13(5): 740-746, 2009 (IF: 1.939)
#Y. Liu, D. Maskell, __B. Schmidt__: //CUDASW++: optimizing ~Smith-Waterman sequence database searches for ~CUDA-enabled graphics processing units//, ''BMC Research Notes'' 2:73, 2009 <html> <img src="http://www.staff.uni-mainz.de/schmi033/highlyaccessed.gif" > </html> [[Ranked 3rd in all-time most viewed articles|http://www.biomedcentral.com/bmcresnotes/mostviewedalltime/]]
#A. Wirawan, __B. Schmidt__, H. Zhang, C.K. Kwoh: //High Performance Protein Sequence Database Scanning on the Cell B.E. Processor//, ''Scientific Programming'' 17(1-2):97-111, 2009
#A. Wirawan, C.K. Kwoh, T.H. Nim, __B. Schmidt__: //CBESW: Sequence Alignment on the Playstation 3//, ''BMC Bioinformatics'' 9:377, 2008 (IF: 3.781) <html> <img src="http://www.staff.uni-mainz.de/schmi033/highlyaccessed.gif" > </html>
#T. Oliver, Y.Y. Leow, __B. Schmidt__: //Integrating FPGA Acceleration into ~HMMer//, ''Parallel Computing'' 34(11):681-691, 2008 (IF: 1.309)
#W. Liu, __B. Schmidt__, G. Voss, W. ~Müller-Wittig: //Accelerating Molecular Dynamics simulations using Graphics Processing Units with CUDA//, ''Computer Physics Communications'' 179(9):634-641, 2008 (IF: 2.120)
#D.T. Singh, R.Trehan, __B. Schmidt__, T. Bretschneider: //Comparative Phyloinformatics of Virus Genes at Micro and Macro Levels in a Distributed Computing Environments//, ''BMC Bioinformatics'' 9:S23, 2008 (IF: 3.781)
#A. Singh, C. Chen, W. Liu, W. Mitchell, __B. Schmidt__: //A Hybrid Computational Grid Architecture for Comparative Genomics//, ''IEEE Transactions on Information Technology in Biomedicine'' 12(2):218-225, 2008 (IF: 1.939)
#M. Rajapakse, __B. Schmidt__, F. Lin, V. Brusic: //Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms//, ''BMC Bioinformatics'' 8:459, 2007 (IF: 3.781) <html> <img src="http://www.staff.uni-mainz.de/schmi033/highlyaccessed.gif" > </html>
#W. Liu, __B. Schmidt__, G. Voss, W. ~Müller-Wittig, //Streaming Algorithms for Biological Sequence Alignment on ~GPUs//, ''IEEE Transactions on Parallel and Distributed Systems'' 18(9):1270-1281, 2007 (IF: 1.916)
#F. Lin,, H. Schröder, '__B. Schmidt'__: //Solving the Bottleneck Problem in Bioinformatics Computing: an Architectural Perspective//, ''Journal of VLSI Signal Processing Systems'' 48(3):185-188, 2007 (IF: 0.779)
#W. Liu, __B. Schmidt__, W. ~Müller-Wittig: //Performance Analysis of ~General-Purpose Computation on Commodity Graphics Hardware: A Case Study Using Bioinformatics//, ''Journal of VLSI Signal Processing Systems'' 48(3):209-221, 2007 (IF: 0.779)
#J.P. Walters, X. Meng, V. Chaudhary T. Oliver, Y.Y Leow, __B. Schmidt__, D. Nathan J. Landman: //~MPI-HMMER-Boost: Distributed FPGA Acceleration//, ''Journal of VLSI Signal Processing Systems'' 48(3):223-238, 2007 (IF: 0.779)
#__B. Schmidt__: //A Survey of Desktop Grid Applications for ~E-Science//, ''International Journal of Web and Grid Services'' 3(3):354-368, 2007
#M. Schimmler, __B. Schmidt__, H.-W. Lang, S. Heithecker: //An ~Area-Efficient ~Bit-Serial Integer and GF(2n) Multiplier//, ''Microelectronic Engineering'', 82(2):253-259, 2007. (IF: 1.583)
#M. Rajapakse, G.L. Zhang, K.N. Srinivasan, __B. Schmidt__, N. Petrovsky, V. Brusic: //PREDNOD, a prediction server for peptide binding to the H-2g7 haplotype of the nonobese diabetic mouse//, ''Autoimmunity'' 39(8):645-650, 2006 (IF: 2.525)
#C. Chen, __B. Schmidt__: //Constructing Large Suffix Trees on a Computational Grid//, ''Journal of Parallel and Distributed Computing'' 66(12):1512-1523, 2006 (IF: 1.168)
#W. Liu, __B. Schmidt__: //A Parallel Pattern-based System for High Performance Computational Biology//, ''IEEE Transactions on Parallel and Distributed Systems'', 17(8):750-763, 2006 (IF: 1.916)
#T. Oliver, __B. Schmidt__, D. Maskell, D. Nathan, R. Clemens: //~High-speed multiple sequence alignment on a reconfigurable platform// ''International Journal of Bioinformatics Research and Applications'' 2(4):394-406, 2006
#Z. Du, F. Lin, __B. Schmidt__: //Accomplishments and Challenges in High Performance Computing for Computational Biology//, ''Current Bioinformatics'' 1(2):185-195, 2006 (IF: 1.255)
#W. Liu, __B. Schmidt__: //Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids//, ''IEICE Transactions on Information and Systems'' ~E89-D(2):589-596, 2006 (IF: 0.369)
#T. Oliver, __B. Schmidt__, D. Nathan, R. Clemens, D. Maskell: //Using reconfigurable hardware to accelerate multiple sequence alignment with ~ClustalW//, ''Bioinformatics'' 21(16):3431-3432, 2005 (IF: 4.328)
#T. Oliver, __B. Schmidt__, D. Maskell: //Reconfigurable Architectures for ~Bio-sequence Database Scanning on ~FPGAs//, ''IEEE Transactions on Circuits and Systems II'' 52(12):851-855, 2005 (IF: 1.436)
#C. Chen, __B. Schmidt__: //An Adaptive Grid Implementation of DNA Sequence Alignment// ''Future Generation Computer Systems'', 21(7):988-1003, 2005 (IF: 1.476)
#T. Liu, __B. Schmidt__: //Parallel RNA Secondary Structure Prediction using Stochastic ~Context-Free Grammars//, ''Concurrency and Computation: Practice and Experience'' 17(14):1669-85, 2005 (IF: 1.791)
#__B. Schmidt__, M. Schimmler: //A ~Bit-Serial ~Floating-Point Unit for a massively parallel system on a chip//, ''Journal of Parallel Algorithms and Architectures'' 19(2-3):79-96, 2004
#__B. Schmidt__, F. Lin, A. Laud, Y. Santoso: //Development of Distributed Bioinformatics Applications with GMP//, ''Concurrency and Computation: Practice and Experience'' 16:945-959, 2004 (IF: 1.791)
#__B. Schmidt__, H. Schröder, M. Schimmler: //A hybrid architecture for bioinformatics//, ''Future Generation Computer Systems'', 18:855-862, 2002 (IF: 1.476)
#__B. Schmidt__, H. Schröder: //A hybrid Architecture for Multimedia Processors//, ''Computing and Informatics'' 20(9):225-244, 2001 (IF: 0.492)
