Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)—Taking Metagenomics to Light Speed

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The document discusses the creation of the Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) project. CAMERA aims to provide metagenomic sequencing and analysis of marine microbes at high speeds. It will include data from the Sorcerer II expedition and other projects. The document outlines how CAMERA will utilize Calit2's infrastructure including high-performance computing resources and optical networks to enable remote interactive analysis of large-scale genomic and environmental data sets.

Technology Education

Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)—Taking Metagenomics to Light Speed Invited Talk ONR Review Scripps Institution of Oceanography, UCSD June 27, 2006 Dr. Larry Smarr Director, California Institute for Telecommunications and Information Technologies Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD

Two New Calit2 Buildings Provide New Laboratories for “Living in the Future” ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],UC Irvine www.calit2.net Preparing for a World in Which Distance is Eliminated… UC San Diego

The OptIPuter Project – Creating High Resolution Portals Over Dedicated Optical Channels to Global Science Data ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],NIH Biomedical Informatics NSF EarthScope and ORION Research Network

OptIPuter Scalable Adaptive Graphics Environment (SAGE) Allows Integration of HD Streams Photo: David Lee, NCMIR, UCSD OptIPortal– Termination Device for the OptIPuter Global Backplane

The Sargasso Sea Experiment The Power of Environmental Metagenomics ,[object Object],[object Object],[object Object],[object Object],MODIS-Aqua satellite image of ocean chlorophyll in the Sargasso Sea grid about the BATS site from 22 February 2003 J. Craig Venter, et al. Science 2 April 2004: Vol. 304. pp. 66 - 74

Evolution is the Principle of Biological Systems: Most of Evolutionary Time Was in the Microbial World Source: Carl Woese, et al You Are Here Much of Genome Work Has Occurred in Animals

Marine Genome Sequencing Project Measuring the Genetic Diversity of Ocean Microbes CAMERA will include All Sorcerer II Metagenomic Data

Using the OptIPuter to Couple Data Assimilation Models to Remote Data Sources Including Biology Regional Ocean Modeling System (ROMS) http://ourocean.jpl.nasa.gov/ NASA MODIS Mean Primary Productivity for April 2001 in California Current System

Calit2’s Direct Access Core Architecture Will Create Next Generation Metagenomics Server Traditional User Response Request Source: Phil Papadopoulos, SDSC, Calit2 + Web Services ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Flat File Server Farm W E B PORTAL Dedicated Compute Farm (100s of CPUs) TeraGrid: Cyberinfrastructure Backplane (scheduled activities, e.g. all by all comparison) (10000s of CPUs) Web (other service) Local Cluster Local Environment Direct Access Lambda Cnxns Data- Base Farm 10 GigE Fabric

The Future Home of the Moore Foundation Funded Marine Microbial Ecology Metagenomics Complex First Implementation of the CAMERA Complex Photo Courtesy Joe Keefe, Calit2 Major Buildout of Calit2 Server Room Underway

The Bioinformatics Core of the Joint Center for Structural Genomics will be Housed in the Calit2@UCSD Building Extremely Thermostable -- Useful for Many Industrial Processes (e.g. Chemical and Food) 173 Structures (122 from JCSG) ,[object Object],[object Object],[object Object],[object Object],Source: John Wooley, UCSD

Interactive Visualization of Thermatoga Proteins at Calit2 Source: John Wooley, Jurgen Schulze, Calit2

Calit2 and the Venter Institute Will Combine Telepresence with Remote Interactive Analysis Live Demonstration of 21st Century National-Scale Team Science OptIPuter Visualized Data HDTV Over Lambda 25 Miles Venter Institute

Countries are Aggressively Creating Gigabit Services: Interactive Access to CAMERA Data System www.glif.is Created in Reykjavik, Iceland 2003 Visualization courtesy of Bob Patterson, NCSA.

After billions of years of evolution, prokaryotes have developed a huge diversity of regulatory mechanisms, many of which are probably uncharacterized. Now that the powerful tool of whole-transcriptome analysis can be used to study the RNA of bacteria and archaea, a new set of un expected RNA-based regulatory strategies might be revealed. Metagenomics, together with in vitro evolution and high-throughput screening technologies, provides industry with an unprecedented chance to bring biomolecules into industrial application.

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GigaScience, BGI Hong Kong

This document discusses challenges in comparing metagenomic data from different environments and studies. It argues that when exploring a new environment, multiple methodological approaches should be used to capture natural and methodological variations. When performing global comparisons, methodological variations should be considered for all environments. Defining ecosystems precisely at the microorganism level is important. The author's vision is for projects like the Earth Microbiome Project to use flexible experimental designs informed by different experts to best represent microbial communities.

