Unique Capabilities
Sponsors – Biometrics projects at CUBS
Technology Transfer Record
Current Leveraged Projects
People – Faculty, Staff, Students
Biometrics Community Leadership
Data science remains a high-touch activity, especially in life, physical, and social sciences. Data management and manipulation tasks consume too much bandwidth: Specialized tools and technologies are difficult to use together, issues of scale persist despite the Cambrian explosion of big data systems, and public data sources (including the scientific literature itself) suffer curation and quality problems.
Together, these problems motivate a research agenda around “human-data interaction:” understanding and optimizing how people use and share quantitative information.
I’ll describe some of our ongoing work in this area at the University of Washington eScience Institute.
In the context of the Myria project, we're building a big data "polystore" system that can hide the idiosyncrasies of specialized systems behind a common interface without sacrificing performance. In scientific data curation, we are automatically correcting metadata errors in public data repositories with cooperative machine learning approaches. In the Viziometrics project, we are mining patterns of visual information in the scientific literature using machine vision, machine learning, and graph analytics. In the VizDeck and Voyager projects, we are developing automatic visualization recommendation techniques. In graph analytics, we are working on parallelizing best-of-breed graph clustering algorithms to handle multi-billion-edge graphs.
The common thread in these projects is the goal of democratizing data science techniques, especially in the sciences.
Data science remains a high-touch activity, especially in life, physical, and social sciences. Data management and manipulation tasks consume too much bandwidth: Specialized tools and technologies are difficult to use together, issues of scale persist despite the Cambrian explosion of big data systems, and public data sources (including the scientific literature itself) suffer curation and quality problems.
Together, these problems motivate a research agenda around “human-data interaction:” understanding and optimizing how people use and share quantitative information.
I’ll describe some of our ongoing work in this area at the University of Washington eScience Institute.
In the context of the Myria project, we're building a big data "polystore" system that can hide the idiosyncrasies of specialized systems behind a common interface without sacrificing performance. In scientific data curation, we are automatically correcting metadata errors in public data repositories with cooperative machine learning approaches. In the Viziometrics project, we are mining patterns of visual information in the scientific literature using machine vision, machine learning, and graph analytics. In the VizDeck and Voyager projects, we are developing automatic visualization recommendation techniques. In graph analytics, we are working on parallelizing best-of-breed graph clustering algorithms to handle multi-billion-edge graphs.
The common thread in these projects is the goal of democratizing data science techniques, especially in the sciences.
Web Apollo: Lessons learned from community-based biocuration efforts.Monica Munoz-Torres
This presentation tries to highlight the importance and relevance of community-based curation of biological data. It describes the results of harvesting expertise from dispersed researchers assigning functions to predicted and curated peptides, as well as collaborative efforts for standardization of genes and gene product attributes across species and databases.
Join us in Boston this coming Fall to attend Cambridge Healthtech Institute's (CHI) 2nd Annual FAST: Functional Analysis & Screening Technologies Congress on November 17-19, 2014 and meet with a community of 250+ biologists, screening managers, assay developers, engineers and pharmacologists dedicated to improving in vitro cell models and phenotypic screening to advance drug discovery and development at 6 conferences: Phenotypic Drug Discovery (Part I & II), Engineering Functional 3D Models, Screening and Functional Analysis of 3D Models, Organotypic Culture Models for Toxicology and Physiologically-Relevant Cellular Tumor Models for Drug Discovery. Delegates have the opportunity to share insights in interactive panel discussions and connect during networking breaks. View innovative technologies and scientific research revolutionizing early-stage drug discovery in the exhibit/poster hall.
VIVO: enabling the discovery of research and scholarshipPaul Albert
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Precise elucidation of the many different biological features encoded in any genome requires careful examination and review by researchers, who gather and evaluate the available evidence to corroborate and modify gene predictions and other biological elements. This curation process allows them to resolve discrepancies and validate automated gene model hypotheses and alignments. This approach is the well-established practice for well-known genomes such as human, mouse, zebrafish, Drosophila, et cetera. Desktop Apollo was originally developed to meet these needs.