#__B. Schmidt__, M. Schimmler, H. Schröder: //Tomographic Image Reconstruction on the Instruction Systolic Array//, ''Computing and Informatics'' 20(1):27-42, 2001 (IF: 0.492)
#__B. Schmidt__, M. Schimmler: //KPROC - An Instruction Systolic Architecture for Parallel Prefix Applications//, ''Parallel and Distributed Computing Practices'' 3(2), 2000
#__B. Schmidt__, H. Schröder, M. Schimmler: //A Morphological Approach to Hough Transform on the Instruction Systolic Array//, ''Computers and Artificial Intelligence'' 18(6):541-557, 1999 (IF: 0.492)
!Conferences
#H.V. Dang, __B. Schmidt__: //The Sliced COO format for Sparse ~Matrix-Vector Multiplication on ~CUDA-enabled ~GPUs//, The International Conference on Computational Science 2012 (''ICCS 2012''), Omaha, Nebraska, 2012, (to appear)
#Y. Liu, __B. Schmidt__: //Evaluation of ~GPU-based seed generation for computational genomics using ~Burrows-Wheeler transform//, 11th IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2012''), Shanghai, China, 2012, (to appear)
#W. Liu, __B. Schmidt__, Y. Liu, W. ~Müller-Wittig: //Mapping of the BLASTP Algorithm onto GPU Clusters//, 17th IEEE International Conference on Parallel and Distributed Systems (''IEEE ICPADS 2011''), Tainan, Taiwan, IEEE Computer Society, pp. 236-243, 2011
#Z. Zheng, T.D. Nguyen, __B. Schmidt__: //~CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA//, 6th IAPR International Conference on Pattern Recognition in Bioinformatics (''PRIB 2011''), Deft, Netherlands, Springer LNCS 7036, pp. 37-49, 2011
#__B. Schmidt__, H. Aribowo, H.V. Dang: //Iterative Sparse ~Matrix-Vector Multiplication for Integer Factorization on ~GPUs//, ''~Euro-Par 2011'', Bordeaux, France, Springer LNCS 6853, 413-424, 2011
#Y. Liu, __B. Schmidt__, D. Maskell: //An ultrafast scalable many-core motif discovery algorithm for multiple ~GPUs//, 10th IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2011''), Anchorage, Alaska, 2011
#Z. Zheng, G. Bourque, __B. Schmidt__: //Prediction of Low Coverage Prone Regions for Illumina Sequencing Projects using a Support Vector Machine//, IEEE International Conference on Bioinformatics & Biomedicine (''IEEE BIBM 2010''), Hong Kong, IEEE Press, 2010
#H. Shi, __B. Schmidt__, W. Liu, W. ~Müller-Wittig: //~Quality-Score Guided Error Correction for ~Short-Read Sequencing Data using CUDA//, The International Conference on Computational Science 2010 (''ICCS 2010''), Amsterdam, Netherlands, Procedia 1(1):1123-1132, 2010
#Y. Liu, __B. Schmidt__, D.L. Maskell: //~MSA-CUDA: "Multiple Sequence Alignment on Graphics Processing Units with CUDA//, 20th IEEE International Conference on Application-specific Systems, Architectures and Processors (''ASAP 2009''), Boston, MA, IEEE Press, 121-128, 2009 (''//BEST PAPER AWARD//'')
#A. Wirawan, __B. Schmidt__, C.K. Kwoh: //Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine//, The International Conference on Computational Science 2009 (''ICCS 2009''), Baton Rouge, Louisiana, Springer, LNCS 5544, 962-971, 2009
#H. Shi, __B. Schmidt__, W. Liu, K. ~Müller-Wittig: //Accelerating Error Correction in ~High-Throughput ~Short-Read DNA Sequencing Data with CUDA//, 8th IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2009''), Rome, Italy, IEEE Press, 2009
#Y. Liu, __B. Schmidt__, D. Maskell: //Parallel Reconstruction of ~Neighbor-Joining Trees for Large Multiple Sequence Alignments using CUDA//, 8th IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2009''), Rome, Italy, IEEE Press, 2009
#Y. Chen, __B. Schmidt__, D. Maskell: //A Reconfigurable Bloom Filter Architecture for BLASTN//, 22nd International Conference on Architectures of Computing Systems (''ARCS 2009''), Delft, Netherlands, Springer, LNCS 5455, 40-49, 2009
#C. Chen, __B. Schmidt__, W. Liu, W. ~Müller-Wittig: //~GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Seqeunces//, ''PRIB 2008'', Melbourne, Australia, Springer, LNCS Vol. 5265, 448-459, 2008.
#H. Zhang, __B. Schmidt__, W. ~Müller-Wittig: //Accelerating BLASTP on the Cell Broadband Engines//, ''PRIB 2008'', Melbourne, Australia, Springer, LNCS 5265, 460-470, 2008.
#W. Liu, __B. Schmidt__, G.Voss, W. ~Müller-Wittig: //Molecular Dynamics Simulations on Commodity ~GPUs With CUDA//, 14th IEEE International Conference on High Performance Computing (''~HiPC 2007''), Goa, India, Springer, LNCS 4873, 2007
#M.Y.H. Low, W. Liu, __B. Schmidt__: //A Parallel BSP Algorithm for Irregular Dynamic Programming//, 7th International Symposium on Advanced Parallel Processing Technologies (''APPT 2007''), Springer, LNCS 4847, 151-160, 2007
#A. Wirawan, __B. Schmidt__, C.K. Kwoh: //Parallel DNA Sequence Alignment on the Cell Broadband Engine//,7th International Conference on Parallel Processing and Applied Mathematics (''PPAM 2007''), Gdansk, Poland, Springer, LNCS 4967, 1249-1256, 2008
#L.A. Aung, D. Maskell, T. Oliver, __B. Schmidt__: //~C-based Design Methodology for ~FPGA Implementation of ~ClustalW MSA//, ''PRIB 2007'', Singapore, Springer LNCS 4774, pp. 11-18, 2007
#R. Trehan, D.T. Singh, __B. Schmidt__: //Phylogenetic Analysis of Neuraminidase Genes of ~H5N1 Isolates using HPC technologies//, 9th International Conference on e-Health Networking, Application and Services (''IEEE Healthcom 2007''), IEEE Press, 285-288, 2007
#C. Chen, A. Singh, W. Mitchell, __B. Schmidt__: //Phenotype Genotype Exploration on a Desktop GPU Grid//, 3rd International Workshop on Grid Computing and Applications, World Scientific, 154-165, 2007
#W. Liu, W. ~Müller-Wittig, B. Schmidt: //Performance Predictions for ~General-Purpose Computation on ~GPUs//, International Conference on Parallel Processing (''ICPP 2007''), ~XiAn, China, IEEE Press, 2007
#T. Oliver, Y.Y. Leow, __B. Schmidt__: //High Performance Database Searching with ~HMMer on ~FPGAs//, 6th IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2007''), Long Beach, CA, IEEE Press, 2007.
