Building an Information Infrastructure to Support Microbial Metagenomic SciencesLarry Smarr
06.01.14
Presentation for the Microbe Project Interagency Team
Title: Building an Information Infrastructure to Support Microbial Metagenomic Sciences
La Jolla, CA
Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research...Larry Smarr
06.06.27
Invited Talk
ONR Review
Scripps Institution of Oceanography, UCSD
Title: Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)—Taking Metagenomics to Light Speed
La Jolla, CA
Large scale machine learning challenges for systems biologyMaté Ongenaert
Large scale machine learning challenges for systems biology
by dr. Yvan Saeys - Machine Learning and Data Mining group, Bioinformatics and Systems Biology Division, VIB-UGent Department of Plant Systems Biology
Due to technological advances, the amount of biological data, and the pace at which it is generated has increased dramatically during the past decade. To extract new knowledge from these ever increasing data sets, automated techniques such as data mining and machine learning techniques have become standard practice.
In this talk, I will give an overview of large scale machine learning challenges in bioinformatics and systems biology, highlighting the importance of using scalable and robust techniques such as ensemble learning methods implemented on large computing grids.
I will present some of our state-of-the-art tools to solve problems such as biomarker discovery, large scale network inference, and biomedical text mining at PubMed scale.
The Emerging Global Collaboratory for Microbial Metagenomics ResearchersLarry Smarr
08.07.30
Invited Talk
Delivered From Calit2@UCSD
Monash University MURPA Lecture
Title: The Emerging Global Collaboratory for Microbial Metagenomics Researchers
Melbourne, Australia
Microbial Metagenomics Drives a New CyberinfrastructureLarry Smarr
06.03.03
Invited Talk
School of Biological Sciences
University of California, Irvine
Title: Microbial Metagenomics Drives a New Cyberinfrastructure
Irvine, CA
Building an Information Infrastructure to Support Microbial Metagenomic SciencesLarry Smarr
06.01.14
Presentation for the Microbe Project Interagency Team
Title: Building an Information Infrastructure to Support Microbial Metagenomic Sciences
La Jolla, CA
Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research...Larry Smarr
06.06.27
Invited Talk
ONR Review
Scripps Institution of Oceanography, UCSD
Title: Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)—Taking Metagenomics to Light Speed
La Jolla, CA
Large scale machine learning challenges for systems biologyMaté Ongenaert
Large scale machine learning challenges for systems biology
by dr. Yvan Saeys - Machine Learning and Data Mining group, Bioinformatics and Systems Biology Division, VIB-UGent Department of Plant Systems Biology
Due to technological advances, the amount of biological data, and the pace at which it is generated has increased dramatically during the past decade. To extract new knowledge from these ever increasing data sets, automated techniques such as data mining and machine learning techniques have become standard practice.
In this talk, I will give an overview of large scale machine learning challenges in bioinformatics and systems biology, highlighting the importance of using scalable and robust techniques such as ensemble learning methods implemented on large computing grids.
I will present some of our state-of-the-art tools to solve problems such as biomarker discovery, large scale network inference, and biomedical text mining at PubMed scale.
The Emerging Global Collaboratory for Microbial Metagenomics ResearchersLarry Smarr
08.07.30
Invited Talk
Delivered From Calit2@UCSD
Monash University MURPA Lecture
Title: The Emerging Global Collaboratory for Microbial Metagenomics Researchers
Melbourne, Australia
Microbial Metagenomics Drives a New CyberinfrastructureLarry Smarr
06.03.03
Invited Talk
School of Biological Sciences
University of California, Irvine
Title: Microbial Metagenomics Drives a New Cyberinfrastructure
Irvine, CA
10.02.19
Invited talk
Symposium #1816, Managing the Exaflood: Enhancing the Value of Networked Data for Science and Society
Title: Advancing the Metagenomics Revolution
San Diego, CA
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.15
Invited Talk
2006 Synthetic Biology Symposium
Aliso Creek Inn
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
Laguna Beach, CA
Cross-Kingdom Standards in Genomics, Epigenomics and MetagenomicsChristopher Mason
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single cells, RNA profiling, and metagenomics. Technical artifacts and contaminations can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous.
Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data.