The cost of sequencing a genome has been dramatically reduced by several orders of magnitude in the last decade, and the natural consequence is that more and more researchers are sequencing more and more new genomes, both within populations and across species. Because individual researchers can now readily sequence many genomes of interest, the need for a universally accessible genomic curation tool logically follows. Each new exome or genome sequenced requires visualization and curation to obtain biologically accurate genomic features sets, even for limited set of genes, because computational genome analysis remains an imperfect art. Additionally, unlike earlier genome projects, which had the advantage of more highly polished genomes, recent projects usually have lower coverage. Therefore researchers now face additional work correcting for more frequent assembly errors and annotating genes split across multiple contigs.
Genome annotation is an inherently collaborative task; researchers only very rarely work in isolation, turning to colleagues for second opinions and insights from those with with expertise in particular domains and gene families. The new JavaScript based Apollo, allows researchers real-time interactivity, breaking down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. We are also focused on training the next generation of researchers by reaching out to educators to make these tools available as part of curricula via workshops and webinars, and through widely applied systems such as iPlant and DNA Subway. Here we offer details of our progress.
Presentation at Genome Informatics, Session (3) on Databases, Data Mining, Visualization, Ontologies and Curation.
Authors: Monica C Munoz-Torres, Suzanna E. Lewis, Ian Holmes, Colin Diesh, Deepak Unni, Christine Elsik.
Mapping Genotype to Phenotype using Attribute Grammar, Laura Adammadalladam
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Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
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2006 Synthetic Biology Symposium
Aliso Creek Inn
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
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Introduction to Web Apollo for the i5K Pilot species project. WebApollo is genome annotation editor; it provides a web-based environment that allows multiple distributed users to review, edit, and share manual annotations. Let's get started!
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This presentation tries to highlight the importance and relevance of community-based curation of biological data. It describes the results of harvesting expertise from dispersed researchers assigning functions to predicted and curated peptides, as well as collaborative efforts for standardization of genes and gene product attributes across species and databases.
Join us in Boston this coming Fall to attend Cambridge Healthtech Institute's (CHI) 2nd Annual FAST: Functional Analysis & Screening Technologies Congress on November 17-19, 2014 and meet with a community of 250+ biologists, screening managers, assay developers, engineers and pharmacologists dedicated to improving in vitro cell models and phenotypic screening to advance drug discovery and development at 6 conferences: Phenotypic Drug Discovery (Part I & II), Engineering Functional 3D Models, Screening and Functional Analysis of 3D Models, Organotypic Culture Models for Toxicology and Physiologically-Relevant Cellular Tumor Models for Drug Discovery. Delegates have the opportunity to share insights in interactive panel discussions and connect during networking breaks. View innovative technologies and scientific research revolutionizing early-stage drug discovery in the exhibit/poster hall.
VIVO: enabling the discovery of research and scholarshipPaul Albert
An introduction to VIVO, an open source, semantic web application that enables discovery of research and scholarship across institutions and one library's role in its implementation and development.
Precise elucidation of the many different biological features encoded in any genome requires careful examination and review by researchers, who gather and evaluate the available evidence to corroborate and modify gene predictions and other biological elements. This curation process allows them to resolve discrepancies and validate automated gene model hypotheses and alignments. This approach is the well-established practice for well-known genomes such as human, mouse, zebrafish, Drosophila, et cetera. Desktop Apollo was originally developed to meet these needs.
The cost of sequencing a genome has been dramatically reduced by several orders of magnitude in the last decade, and the natural consequence is that more and more researchers are sequencing more and more new genomes, both within populations and across species. Because individual researchers can now readily sequence many genomes of interest, the need for a universally accessible genomic curation tool logically follows. Each new exome or genome sequenced requires visualization and curation to obtain biologically accurate genomic features sets, even for limited set of genes, because computational genome analysis remains an imperfect art. Additionally, unlike earlier genome projects, which had the advantage of more highly polished genomes, recent projects usually have lower coverage. Therefore researchers now face additional work correcting for more frequent assembly errors and annotating genes split across multiple contigs.