#J. Feng, S. Chakraborty, __B. Schmidt__, W. Liu, U.D. Bordoloi: //Fast Schedulability Analysis Using Commodity Graphics Hardware//, 13th IEEE International Conference on Embedded and ~Real-Time Computing Systems and Applications (''RTCSA 2007''), IEEE Press, 400-408, 2007
#W. Liu, __B. Schmidt__, G. Voss, W. ~Müller-Wittig: //~GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment//, 13th IEEE International Conference on High Performance Computing (''~HiPC 2006''), Bangalore, India, Springer, LNCS 4297, pp. 363-374, 2006.
#A. Wirawan, __B. Schmidt__: //Parallel Discovery of Transcription Factor Binding Sites//, IEEE Asia Pacific Conference on Circuits and Systems (''APCCAS 2006''), Singapore, IEEE Press, 2006
#T. Oliver, __B. Schmidt__, J. Yanto, D. Maskell: //Accelerating the Viterbi Algorithm for Profile Hidden Markov Models using Reconfigurable Hardware//, International Conference on Computational Science (''ICCS 2006''), Reading, UK, Springer LNCS 3991, 522-529, 2006
#M. Rajapakse, __B. Schmidt__, V. Brusic: //~Multi-Objective Evolutionary Algorithm for Discovering Peptide Binding Motifs//, 4th European Workshop on Evolutionary Computation and Machine Learning in Bioinformatics (''~EvoBIO 2006''), Budapest, Hungary, Springer, LNCS 3907, 149-158, 2006
#W. Liu, B. Schmidt, G. Voss, A. Schröder, W. ~Müller-Wittig: //~Bio-Sequence Database Scanning on a GPU//, 5th IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2006''), Rhode Island, Greece, IEEE Press, 2006
#M. Rajapakse, __B. Schmidt__, V. Brusic: //~Pareto-Optimal Motif for Predicting Peptide Binders//, 16th International Conference on Genomic Informatics (''GIW 2005''), Yokohama, Japan, 2005
#G. Voss, A. Schröder, W. ~Müller-Wittig, B. Schmidt: //Using Graphics Hardware to Accelerate Biological Sequence Analysis//, ''IEEE Tencon 2005'', Melbourne, Australia, 2005
#W. Liu, __B. Schmidt__: //Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids//, ''IEEE Tencon 2005'', Melbourne, Australia, 2005.
#J. Yanto, T. Oliver, __B. Schmidt__, D. Maskell: //Biological Sequence Analysis with Hidden Markov Models on an FPGA//, 10th ~Asia-Pacific Computer Systems Architecture Conference (''ACSAC 2005''), Singapore, Springer LNCS 3740, 2005.
#C. Chen, __B. Schmidt__: //Parallel Construction of Large Suffix Trees on a PC Cluster//, ''~Euro-Par 2005'', Lisbon, Portugal, Springer LNCS 3648, 2005.
#M. Rajapakse, L. Wyse, ''B. Schmidt'', V. Brusic: //Deriving Matrix of ~Peptide-MHC Interactions in Diabetic Mouse by Genetic Algorithm//, 6th International Conference on Intelligent Data Engineering and Automated Learning (''IDEAL 2005''), Brisbane, Australia, Springer LNCS, 2005
#T. Oliver, __B. Schmidt__, D. Nathan, R. Clemens, D. Maskell: //Multiple Sequence Alignment on an FPGA//, 11th International Conference on Parallel and Distributed Systems (''ICPADS 2005''), IEEE Computer Society Press, Fukuoka, Japan, 2005
#W. Liu, __B. Schmidt__: //A Case Study on Pattern-based Systems for High Performance Computational Biology//, 4th IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2005''), Denver, CO, IEEE Press, 2005
#T. Oliver, __B. Schmidt__, D. Maskell: //Hyper Customized Processors for ~Bio-Sequence Database Scanning on ~FPGAs//, ''ACM FPGA 2005'', Monterrey, CA, 2005.
#T. Liu, __B. Schmidt__: //Optimal local alignment in RNA secondary structures//, ''~BioMED 2005'', Innsbruck, Austria, 2005.
#W. Liu, __B. Schmidt__: //A Tunable ~Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications//, 11th Annual International Conference on High Performance Computing (''~HiPC 2004''), Bangalore, India, Springer LNCS 3296, 2004.
#C.Chen, __B. Schmidt__: //Load Balancing for Hierarchical Grid Computing: A Case Study//, 11th Annual International Conference on High Performance Computing (''~HiPC 2004''), Bangalore, Springer, LNCS 3296, 2004.
#W. Liu, __B. Schmidt__: //A Generic Parallel Pattern-based System for Bioinformatics//, ''~Euro-Par 2004'', Pisa, Italy, Springer, LNCS 3149, 2004
#C.S.S. Tan, __B. Schmidt__: //Combining ~message-passing and ~inter-process communication in ~SMP-hybrid cluster for efficient parallel medical image analysis//, APPLICATIONS OF DIGITAL IMAGE PROCESSING XXVII, Denver, CO, SPIE 5558, 2004
#T. Oliver, __B. Schmidt__: //High Performance Biosequence Database Scanning on Reconfigurable Platforms//, 3rd IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2004''), Santa Fe, NM, IEEE Press, 2004
#T. Liu, ___B. Schmidt__: //Parallel RNA ~Sequence-Structure Alignment//, 3rd IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2004''), Santa Fe, NM, IEEE, 2004
#C. Chen, __B. Schmidt__: //Performance Analysis of Computational Biology Applications on Hierarchical Grid Systems//, 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (''~CCGrid 2004''), Chicago, IL, IEEE, 2004.
#C. Chen, __B. Schmidt__: //Computing ~Large-Scale Alignments on a ~Multi-Cluster//, IEEE International Conference on Cluster Computing (''Cluster 2003''), Hong Kong, 2003.