This webinar will review work to develop standards and their applications in genomics, including the ABRF-NGS Phase II NGS Study on DNA Sequencing; the FDA’s Sequencing Quality Control Consortium (SEQC2); metagenomics standards efforts (ABRF, ATCC, Zymo, Metaquins), and the Epigenomics QC group of the SEQC2. The webinar will also review he computational methods for detection, validation, and implementation of these genomic measures.
Using Supercomputers and Supernetworks to Explore the Ocean of LifeLarry Smarr
07.06.07
Director's Colloquium
Los Alamos National Laboratory
Title: Using Supercomputers and Supernetworks to Explore the Ocean of Life
Los Alamos, NM
Presentation for teaching faculty about resources, data, issues, and strategies for including personal genomics in the classroom, within the context of precision medicine as an overarching theme.
Viral Metagenomics (CABBIO 20150629 Buenos Aires)bedutilh
This is a one-hour lecture about metagenomics, focusing on discovery of viruses and unknown sequence elements. It is part of a one-day workshop about metagenome assembly of crAssphage, a bacteriophage virus found in human gut. The hands-on workflow can be found at http://tbb.bio.uu.nl/dutilh/CABBIO/ and should be doable in one afternoon with supervision. There is also an iPython notebook about this here: https://github.com/linsalrob/CrAPy
Genomics, Cellular Networks, Preventive Medicine, and SocietyLarry Smarr
09.12.11
Invited Talk
Guest Lecture to UCSD Medical and Pharmaceutical Students
Genetics in Medicine Course
Amphitheater of the Pharmaceutical Sciences Bldg
Title: Genomics, Cellular Networks, Preventive Medicine, and Society
La Jolla, CA
The presentation includes preliminary information about the big data mainly metagenomic data and discussions related to the hurdles in analyzing using conventional approaches. In the later part, brief introduction about machine learning approaches using biological example for each. In the last, work done with special focus on implementation of a machine learning approach Random Forest for the functional annotation and taxonomic classification of metagenomic data.
Quantified Self On Being A Personal Genomic ObservatoryLarry Smarr
Larry Smarr's presentation on the "Quantified Self On Being A Personal Genomic Observatory", Keynote in the "Humans as Genomic Observatories" Meeting Session in the Genomics Standards Consortium, GSC 15, April 24, 2013
Deciphering the genome of Diaphorina citri to develop solutions for the citru...Surya Saha
The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for the citrus greening or Huanglongbing disease which threatens citrus industry worldwide. This vector is the primary target of approaches to stop the transmission of the pathogen. Accurate structural and functional annotation of the psyllid’s gene models and understanding its interactions with the pathogenic bacterium, CLas, is required for precise targeting using molecular methods such as RNAi. We opted for manual curation of gene families in the draft genome of D. citri (Diaci v1.1, contig N50 34.4Kb) that have key functional roles in D. citri biology and pathology. The community effort resulted in Official Gene Set v1.0 with more than 500 manually curated gene models across developmental, RNAi regulatory, and immune-related pathways.
Single copy marker analysis of the current genome shows a significant proportion of 3,350 markers conserved in Hemipterans to be missing (25%) with only 74% present in full-length copies. The manual genome annotation also identified a number of misassemblies and missing genes in the current genome. This is, in-part, due to the complexity introduced when assembling a heterogeneous sample containing DNA from multiple psyllids and exacerbated by the use of short reads. This challenge is common with insect genomes due to the size of individuals. To improve quality of genome assembly, we generated 36.2Gb of Pacbio long reads with a coverage of 80X for the 450Mb psyllid genome. The Canu assembler followed by Dovetail Chicago-based scaffolding was used to create an improved assembly (Diaci v2.0) with a contig N50 of 758.7kb and 1906 contigs. The assembly was polished with Pacbio and Illumina paired-end reads to remove indel and SNP errors. We are employing Dovetail Chicago and 10X Illumina libraries generated from a single psyllid in conjunction with Bionano optical maps to achieve long-range scaffolding of the genome. We have also generated full-length cDNA transcripts from diseased and healthy tissue from multiple life stages with the Pacbio IsoSeq technology. This will be the first time all these methods have been applied to resolve a complex insect genome from a highly heterogeneous sample. The new assembly will be available on https://citrusgreening.org/ which is our portal for all omics resources for the citrusgreening disease. We are continuing with the manual curation effort using the improved genome. We will also present how the improved genome and annotation is contributing to the development of molecular interdiction methods to disrupt the vectoring ability of D. citri.