Genome annotation is an inherently collaborative task; researchers only very rarely work in isolation, turning to colleagues for second opinions and insights from those with with expertise in particular domains and gene families. The new JavaScript based Apollo, allows researchers real-time interactivity, breaking down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. We are also focused on training the next generation of researchers by reaching out to educators to make these tools available as part of curricula via workshops and webinars, and through widely applied systems such as iPlant and DNA Subway. Here we offer details of our progress.
Presentation at Genome Informatics, Session (3) on Databases, Data Mining, Visualization, Ontologies and Curation.
Authors: Monica C Munoz-Torres, Suzanna E. Lewis, Ian Holmes, Colin Diesh, Deepak Unni, Christine Elsik.
Mapping Genotype to Phenotype using Attribute Grammar, Laura Adammadalladam
Defense -- thesis: “Mapping Genotype to Phenotype using Attribute Grammar.”
PhD degree in Genetics, Bioinformatics and Computational Biology (GBCB) in the tracks of Computer Science, Mathematics and Life Sciences.
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2. Overview Unique Capabilities Sponsors – Biometrics projects at CUBS Technology Transfer Record Current Leveraged Projects People – Faculty, Staff, Students Biometrics Community Leadership
3. Unique Capabilities Faculty strengths in multiple disciplines Behavioral Sciences, Social Issues Computer Vision, Visualization Chemical and Biological Sensors Pattern Recognition, Machine Learning Smart Environments, Pervasive Computing Spectroscopy Solid record of transferring of technology to field Large pool of current PhD students Growing pool of PhD alumni in industry Several current projects with industry
18. Unobtrusive People Tracking Freedom from Continuous Surveillance RECOGNIZE REASON Evolutionary Recognition RETRIEVE Did Bob and Frank meet at the library yesterday? Given building map, occupants, schedules, sensor locations
21. Soft BiometricsExpressions + = AU 6 AU 12 AU 6 & 12 + + = AU 1 AU 2 AU 4 AU 1, 2 & 4 + + = AU 1 AU 4 AU 15 AU 1, 4 & 15 FACS FEAR HAPPY ANGER SAD FEAR HAPPY SAD Facial Expression Manifold
23. Q: The suspect is male 1st Iteration Pruned Set Q: The suspect has a beard 2nd Iteration Pruned Set Q: The suspect wears spectacles 3rd Iteration SUSPECT Soft BiometricsSemantic Face Retrieval Original Set
26. PeopleFaculty Frank Bright SUNY Distinguished Professor Biological, Chemical Sensors VenuGovindaraju SUNY Distinguished Professor Machine Learning Director Mark Frank Professor Behavioral Sciences Raymond Fu Assistant Professor Computer Vision, Visualization Alex Cartwright Professor Spectroscopy, Photonics AtriRudra Assistant Professor Cryptography, Coding theory
27.
28. PeopleCurrent PhD students; Research topics Xi Cheng Biometric Fusion Gaurav Kumar Mobile Device Apps UtkarshPoruwal People Tracking ChetanRamaiah Writer Identification Manavender Reddy Gesture Recognition Ricardo N. Rodriguez Multimodal Fusion ArtiShivaram Mobile Device Apps SafwanWshah Arabic Handwriting Recognition Daekeun You Medical Analytics Yingbou Zhou Image Segmentation
30. Leadershipin Biometrics Community Program ChairCVPR Biometrics Workshop Series 2006-2011Program Co-ChairBiometrics: Theory, Applications, and Systems, BTAS 2007-2008General ChairAutomatic Identification Advanced Technologies AutoID 05Program CommitteeBTAS 2008-10, Biometric Symposium 2006-08, International Conference on Biometrics, 2007, SPIE Biometric Technology for Human Identification2009-10, International Joint Conference on Biometrics, 2011 IEEE Biometric Council Website Initiative 2011 Website Design, Construction, Hosting, and Maintenance
31. Contact VenuGovindaraju venu@cubs.buffalo.edu University at Buffalo State University of New York