#W. Liu, __B. Schmidt__: //Parallel Design Pattern for Computational Biology and Scientific Computing//, IEEE International Conference on Cluster Computing (''Cluster 2003''), Hong Kong, 2003
#M. Schimmler, __B. Schmidt__, S. Heithecker: //An ~Area-Efficient ~Bit-Serial Integer Multiplier//, The 2003 International Conference on VLSI (''VLSI 2003''), Las Vegas, NV, 2003
#M. Schimmler, __B. Schmidt__, H.-W. Lang: //Design of a ~Bit-serial ~Floating-Point Unit for a ~Fine-Grained Parallel Processor Array//, The 2003 International Conference on Parallel and Distributed Processing Techniques and Applications (''PDPTA 2003''), Las Vegas, NV, 2003
#__B. Schmidt__, F. Lin, A. Laud, Y. Santoso: //Parallel Detection of Regulatory Elements with gMP//, 2nd IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2003''), Nice, France, IEEE Press, 2003
#L. Wang, W. Cai, __B. Schmidt__, B.S. Lee, W. Jie: //Biogrid Computing Platform: Parallel computing for protein alignment analysis//, ''HPC Asia 2002'', Bangalore, India, 2002
#H. Schröder, __B. Schmidt__, J. Zhu: //A new approach to protein structure prediction//, The International Conference on Bioinformatics (''~InCoB 2002''), Bangkok, Thailand, 2002
#__B. Schmidt__, M. Schimmler, W. Adi: //Area efficient modular arithmetic for mobile security//, The 2002 International Conference on Wireless Networks (''ICWN 2002''), Las Vegas, NV, 2002
#__B. Schmidt__, H. Schröder, M. Schimmler: //Massively Parallel Solutions for Molecular Sequence Analysis//, IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2002''), Ft Lauderdale, FL, IEEE Press, 2002
#__B. Schmidt__, H. Schröder: //Massively Parallel Sequence Analysis with Hidden Markov Models//, International Conference on Scientific & Engineering Computation (''~IC-SEC 2002''), Singapore, World Scientific, 2002
#L. Wang, W. Cai, __B. Schmidt__, B.S. Lee, W. Jie: //Replica Selection Framework for ~Bio-Grid Computing//, International Conference on Scientific & Engineering Computation (''~IC-SEC 2002''), Singapore, World Scientific, 2002
#H. Schröder, __B. Schmidt__: //Image Processing Algorithms for on-board Computing//, 3rd International Conference on Information, Communications & Signal Processing (''ICICS 2001''), Singapore, 2001
#L.S. Chin, H. Schröder, __B. Schmidt__: //Parallel Volume Rendering using Slice Orientation//, 3rd International Conference on Information, Communications & Signal Processing (''ICICS 2001''), Singapore 2001
#__B. Schmidt__, H. Schröder, M. Schimmler: //Protein Sequence Comparison on the Instruction Systolic Array//, 6th International Conference on Parallel Computing Technologies (''~PaCT 2001''), Novosibirsk, Russia, Springer LNCS 2127, 2001
#__B. Schmidt__, H. Schröder, M. Schimmler: //Scanning Biosequence Databases on a Hybrid Parallel Architecture//, ''~Euro-Par 2001'', Manchester, UK, Springer LNCS 2150, 2001.
#__B. Schmidt__, H. Schröder, T. Srikanthan: //A SIMD Solution to Biosequence Database Scanning//, Parallel Computing 2001 (''~ParCo 2001''), Naples, Italy, Imperial College Press, 2001.
#L.S. Chin, __B. Schmidt__, H. Schröder: //Volume Rendering Using the Instruction Systolic Array Concept//, ~Asia-Pacific Conference on Computational Mechanics, Sydney, Australia, 2001
#__B. Schmidt__: //Design of a Parallel Accelerator for Volume Rendering//, ''~Euro-Par 2000'', Munich, Germany, Springer LNCS 1900, 1095-1104, 2000.
#__B. Schmidt__, H. Schröder: //Volume Visualisation on a Hybrid Parallel Architecture//, 7th Australasian Conference on Parallel and ~Real-Time Systems (''PART 2000''), Sydney, Australia, Springer, 2000.
#__B. Schmidt__, M. Schimmler: //A Parallel Accelerator Architecture for Multimedia Video Compression//, ''~Euro-Par 1999'', Toulouse, France, Springer LNCS 1685, 1999.
#__B. Schmidt__, M. Schimmler, H. Schröder: //Long Operand Arithmetic on Instruction Systolic Computer Architectures and its Application for RSA Cryptography//, ''~Euro-Par 1998'', Southampton, UK, Springer LNCS 1470, 1998
#__B. Schmidt__, M. Schimmler, H. Schröder: //The Instruction Systolic Array in Tomographic Image Reconstruction Applications//, 5th Annual Australasian Conference on Parallel and Real-time Systems (''PART 1998''), Adelaide, Australia, Springer, 1998
#__B. Schmidt__, M. Schimmler, H. Schröder: //Morphological Hough Transform on the Instruction Systolic Array//, ''~Euro-Par 1997'', Passau, Germany, Springer LNCS 1300, 1997
#U. Mahlmeister, __B. Schmidt__, G. Sommer: //Preattentive Colour Features by Steerable Filters//, 17th DAGM Symposium Pattern Recognition (''DAGM 1995''), Bielefeld, Germany, Springer, 1995
!EDUCATION: !!<html> <img src="http://www.staff.uni-mainz.de/schmi033/lulogo.gif" width="120"> </html> Ph.D. in Computer Science *1999, [[Loughborough University|http://www.lboro.ac.uk/]] *Thesis title: //Algorithm Design on the Instruction Systolic Array// *Advisor: [[Prof. Dr. Heiko Schröder|http://goanna.cs.rmit.edu.au/~heiko/]] !! <html> <img src="http://www.staff.uni-mainz.de/schmi033/cau.png" width="120"> </html> ~Diplom-Informatiker *1995, Major: Computer Science, Minor: Mathematics, [[Christian-Albrechts-Universität zu Kiel|http://www.uni-kiel.de/index-e.shtml]] *Award: ''//Best Degree in Computer Science in 1995//'' * Thesis advisor: [[Prof. Dr. Gerald Sommer|http://www.informatik.uni-kiel.de/inf/Sommer/]] !ACADEMIC EXPERIENCE: !! <html> <img src="http://www.staff.uni-mainz.de/schmi033/mainzlogo.gif" width="120"> </html> Johannes Gutenberg University Mainz (Germany) *07/2011 - present: Tenured Full Professor (W3) and Chair for Parallel and Distributed Systems, Insitut für Informatik !! <html> <img src="http://www.staff.uni-mainz.de/schmi033/ntu_logo2.jpg" width="120"> </html>Nayang Technological University (NTU) *06/2008 - 06/2011: Associate Professor, School of Computer Engineering *05/2001 - 12/2006: Assistant Professor, School of Computer Engineering *09/1999 - 04/2001: Research Fellow, School of Computer Engineering !!