10.02.19
Invited talk
Symposium #1816, Managing the Exaflood: Enhancing the Value of Networked Data for Science and Society
Title: Advancing the Metagenomics Revolution
San Diego, CA
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.15
Invited Talk
2006 Synthetic Biology Symposium
Aliso Creek Inn
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
Laguna Beach, CA
Cross-Kingdom Standards in Genomics, Epigenomics and MetagenomicsChristopher Mason
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single cells, RNA profiling, and metagenomics. Technical artifacts and contaminations can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous.
Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data.
This webinar will review work to develop standards and their applications in genomics, including the ABRF-NGS Phase II NGS Study on DNA Sequencing; the FDA’s Sequencing Quality Control Consortium (SEQC2); metagenomics standards efforts (ABRF, ATCC, Zymo, Metaquins), and the Epigenomics QC group of the SEQC2. The webinar will also review he computational methods for detection, validation, and implementation of these genomic measures.
Using Supercomputers and Supernetworks to Explore the Ocean of LifeLarry Smarr
07.06.07
Director's Colloquium
Los Alamos National Laboratory
Title: Using Supercomputers and Supernetworks to Explore the Ocean of Life
Los Alamos, NM
Presentation for teaching faculty about resources, data, issues, and strategies for including personal genomics in the classroom, within the context of precision medicine as an overarching theme.
Viral Metagenomics (CABBIO 20150629 Buenos Aires)bedutilh
This is a one-hour lecture about metagenomics, focusing on discovery of viruses and unknown sequence elements. It is part of a one-day workshop about metagenome assembly of crAssphage, a bacteriophage virus found in human gut. The hands-on workflow can be found at http://tbb.bio.uu.nl/dutilh/CABBIO/ and should be doable in one afternoon with supervision. There is also an iPython notebook about this here: https://github.com/linsalrob/CrAPy
Genomics, Cellular Networks, Preventive Medicine, and SocietyLarry Smarr
09.12.11
Invited Talk
Guest Lecture to UCSD Medical and Pharmaceutical Students
Genetics in Medicine Course
Amphitheater of the Pharmaceutical Sciences Bldg
Title: Genomics, Cellular Networks, Preventive Medicine, and Society
La Jolla, CA
The presentation includes preliminary information about the big data mainly metagenomic data and discussions related to the hurdles in analyzing using conventional approaches. In the later part, brief introduction about machine learning approaches using biological example for each. In the last, work done with special focus on implementation of a machine learning approach Random Forest for the functional annotation and taxonomic classification of metagenomic data.
Quantified Self On Being A Personal Genomic ObservatoryLarry Smarr
Larry Smarr's presentation on the "Quantified Self On Being A Personal Genomic Observatory", Keynote in the "Humans as Genomic Observatories" Meeting Session in the Genomics Standards Consortium, GSC 15, April 24, 2013
Deciphering the genome of Diaphorina citri to develop solutions for the citru...Surya Saha
The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for the citrus greening or Huanglongbing disease which threatens citrus industry worldwide. This vector is the primary target of approaches to stop the transmission of the pathogen. Accurate structural and functional annotation of the psyllid’s gene models and understanding its interactions with the pathogenic bacterium, CLas, is required for precise targeting using molecular methods such as RNAi. We opted for manual curation of gene families in the draft genome of D. citri (Diaci v1.1, contig N50 34.4Kb) that have key functional roles in D. citri biology and pathology. The community effort resulted in Official Gene Set v1.0 with more than 500 manually curated gene models across developmental, RNAi regulatory, and immune-related pathways.