<html> <img src="http://www.staff.uni-mainz.de/schmi033/melb.jpg" width="120"> </html>University of Melbourne: *01/2008 - 06/2008: Senior Researcher, NICTA VRL !! <html> <img src="http://www.staff.uni-mainz.de/schmi033/UNSW.jpg" width="120"> </html>University of New South Wales: *01/2007 - 08/2007: Associate Professor, Computer Engineering and Information Technology (Asia Campus) !!UNIVERSITY SERVICE *08/2011 - present: University HPC Comittee Member *07/2010 - 06/2011: Course Lead in HPC Stream *11/2009 - 06/2011: Search Committee Member for Faculty Positions in High Performance Computing and Distributed Systems *01/2006 - 12/2006: Programme Director, M.Sc. in Bioinformatics *05/2003 - 05/2005: Deputy Director, ~BioMedical Engineering Research Center (BMERC) !INDUSTRIAL CONSULTATION *[[Progeniq Pte Ltd|http://www.progeniq.com/]] (Singapore): //BLAST on ~FPGAs//, //Speech Recognition on ~FPGAs//, //Ray Tracing on SGI RASC ~RC100//, //Development of biological sequence analysis applications on ~FPGAs// *[[Matrixview Ltd|http://www.matrixview.com/]] (Singapore): //Evaluation of computational platforms for real-time medical imaging compression// *Helixense Pte Ltd (Singapore): //Development of a software system for bioinformatics applications on PC clusters// *Siemens AG (Munich, Germany): //Design of an embedded system for H.263 video compression// *ISATEC ~GmbH (Kiel, Germany): //Parallelization of scientific computing applications on Systola1024 (image and signal processing, FFT, medical image reconstruction, cryptography, and multimedia video compression)// !AWARDS AND HONORS *[[NVIDIA Academic Partnership Award|http://research.nvidia.com/content/bertil-schmidt ]] *[[CUDA Research Center (CRC) Award|http://research.nvidia.com/content/ntu-crc-summary]] *GPU Computing Champion for the "Bioinformatics and Computational Biology" community on [[gpucomputing.net|http://gpucomputing.net/]] *Best Paper Award, 20th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2009), July, 7-9, 2009, Boston, MA *Award for the best degree in Computer Science at University of Kiel in 1995 *Nominated for the Excellence in Teaching Award for contributions in teaching at Nanyang Technological University in 2005 *Best Paper Award "Systems Category", Fraunhofer Institute (IGD in Darmstadt) in 2007 *NVIDIA Professor Partnership Award !LIST OF PUBLICATIONS [[Publications]] !RESEARCH GRANTS: !!External Research Grants *//Modeling, validation, and analysis of gene regulatory networks including delays//, Source: MOE Tier 2, Amount and Period: S$1,191,620 (2010-13), Role: ~Co-PI *//Development of Scalable Bioinformatics Algorithms and Tools for Emerging Sequencing Technologies//, Source: MOE Tier 1, Amount and Period: S$150,000 (2009-12), Role: PI *//NVIDIA Academic Paternership Award//, Source: NVIDIA, Amount and Period: US$25,000 (2010-11), Role: PI *//Amazon Cloud Computing Grant//, Source: Amazon, Period: 2010-11, Role: PI *//CUDA Research Center Award//, Period: 2010-11, Source: NVIDIA, Role: PI *//Scalable Algorithm Design for Emerging Parallel Architectures//, Source: ~MoD, Period and Amount: 2010-11, S$135,000 Role: PI *//NVIDIA Professor Partnership Award//, Source: NVIDIA, Amount and Period: US$25,000 (2008-09), Role: PI *//Dynamic Reconfigurable Computing: The next generation high performance computing platform for embedded applications//, Source: MOE Tier 2, Amount and Period: S$527,695 (2007-10), Role: ~Co-PI *//Development of a Grid System with Applications to ~Large-Scale Bio and Nanomaterial-systems//, Source: A*Star, Amount and Period: S$297,145 (2005-08), Role: PI *//Hybrid Computing//, Source: ISAVISION ~GmbH, Amount and Period: S$200,000 (2000-2003), Role: PI !!University Research Grants: *//Algorithms and Architectures for Emerging High Performance Computing Applications//, Source: Group Seed Funding Scheme Award (UNSW), Amount: S$80,000 (2007-08), Role: PI *//Using a ~PlayStation3 Cluster for Biological Sequence Analysis//, Source: Small Research Grant Award (UNSW), Amount: S$9,000 (2007-08), Role: PI *//GPGPU Grid//, Source: NTU Office of Research (2005-06), Amount: S$16,000, Role:PI *//Ph.D. scholarships//, Source: NTU, Amount and Period: approx. S$100,000 (2005-10), Role: Supervisor *//DNA Chip Design Program//, Source: ~ER-Lab Research Program Grant, NTU, Amount and Period: S$40,000 (2005-07), Role: ~Co-PI !PROFESSIONAL SERVICE !!Professional Associations *Senior Member, IEEE and IEEE Computer Society *Member, ISCB !!Journal Editorial Board *Associate Editor, BMC Research Notes (~BioMed Central) *Editoral Board Member, Journal of Computational Science (Elsevier) *Editor for Life Sciences, GPU Computing Gems (NVIDIA) *Guest Editor, Pattern Recognition Letters (Elsevier), Special Issue on Bioinformatics, Vol. 31, No. 14, 2010 *Guest Editor, The Journal of VLSI Signal Processing Systems (Springer), Special Issue on Computing Architectures and Acceleration for Bioinformatics Algorithms, Vol. 48, No. 3, 2007 *Guest Editor, International Journal of Web and Grid Services, Special Issue on Selected paper from ~CCGrid Workshop on Grid Testbeds, Vol. 3, No. 3, 2007 !!Organizing Committees *Program ~Vice-Chair, //IEEE ICPADS 2012//, Singapore, December 2012 *~Program Chair, Applications Track, //Fourth International Conference on Contemporary Computing (~IC3-2011)//, NOIDA, India August, 2011 *Workshop Chair: //3rd Workshop on using Emerging Parallel Architectures (WEPA 2011)//, held at the ICCS 2011, Tsukuba, Japan *Workshop ~Co-chair: //Parallel Programming and Applications on Accelerator Clusters (PPAAC 2010)//, held at IEEE Cluster 2010, Heraklion, Greece, Sep 20-24, 2010 *Workshop Chair: //2nd Workshop on using Emerging Parallel Architectures (WEPA 2010)//, held at ICCS 2010, Amsterdam, Netherlands *Workshop Chair, //1st Workshop on using Emerging Parallel Architectures (WEPA 2009)//, held at ICCS 2009, Baton Rouge, Louisiana *Program Chair, //7th IEEE International Workshop on High Performance Computational Biology (~HiCOMB 2008)//, Miami, FL, 2008 *Program ~Co-Chair, //2nd IAPR Workshop on Pattern Recognition in Bioinformatics (PRIB 2007)//, Singapore, 2007 *Technical ~Co-Chair, //3rd IAPR Workshop on Pattern Recognition in Bioinformatics (PRIB 2008)//, Melbourne, Australia, 2008 *Scientific Organizing Committee, //World Wide Work Flow Grid Workshop (~W4G 2007)//, Singapore, 5-7 June 2007 *Workshop Organizer, //International Workshop on Grid Testbeds//, held at ACM/IEEE ~CCGrid 2006, Singapore, May, 16-19, 2006 *Track Chair, //IEEE International Conference in Biomedical and Pharmaceutical Engineering 2006 (ICBPE 2006)//, Singapore, December 11-14, 2006 *Workshops Chair, //6th ACM/IEEE Symposium on Cluster Computing and the Grid (~CCGrid 2006)//, Singapore, May 16-19, 2006. *Program ~Vice-Chair, //7th ~NTU-SGH Symposium//, Singapore, August 11-12, 2005 *Cyberchair, //11th Annual International Conference on High Performance Computing (~HiPC 2004)//, Bangalore, India, December 19-22, 2004 *Publicity Chair, //The 2004 IEEE International Conference on Cluster Computing (Cluster 2004)//, San Diego, CA, September 20-23, 2004 *Exhibits/Sponsorship Chair, //1st International ~BioEngineering Conference 2004 (IBEC 2004)//, Singapore, September 8-10, 2004. *Topic ~Vice-Chair, //~Euro-Par 2003//, Klagenfurt, Austria, August 26-29, 2003 !!Program Committee Memberships *11th IEEE International Workshop on High Performance Computational Biolog (~HiCOMB 2012), Shanghai, China, 2012 *12th IEEE International Symposium on Cluster, Cloud and Grid Computing (~CCGrid 2012), Ottawa, Canada, 2012 *18th IEEE International Conference on High Performance Computing (~HiPC 2011), Bangalore, India, Dec. 18-21, 2011. *13th IEEE International Conference on High Performance Computing and Communications (~HPCC 2011), Banff, Alberta, Sep 2-4, 2011 *12th IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing (~PDSEC-11), Anchorage, Alaska, May 16-20, 2011 *4th Workshop on Parallel Computational Biology (PBC 2011), Torun, Poland, September, 2011. *IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology (HISB 2011), San Jose, CA, July 27-29, 2011. *10th IEEE International Workshop on High Performance Computational Biolog (~HiCOMB 2011), Anchorage, Alaska, 2011 *12th IEEE International Conference on High Performance Computing and Communications (~HPCC-2010), Melbourne, Australia, September 1-3, 2010 *11th International Conference on Parallel and Distributed Computing, Applications and Technologies (~PDCAT-2010), Wuhan, China, December 8-11, 2010 *6th Workshop on Large Scale Computations on Gridsa and 1st Workshop on Scalable Computing in Distributed Systems (~LaSCoG-SCoDiS'10), Wisla, Poland, October 18-20, 2010 *Third International Conference on Contemporary Computing (~IC3-2010), India August 9-11, 2010 *2010 International Workshop on ~Multi-Core Computing Systems (~MuCoCoS 2010), Feb. 15, Krakow, Poland, 2010 *15th International Conference on Parallel and Distributed Systems (ICPADS 2009), Dec. 9-11, Shenzhen, China, 2009 *The International Conference on Bioinformatics (~InCoB 2009), Singapore, Sep 7-11, 2009 *2nd International Conference on Contemporary Computing, Noida, India, August 17-19, 2009 *3rd Workshop on Parallel Computational Biology (PBC 2009), Wroclaw, Poland, September 13-16, 2009. *2009 IEEE Congress on Evolutionary Computation (IEEE CEC 2009), Trondheim, Norway, 2009 *8th IEEE International Workshop on High Performance Computational Biology (~HiCOMB 2009), Rome, Italy, 2009 *6th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA 2008), Doha, Qatar, March 31 - April 4, 2008 *14th Annual International Conference on High Performance Computing (~HiPC 2007), Goa, India, December 18-21, 2007 *10th International Conference on e-Health Networking, Applications and Services (IEEE Healthcom 2008), Singapore, July, 7-9, 2008 *9th International Conference on e-Health Networking, Applications and Services (IEEE Healthcom 2007), Taipei, Taiwan, June, 19-22 2007 *21st IEEE International Parallel & Distributed Processing Symposium (IPDPS 2007), Long Beach, California, March 26-30, 2007 *2007 IEEE International Symposium on Bioinformatics and Life Science Computing (BLSC 2007), Niagara Fall, Ontario, Canada *Parallel ~Bio-Computing (PBC 2007) Workshop, Gdansk, Poland, September 9-12, 2007 *2006 Workshop on Pattern Recognition in Bioinformatics (PRIB 2006), Hong Kong, 20-24 August, 2006 *IEEE Workshop on Biomedical Computations on the Grid (~BioGrid 2007), held at ~CCGrid 07, Rio de Janero, Brazil, May 14-17, 2007 *IEEE Workshop on Biomedical Computations on the Grid (~BioGrid 2006), held at ~CCGrid 06, Singapore, May 16-19, 2006 *IEEE Workshop on ~High-Performance Computing in Medicine and Biology (~HiPCoMB 2006), April 18-20, 2006, Vienna, Austria, held at AINA 2006 *IEEE Workshop on ~High-Performance Computing in Medicine and Biology (~HiPCoMB 2005), July 20-22, 2005, Fukuoka, Japan, held at ICPADS 2005 *4th IASTED International Conference on Biomedical Engineering (~BioMED 2006), Innsbruck, Austria, February 15-17, 2006, *5th IASTED International Conference on Biomedical Engineering (~BioMED 2007), Innsbruck, Austria, February, 14-16, 2007, *6th IASTED International Conference on Biomedical Engineering (~BioMED 2008), Innsbruck, Austria, February, 14-16, 2008 *1st IEEE International Conference on e-Science and Grid Computing (~E-Science 2005) December 5-8, 2005, Melbourne, Australia *2nd IEEE International Conference on e-Science and Grid Computing (~E-Science 2006) , December 4-6, 2006, Amsterdam, Netherland !!Journal Reviewing *Genome Biology *Information Systems *ACM Transactions on Reconfigurable Technology and Systems *IEEE Transactions on Information Technology in Biomedicine *IEEE Transactions on Computers *IEEE Transactions on Nanobiosciences *IEEE Transactions on Circuits and Systems II *IEEE/ACM Transactions on Computational Biology and Bioinformatics *IEEE Computer Magazine *IEEE Transactions on Parallel and Distributed Computing *IEEE Transactions on VLSI *Journal of Computational Biology *Bioinformatics *BMC Bioinformatics *Parallel Computing *Journal of Parallel and Distributed Computing *Computer Physics Communications *Comparative and Functional Genomics *Virus Genes *Pattern Recognition Letters *The Computer Journal *Journal of ~Real-Time Imaging *International Journal of Data Mining and Bioinformatics *Journal of Signal Processing Systems !!Panelist for Funding Agencies *European Cooperation in Science and Technology (COST) *Microsoft Research ~PhD Scholarship Programme *SPRING Singapore, Technology Enterprise Commercialisation Scheme *Landesstiftung ~Baden-Wuerttemberg, HPC funding program *Kentucky Science and Engineering Foundation, R&D Excellence program !TEACHING ACTVITIES [[Teaching]] !Current Group Members !!Current Ph.D. and M.Eng. Students: *[[Liu Yongchao|http://sites.google.com/site/yongchaosoftware/]] *Chen Yupeng *[[Nguyen Thuy Diem|http://pdcc.ntu.edu.sg/content/nguyen-thuy-diem]] *Robert Guziolowski *Karan Shetti (external M.Eng. with EADS) !!Researchers (as members of my research team): *[[Dr Liu Weiguo|http://sites.google.com/site/liuweiguohome/home]] *Dr Zejun Zheng *Dang Hoang Vu !Former Group Members !!Graduated Ph.D. Students: *[[Adrianto Wirawan|http://sites.google.com/site/adrianto/home]]: //Heterogeneous ~Multi-Core Systems for Bioinformatics//, 2010 *Menaka Rajapakse: //Evolutionary Approaches for Predicting MHC Peptide Binding//, 2009 *[[Weiguo Liu|http://sites.google.com/site/liuweiguohome/home]], Dissertation: //Parallel and Distributed Algorithms for Computational Biology//, 2007 *Chunxi Chen, Dissertation: //Computational Genomics on the Grid//, 2007 !!Former Researchers *Hans Aribowo *Dr Shi Haixiang *Dr Chen Chen *Dr Zhang Huiliang
Professor of Computer Science
<html> <html> <img src="http://www.staff.uni-mainz.de/schmi033/Bertil2" width="120" align="left"> </html> Bertil Schmidt
''Publicly available Bioinformatics Software developed by my research group.''