Single copy marker analysis of the current genome shows a significant proportion of 3,350 markers conserved in Hemipterans to be missing (25%) with only 74% present in full-length copies. The manual genome annotation also identified a number of misassemblies and missing genes in the current genome. This is, in-part, due to the complexity introduced when assembling a heterogeneous sample containing DNA from multiple psyllids and exacerbated by the use of short reads. This challenge is common with insect genomes due to the size of individuals. To improve quality of genome assembly, we generated 36.2Gb of Pacbio long reads with a coverage of 80X for the 450Mb psyllid genome. The Canu assembler followed by Dovetail Chicago-based scaffolding was used to create an improved assembly (Diaci v2.0) with a contig N50 of 758.7kb and 1906 contigs. The assembly was polished with Pacbio and Illumina paired-end reads to remove indel and SNP errors. We are employing Dovetail Chicago and 10X Illumina libraries generated from a single psyllid in conjunction with Bionano optical maps to achieve long-range scaffolding of the genome. We have also generated full-length cDNA transcripts from diseased and healthy tissue from multiple life stages with the Pacbio IsoSeq technology. This will be the first time all these methods have been applied to resolve a complex insect genome from a highly heterogeneous sample. The new assembly will be available on https://citrusgreening.org/ which is our portal for all omics resources for the citrusgreening disease. We are continuing with the manual curation effort using the improved genome. We will also present how the improved genome and annotation is contributing to the development of molecular interdiction methods to disrupt the vectoring ability of D. citri.
The United States’ leadership position in biomedical research is no longer assured, especially as the governments of an increasing number of countries are investing more in life sciences research as a share of their GDP than the United States.
A National Network of Biomedical Research ExpertiseManinder Kahlon
Overview of status on a Clinical & Translational Science Award Consortium project co-lead by UCSF and Harvard to link biomedical experts across the country.
Slides from the presentation at IDAMO 2016, Rostock. May 2016.
Most scientific discoveries rely on previous or other findings. A lack of transparency and openness led to what many consider the "reproducibility crisis" in systems biology and systems medicine. The crisis arose from missing standards and inappropriate support of
standards in software tools. As a consequence, numerous results in low-and high-profile publications cannot be reproduced.
In my presentation, I summarise key challenges of reproducibility in systems biology and systems medicine, and I demonstrate available solutions to the related problems.
dkNET Webinar: The Collaborative Microbial Metabolite Center – Democratizing ...dkNET
Presenter: Pieter Dorrestein, PhD, Professor, Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmacology and Pediatrics, University of California San Diego
Abstract
In the analysis of organs, volatilome, or biofluids, the microbiome influences 15-70% of detectable mass spectrometry molecules. Typically, only 10% of human untargeted metabolomics data can be assigned a molecular structure, with merely 1-2% traceable to microbial origins. Human microbiomes contribute metabolites through the microbial metabolism of host-derived substances, digestion of food and beverage molecules, and de novo assembly using proteins encoded by genetic elements. Despite the significance of microbiome-derived metabolites to human health, there is no centralized knowledge base for community access. To address this, the "Collaborative Microbial Metabolite Center" (CMMC) leverages expertise in mass spectrometry, microbiome innovation, and the GNPS ecosystem to built a knowledgebase. It aims to create a user-accessible microbiome resource, enrich bioactivity knowledge, and facilitate data deposition. The CMMC includes the construction of a knowledge base, MicrobeMASST tool, and health phenotype enrichment workflows, the construction and use will be discussed in this presentation. The use of this ecosystem will be exemplified by the discovery of 20,000 bile acids, many of which were shown to be of microbial origin and linked to diet and IBD.
The top 3 key questions that this resource can answer:
1. How can we leverage the 1000’s of public metabolomics studies to discover microbial metabolites and their organ distributions as well as their phenotypic, including health, associations?
2. If one has an unknown molecule, how can one assess what microbes make a molecule without known structure?
3. How can one contribute to the expansion of the knowledgebase on microbial metabolites?
Upcoming webinars schedule: https://dknet.org/about/webinar
Global Telepresence in Support of Global Public HealthLarry Smarr
08.04.17
Briefing
University of California School of Global Health
All Campuses Planning Committee
Calit2@UCSD
Title: Global Telepresence in Support of Global Public Health
La Jolla, CA
High Performance Cyberinfrastructure to Support Data-Intensive Biomedical Res...Larry Smarr
08.06.16
Invited Talk
Association of University Research Parks BioParks 2008
"From Discovery to Innovation"
Salk Institute
Title: High Performance Cyberinfrastructure to Support Data-Intensive Biomedical Research Instruments
La Jolla, CA
Developing data services: a tale from two Oregon universitiesAmanda Whitmire
While the generation or collection of large, complex research datasets is becoming easier and less expensive all the time, researchers often lack the knowledge and skills that are necessary to properly manage them. Having these skills is paramount in ensuring data quality, integrity, discoverability, integration, reproducibility, and reuse over time. Librarians have been preserving, managing and disseminating information for thousands of years. As scholarly research is increasingly carried out digitally, and products of research have expanded from primarily text-based manuscripts to include datasets, metadata, maps, software code etc., it is a natural expansion of scope for libraries to be involved in the stewardship of these materials as well. This kind of evolution requires that libraries bring in faculty with new skills and collaborate more intimately with researchers during the research data lifecycle, and this is exactly what is happening in academic libraries across the country. In this webinar, two researchers-turned-data-specialists, both based in academic libraries, will share their experiences and perspectives on the development of research data services at their respective institutions. Each will share their perspective on the important role that libraries can play in helping researchers manage, preserve, and share their data.
Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analys...Larry Smarr
06.03.13
Invited Keynote
Annual Meeting CENIC 2006
Title: Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)
Oakland, CA
Discovery on Target 2014 - The Industry's Preeminent Event on Novel Drug TargetsJaime Hodges
Cambridge Healthtech Institute's 12th Annual Discovery on Target will showcase current and emerging “hot” targets for the pharmaceutical industry, October 8 – 10, 2014 in Boston, MA. Spanning three days, the meeting will bring together more than 900 global attendees, including scientists/technologists, executives, directors, and managers from biopharma, academic, and healthcare organizations. In 2014 the event is comprised of 14 conference tracks which include Epigenetic Readers, Ubiquitin Proteasome, Big Data Discovery, GPCR Drug Discovery, RNAi-Screens-Functional-Genomics, PPI Targets, Protein-Targets, Histone-Methyltransferases-Demethylases, Drug Transporters, Maximizing Efficiency, GPCR Therapeutics, Genomics Screening, Cancer Metabolism and Membrane Production. The 2014 event will offer 200+ scientific presentations across 14 conference tracks, 1 Symposium and 15 conference short courses, 40+ interactive breakout discussion groups, an exhibit hall of 40+ companies, and dedicated poster viewing and networking sessions.
Mapping the Human Gut Microbiome in Health and Disease Using Sequencing, Supe...Larry Smarr
Invited Talk Delivered by Mehrdad Yazdani, Calit2 Ayasdi Sponsored Lunch & Learn American Society of Human Genetics (ASHG) San Diego Convention Center October 19, 2014
Genomics in Society: Genomics, Cellular Networks, Preventive Medicine, and So...Larry Smarr
10.10.06
Guest Lecture
UCSD Medical and Pharmaceutical Students Foundations of Human Biology--Lecture #41
Title: Genomics in Society: Genomics, Cellular Networks, Preventive Medicine, and Society
La Jolla, CA
Neuro-symbolic is not enough, we need neuro-*semantic*Frank van Harmelen
Neuro-symbolic (NeSy) AI is on the rise. However, simply machine learning on just any symbolic structure is not sufficient to really harvest the gains of NeSy. These will only be gained when the symbolic structures have an actual semantics. I give an operational definition of semantics as “predictable inference”.
All of this illustrated with link prediction over knowledge graphs, but the argument is general.
The Art of the Pitch: WordPress Relationships and SalesLaura Byrne
Clients don’t know what they don’t know. What web solutions are right for them? How does WordPress come into the picture? How do you make sure you understand scope and timeline? What do you do if sometime changes?
All these questions and more will be explored as we talk about matching clients’ needs with what your agency offers without pulling teeth or pulling your hair out. Practical tips, and strategies for successful relationship building that leads to closing the deal.
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024
https://alandix.com/academic/papers/synergy2024-epistemic/
As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.
UiPath Test Automation using UiPath Test Suite series, part 4DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 4. In this session, we will cover Test Manager overview along with SAP heatmap.
The UiPath Test Manager overview with SAP heatmap webinar offers a concise yet comprehensive exploration of the role of a Test Manager within SAP environments, coupled with the utilization of heatmaps for effective testing strategies.
Participants will gain insights into the responsibilities, challenges, and best practices associated with test management in SAP projects. Additionally, the webinar delves into the significance of heatmaps as a visual aid for identifying testing priorities, areas of risk, and resource allocation within SAP landscapes. Through this session, attendees can expect to enhance their understanding of test management principles while learning practical approaches to optimize testing processes in SAP environments using heatmap visualization techniques
What will you get from this session?