!PASHA
PASHA is a parallelized short read assembler for large genomes using de Bruijn graphs. The proof-of-concept implementation takes advantange of hybrid computing systems comprising shared-memory multi-core CPUs and distributed-memory compute clusters to assemble human genomes in reasonably short time with only modest compute resources.
*Download: [[Google|http://sites.google.com/site/yongchaosoftware/pasha]]
*Citation:
**Y. Liu, __B. Schmidt__, D. Maskell: //Parallelized short read assembly of large genomes using de Bruijn graphs//, ''BMC Bioinformatics'' 12:354, 2011 <html> <img src="http://www.staff.uni-mainz.de/schmi033/highlyaccessed.gif" > </html>
!~CUDA-MI
~CUDA-MI accelerates MI (mutual information) estimation using the B-spline function. In order to exploit the GPU's capabilities to accelerate MI estimation, we have used the fast shared memory, fine-grained parallelism, and partitioning to implement our algorithm. Our implementation achieves speedups up to 82 compared to the multi-threaded MIBE on a modern Intel quad-core. We also have used the output of ~CUDA-MI to infer ~GRNs. Our experiments show that compared to ARACNE and ~TINGe, ~CUDA-MI can achieve better performance in terms of both runtime and inferred ~GRNs' quality.
*Download: [[Google|http://sites.google.com/site/liuweiguohome/cuda-mi]]
*Citation
**H. Shi, __B. Schmidt__, W. Liu, W. ~Müller-Wittig: //Parallel Mutual Information Estimation for Inferring Gene Regulatory Networks on ~GPUs//, ''BMC Research Notes'' 4:189, 2011
!CUDASW++
CUDASW++ is a bio-informatics software for ~Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla ~GPUs to perform sequence searches faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, ~GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. This algorithm is publicly available open-source software, complying with the GNU General Public License (GPL) version 3.
*Download: [[NVIDIA Tesla BioWorkbench|http://www.nvidia.com/object/swplusplus_on_tesla.html]], [[SourceForge|http://sourceforge.net/projects/cudasw/]]
*Citation:
**Y. Liu, __B. Schmidt__, D. Maskell://CUDASW++2.0: enhanced ~Smith-Waterman protein database search on ~CUDA-enabled ~GPUs based on SIMT and virtualized SIMD abstractions//, ''BMC Research Notes'' 3:93, 2010 <html> <img src="http://www.staff.uni-mainz.de/schmi033/highlyaccessed.gif" > </html>
**Y. Liu, D. Maskell, __B. Schmidt__: //CUDASW++: optimizing ~Smith-Waterman sequence database searches for ~CUDA-enabled graphics processing units//, ''BMC Research Notes'' 2:73, 2009 <html> <img src="http://www.staff.uni-mainz.de/schmi033/highlyaccessed.gif" > </html> [[Ranked 3rd in all-time most viewed articles|http://www.biomedcentral.com/bmcresnotes/mostviewedalltime/]]
**L. Ligowski, W. Rudnicki, Y. Liu, __B. Schmidt__: //Accurate scanning of sequence databases with the ~Smith-Waterman algorithm//, in ''GPU Comuting Gems'', Emerald Edition, Morgan Kaufmann, 2011
!~CUDA-BLASTP
~CUDA-BLASTP and mpiCUDA-BLASTP are available under the BSD license agreement. Both are designed to accelerate NCBI BLASTP for scanning protein sequence databases on ~GPUs, it is implemented using the CUDA and MPI programming model and has been tested on NVIDIA ~GeForce GTX 280, GTX 295, and Tesla C1060 graphics cards.
*Download: [[NVIDIA Tesla BioWorkbench|http://www.nvidia.com/object/blastp_on_tesla.html]], [[Google|https://sites.google.com/site/liuweiguohome/mpicuda-blastp]]
*Citation:
**W. Liu, __B. Schmidt__, W. ~Müller-Wittig: //~CUDA-BLASTP: Accelerating BLASTP on ~CUDA-enabled Graphics Hardware//, ''IEEE/ACM Transactions on Computational Biology and Bioinformatics'' in press, doi: 10.1109/TCBB.2011.33 (IF: 2.246)
**W. Liu, __B. Schmidt__, Y. Liu, W. ~Müller-Wittig: //Mapping of the BLASTP Algorithm onto GPU Clusters//, 17th IEEE International Conference on Parallel and Distributed Systems (''IEEE ICPADS 2011''), Tainan, Taiwan, to appear
!~CUDA-MEME
~CUDA-MEME and mCUDA-MEME are motif discovery software based on the sequential MEME algorithm for a single GPU device and a GPU Cluster using the CUDA and MPI programming models. ~CUDA-MEME supports the OOPS and ZOOPS models. This algorithm has been fully tested on a Tesla C1060 and a ~GeForce GTX 280 graphics card, and has been incorporated to NVIDIA Tesla Bio Workbench. mCUDA-MEME is an ultrafast scalable motif discovery algorithm based on MEME (version 4.4.0) algorithm for mutliple ~GPUs using a hybrid combination of CUDA, MPI and ~OpenMP parallel programming models. This algorithm is a further extension of ~CUDA-MEME with respect to accuracy and speed and has been tested on a GPU cluster with eight compute nodes and two Fermi-based Tesla S2050 (and Tesla-based Tesla S1070) quad-GPU computing systems, running the Linux OS with the ~MPICH2 library. The experimental results showed that our algorithm scales well with respect to both dataset sizes and the number of ~GPUs. ~CUDA-MEME is used in the [[CompleteMOTIFs|http://cmotifs.tchlab.org/]] developed by Harvard Medical School. ~CompleteMOTIFs is motif discovery platform developed to help biologists to find novel as well as known motifs in their peak datasets from transcription factor (TF) binding experiments such as ~ChIP-seq and ~ChIP-chip.
*Download: [[NVIDIA BioWorkbench|http://www.nvidia.com/object/meme_on_tesla.html]], [[Google|http://sites.google.com/site/yongchaosoftware/mcuda-meme]]
*Citation:
**Y. Liu, __B. Schmidt__, W. Liu, D. Maskell: //~CUDA-MEME: Accelerating Motif Discovery in Biological Sequences Using ~CUDA-enabled Graphics Processing Units//, ''Pattern Recognition Letters'' 31(14):2170 - 2177, 2010 (IF: 1.559)
**Y. Liu, __B. Schmidt__, D. Maskell: //An ultrafast scalable many-core motif discovery algorithm for multiple ~GPUs//, 10th IEEE International Workshop on High Performance Computational Biology (''~HiCOMB 2011''), Anchorage, Alaska, 2011
**L. Kuttippurathu, M Hsing, Y. Liu, __B. Schmidt__, D. Maskell, K. Lee, A. He, W.T. Pu, S.W. Kong: //~CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments//, ''Bioinformatics'' 27(5):715-717, 2011 (IF: 4.926) <html> <img src="http://www.staff.uni-mainz.de/schmi033/cmotif.gif" width="150" > </html>
!~DecGPU
~DecGPU (Distributed Error Correction on ~GPUs) is the first parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming model. Using simulated and real datasets, our algorithm demonstrates superior performance, in terms of error correction quality and execution speed, to the existing error correction algorithms. The distributed feature of our algorithm makes it feasible and flexible for the error correction of large-scale datasets. This algorithm is publicly available open-source software, complying with the GNU General Public License (GPL) version 3.
*Download: [[Google|http://sites.google.com/site/yongchaosoftware/decgpu]]
*Citation:
**Y. Liu, __B. Schmidt__, D. Maskell: //~DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI//, ''BMC Bioinformatics'' 12:85, 2011 (IF: 3.43) <html> <img src="http://www.staff.uni-mainz.de/schmi033/highlyaccessed.gif" > </html>
**H. Shi, __B. Schmidt__, W. Liu, W. ~Müller-Wittig: //A Parallel Algorithm for Error Correction in ~High-Throughput ~Short-Read Data on ~CUDA-enabled Graphics Hardware//, ''Journal of Computational Biology'' 17(4):603-615, 2010 (IF: 1.563)
!~MSAProbs
~MSAProbs is a new and practical multiple alignment algorithm for protein sequences. The design of ~MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: ~BAliBASE, PREFAB, ~SABmark and OXBENCH, ~MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ~ClustalW, MAFFT, MUSCLE, ~ProbCons and Probalign. Furthermore, ~MSAProbs is optimized for multi-core ~CPUs by employing a multi-threaded design, leading to a competitive execution time compared to other aligners. This algorithm is publicly available open-source software, complying with the GNU General Public License (GPL) version 3.
*Download: [[SourceForge|http://sourceforge.net/projects/msaprobs/]]
*Citation:
**Y. Liu, __B. Schmidt__, D. Maskell: //~MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities//, ''Bioinformatics'' 26(16):1958-1964, 2010 (IF: 4.926)
!SHREC
SHREC is a new error correction method based on a suffix tree running on standard multi-cores with Java.
*Download: [[SourceForge|http://sourceforge.net/projects/shrec-ec/]]
*Citation:
**J. Schroder, H. Schroder, S. Puglisi, R. Sinha, __B. Schmidt__: //SHREC: A short-read error correction method//, ''Bioinformatics'' 25(17):2157-2163, 2009 (IF: 4.926)
!Taipan
Taipan is a fast algorithm for single end short read assembly with Illumina reads. A recent comparison published in [[A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies|http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0017915]] has ranked [[Taipan|http://bioinformatics.oxfordjournals.org/content/25/17/2279.full]] as the ''best performing assembler'' for small genomes from single end reads of length 36 to 75.
*Download: [[SourceForge|http://sourceforge.net/projects/taipan/]]
*Citation:
**__B. Schmidt__, R. Sinha, B. ~Beresford-Smith, S. Puglisi: //A Fast Hybrid Short Read Fragment Assembly Algorithm//, ''Bioinformatics'' 25(17),2279-2280, 2009 (IF: 4.926)
!TEACHING ACTVITIES !!Lecturer and Course Coordinator !!!//Data Mining// (at JGU Mainz) #Fall 2011, Class size = TBA !!!//Technische Informatik// (at JGU Mainz) #Fall 2011, Class size = TBA !!!//Seminar: Parallel Computing with CUDA// (at JGU Mainz) #Fall 2011, Class size = TBA !!!//Discrete Mathematics// (~XMTH1040 at UNSW, ~SC109, B.Eng. in Computer Engineering at NTU) #Spring 2007, Class size = 12 #Spring 2004, Class size = 485 #Spring 2003, Class size = 551 #Spring 2002, Class size = 537 !!!//Algorithms for Bioinformatics// (~BI6106, M.Sc. in Bioinformatics) #Fall 2010, Class Size = 40 #Fall 2009, Class Size = 34 #Fall 2008, Class Size = 30 #Fall 2006, Class Size = 40 #Fall 2005, Class size = 36 #Fall 2004, Class size = 35 #Fall 2003, Class size = 57 !!!//High Performance Computing for Bioinformatics// (~BI6121, M.Sc. in Bioinformatics) #Spring 2006, Class size = 16 #Spring 2005, Class size = 12 !!!//Secure Embedded Systems// (~ES6190, M.Sc. in Embedded Systems) #Spring 2011, Class size = 36 #Spring 2010, Class size = 24 #Spring 2009, Class size = 32 !!!"Algortihms to Architectures" (~ES6126, M.Sc. in Embedded Systems) #Spring 2011, Class Size = 12 #Spring 2010, Class size = 16 !!Publications on Learning and Teaching Methods #B. Schmidt, C.K. Kwoh: //The ~MSc in Bioinformatics Program at NTU//, Asia Pacific Biotech News, 10(24) 1487-1489, 2006 !!Tutor *Digital Circuits and Systems (CPE 201): Fall 2008, Fall 2009, Fall 2010 *Logic Design (SC 102): Fall 2001, Fall 2002, Fall 2003, Fall 2004 *Mathematics I (SC 104): Fall 2004 *Discrete Mathematics (SC 109): Spring 2001, Spring 2002, Spring 2003, Spring 2004 *Algorithms (SC 203): Fall 2001, Fall 2002, Fall 2003 *Discrete Mathematics and Algorithms (CPE 204): Fall 2005 *Software Engineering (CPE 207): Spring 2005, Fall 2006 *at University of Karlsruhe: Computer Networks (Winter 1998) *at RWTH Aachen: Algorithms (Spring 1998), Introduction to Computer Science (Fall 1997) *at University of Kiel: Computer Science for Engineers (Spring 1993) !!Laboratories *Digital Circuits and Systems (CPE 201): Fall 2008, Spring 2009, Fall 2009, Spring 2010, Fall 2010 *Software Engineering (CPE 207): Spring 2005, Spring 2006, Fall 2006 *at University of Kiel: Computer Vision (Spring 1995)
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