1. Insights into SAP testing best practices
2. Heatmap utilization for testing
3. Optimization of testing processes
4. Demo
Topics covered:
Execution from the test manager
Orchestrator execution result
Defect reporting
SAP heatmap example with demo
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
Guy Korland, CEO and Co-founder of FalkorDB, will review two articles on the integration of language models with knowledge graphs.
1. Unifying Large Language Models and Knowledge Graphs: A Roadmap.
https://arxiv.org/abs/2306.08302
2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs:
https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/
1. Cross-Disciplinary Biomedical Research at Calit2 Briefing for Pfizer Calit2 @ UCSD La Jolla, CA April 21, 2007 Dr. Larry Smarr Director, California Institute for Telecommunications and Information Technology Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD
2. Calit2 Continues to Pursue Its Initial Mission: Envisioning How the Extension of Innovative Telecommunications and Information Technologies Throughout the Physical World will Transform Critical Applications Important to the California Economy and its Citizens’ Quality Of Life . Calit2 Review Report: p.1
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4. Calit2--A Systems Approach to the Future of the Internet and its Transformation of Our Society www.calit2.net Calit2 Has Assembled a Complex Social Network of Over 350 UC San Diego & UC Irvine Faculty From Two Dozen Departments Working in Multidisciplinary Teams With Staff, Students, Industry, and the Community Integrating Technology Consumers and Producers Into “Living Laboratories”
5. In Spite of the Bubble Bursting, Calit2 Has Partnered with over 130 Companies Industrial Partners > $1 Million $85 Million from Industrial Partners in Matching Funds Broad Range of Companies More Than 80 Have Provided Funds or In-kind
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7. Federal Agencies Have Funded $350 Million to Over 300 Calit2 Affiliated Grants Federal Agency Source of Funds Creating a Rich Ecology of Basic Research 50 Grants Over $1 Million Broad Distribution of Medium and Small Grants OptIPuter Calit2 Review Report p.4,21
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9. Calit2 Facilitated Formation of the Center for Algorithmic and Systems Biology http://casb.ucsd.edu/ CASB Brings Together Faculties from Scripps, Burnham, GNF and Five UCSD Departments
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11. Center for Algorithmic and Systems Biology@Calit2: Bringing World-Class Speakers to Conferences
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16. Nano-Structured Porous Silicon Applied to Cancer Treatment Michael J. Sailor Research Group Chemistry and Biochemistry Nanostructured “Mother Ships” for Delivery of Cancer Therapeutics Nanodevices for In-vivo Detection & Treatment of Cancerous Tumors
17. The New Science of Metagenomics “ The emerging field of metagenomics, where the DNA of entire communities of microbes is studied simultaneously, presents the greatest opportunity -- perhaps since the invention of the microscope – to revolutionize understanding of the microbial world.” – National Research Council March 27, 2007 NRC Report: Metagenomic data should be made publicly available in international archives as rapidly as possible.
20. CAMERA’s Global Microbial Metagenomics CyberCommunity—Can We Employ Social Network Software? Over 1850 Registered Users From Over 50 Countries
21. Marine Genome Sequencing Project – Measuring the Genetic Diversity of Ocean Microbes Sorcerer II Data Will Double Number of Proteins in GenBank! Specify Ocean Data Each Sample ~2000 Microbial Species
22. The Human Kinome: A Protein Family Implicated In Many Human Diseases Crystal Structures EPKs Manning, et al (2002) Science 298 :1912 Over 500 Protein Kinases 2% of the Human Genome Many splice variants Source: Susan Taylor, SOM, UCSD YEAST Mouse C.elegans Drosoph Arabid. Sea Urchin Dicty. Tetrahy.
25. CAMERA Fragment Recruitment Viewer Visualizes Overlap of GOS with Reference Microbial Genome Prochlorococcus marinus str. MIT 9312 , Complete Genome Smallest Known Phototroph--~50% Ocean’s Primary Production 112,688 Hits Shewanella baltica OS155 , complete genome Oxides Organic Material—Found in Baltic 48,725 Hits Thermotoga maritima MSB8 , complete genome Thrives at 80 o C—1/4 of Genome is Archaeal 1,472 Hits Ribosomal RNA Gene
26. Moore Foundation Funded the Venter Institute to Provide the Full Genome Sequence of 155+ Marine Microbes Phylogenetic Trees Created by Uli Stingl, Oregon State Blue Means Contains One of the Moore 155 Genomes www.moore.org/microgenome/trees.aspx Prochlorococcus Shewanella Thermotoga
27. DOE Genomic Encyclopedia of Bacteria and Archaea (GEBA) / Bergey Solution: Deep Sampling Across Phyla Source: Eddie Rubin, DOE JGI 2007 Goal: Finish ~100 Bacterial and Archaeal Genomes from Culture Collections Project Lead -- Jonathan Eisen (JGI/UC Davis) Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter Well sampled phyla No cultured taxa
32. The OptIPuter Project: Creating High Resolution Portals Over Dedicated Optical Channels to Global Science Data Picture Source: Mark Ellisman, David Lee, Jason Leigh Calit2 (UCSD, UCI) and UIC Lead Campuses—Larry Smarr PI Univ. Partners: SDSC, USC, SDSU, NW, TA&M, UvA, SARA, KISTI, AIST Industry: IBM, Sun, Telcordia, Chiaro, Calient, Glimmerglass, Lucent $13.5M Over Five Years Scalable Adaptive Graphics Environment (SAGE)
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34. Use of Tiled Display Wall OptIPortal to Interactively View Microbial Genome Acidobacteria bacterium Ellin345 Soil Bacterium 5.6 Mb
35. Use of Tiled Display Wall OptIPortal to Interactively View Microbial Genome Source: Raj Singh, UCSD
36. Use of Tiled Display Wall OptIPortal to Interactively View Microbial Genome Source: Raj Singh, UCSD
37. Interactive Exploration of Marine Genomes Using 100 Million Pixels Ginger Armburst (UW), Terry Gaasterland (UCSD SIO)
38. Calit2 Microbial Metagenomics Cluster- Next Generation Optically Linked Science Data Server 512 Processors ~5 Teraflops ~ 200 Terabytes Storage 1GbE and 10GbE Switched/ Routed Core ~200TB Sun X4500 Storage 10GbE Source: Phil Papadopoulos, SDSC, Calit2
39. OptIPlanet Collaboratory Persistent Infrastructure Supporting Microbial Research Ginger Armbrust’s Diatoms: Micrographs, Chromosomes, Genetic Assembly Photo Credit: Alan Decker UW’s Research Channel Michael Wellings Feb. 29, 2008 iHDTV: 1500 Mbits/sec Calit2 to UW Research Channel Over NLR
40. ~70 Faculty ~25+ new ~700 people Six floors 225,000 sq ft $98M Molecular Medicine Genomics & Bioinformatics Pharmacology Biomedical Engineering Enabling Genomics Facility Imaging & Vivarium Genome and Medical Biosciences Building First 10Gbps OptIPortal End Point at UC Davis Jonathan Eisen
41. OptIPortals Are Being Adopted Globally [email_address] UZurich SARA- Netherlands Brno-Czech Republic [email_address] U. Melbourne, Australia [email_address] KISTI-Korea [email_address] AIST-Japan CNIC-China NCHC-Taiwan Osaka U-Japan
42. The Calit2 200 Megapixel OptIPortals at UCSD and UCI Are Now a Gbit/s HD Collaboratory Calit2@ UCSD wall NASA Ames is Completing a 245 Mpixel Hyperwall as Project Columbia Interface NASA Ames Visit Feb. 29, 2008 Calit2@ UCI wall
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44. 4Pi Microscope Bar Harbor, Jackson Labs Jeol 4000 #2 Jeol 3200 Jeol 4000#1 Nikon Custom High Speed 2 photon Systems BIRN Rack Electron Microscopes Light Microscopes BioRad/Zeiss Radiance Olympus Co-development Systems Jeol 1.25Mev Daejon, Korea Hitachi 3Mev Osaka, Japan Jeol 200 KV Fully Corrected Oxford, U.K. Computation and Storage Resources Vizualization/Collaboration & Data Exploration Clusters CCDB Optical Networking Storage Calit2 NCMIR EVL External Imaging Instruments Internal Imaging Instruments NCMIR FACILITIES
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46. Lifechips--Merging Two Major Industries: Microelectronic Chips & Life Sciences LifeChips: the merging of two major industries, the microelectronic chip industry with the life science industry LifeChips medical devices 65 UCI Faculty