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

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High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. Forty-five patient samples of known and unknown disease etiology and 20 samples from health individuals were subjected to next-generation sequencing. Subsequent metagenomic analysis identified all microorganisms (bacteria, viruses, fungi and parasites) in the samples, including the expected pathogens in the samples of known etiology. Multiple pathogens were detected in the individual samples, providing evidence for polymicrobial infection. Patients were clearly differentiated from healthy individuals based on microorganism abundance and diversity. The speed, accuracy and actionable features of CosmosID bioinformatics and curated GenBook® databases, implemented in the QIAGEN Microbial Genomics Pro Suite, and the functional analysis, leveraging the QIAGEN functional metagenomics workflow, provide a powerful tool contributing to the revolution in clinical diagnostics, prophylactics and therapeutics that is now in progress globally.

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Metagenomics is the study of microbial communities directly in their natural environments without isolating individual species in the lab. It involves sequencing DNA from environmental samples and analyzing the metagenomes. Some key points are that metagenomics can identify uncultivable microbes, bypassing the need for culture, and it has led to advances in understanding microbial ecology, evolution, and diversity. The rumen, home to a complex microbial community important for ruminant digestion, is a important target of metagenomics study. Next generation sequencing techniques now allow more accessible exploration of microbial systems through metagenomics.

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Machine Learning

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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.

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VHIR Seminar led by Joel Doré. Research Director. Institut National de la Recherche Agronomique (INRA). Jouy-en-Josas, France. Abstract: The human intestinal tract harbours a complex microbial ecosystem which plays a key role in nutrition and health. Interactions between food constituents, microbes and the host organism derive from a long co-evolution that resulted in a mutualistic association. Current investigations into the human faecal metagenome are delivering an extensive gene repertoire representative of functional potentials of the human intestinal microbiota. The most redundant genomic traits of the human intestinal microbiota are identified and thereby its functional balance. These observation point towards the existence of enterotypes, i.e. microbiota sharing specific traits but yet independent of geographic origin, age, sex etc.. It also shows a unique segregation of the human population into individuals with low versus high gene-counts. In the end, it not only gives an unprecedented view of the intestinal microbiota, but it also significantly expands our ability to look for specificities of the microbiota associated with human diseases and to ultimately validate microbial signatures of prognostic and diagnostic value in immune mediated diseases. Metagenomics of the human intestinal tract was applied to specifically compare obese versus lean individuals as well as to explore the dynamic changes associated with a severe calory-restricted diet. Microbiota structure differs with body-mass index and a limited set of marker species may be used as diagnostic model with a >85% predictive value. Among obese subjects; the overall phenotypic characteristics are worse in individuals with low gene counts microbiota, including a worse evolution of morphometric parameters over a period of 10 years, a low grade inflammatory context also associated with insulin-resistance, and the worst response to dietary constraints in terms of weight loss or improvement of biological and inflammatory characteristics. Low gene count microbiota is also associated with less favourable conditions in inflammatory bowel disease, such as higher relapse rate in ulcerative colitis patients. Finally, microbiota transplantation has seen a regain of interest with applications expanding from Clostridium difficile infections to immune mediated and metabolic diseases. The human intestinal microbiota should hence be regarded as a true organ, amenable to rationally designed modulation for human health.

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CENIC is a non-profit organization that operates an 8,000+ mile fiber optic network connecting over 12,000 sites across California, including K-12 schools, universities, libraries, and research organizations. It has over 750 private sector partners and contributes over $100 million annually to the California economy. CENIC's network enables research and education collaborations, innovation, and economic growth statewide. It also operates a wireless research network called PRP that connects wireless sensors to supercomputers, supporting applications like wildfire modeling.

Global Research Platform Workshops - Maxine Brown

Larry Smarr

The document announces a workshop on global research platforms that will be held virtually in 2021 and in Salt Lake City in 2022, with topics including large-scale science, next-generation platforms, data transport, and international testbeds. It also announces the 4th Global Research Platform Workshop to be held in October 2023 in Limassol, Cyprus co-located with the IEEE eScience 2023 conference.

Built around answering questions

Larry Smarr

EPOC and NetSage provide engagement and network monitoring services to support research and education. NetSage collects anonymized network flow data to help understand traffic patterns and troubleshoot performance issues. It provides dashboards and analysis to answer common questions from network engineers and end users. Examples of NetSage deployments and use cases were shown for the CENIC network, including top sources and destinations of traffic, debugging slow flows, and analyzing international traffic patterns by country over time.

Panel: NRP Science Impacts

Larry Smarr

The document discusses accelerating science discovery with AI inference-as-a-service. It describes showcases using this approach for high energy physics and gravitational wave experiments. It outlines the vision of the A3D3 institute to unite domain scientists, computer scientists, and engineers to achieve real-time AI and transform science. Examples are provided of using AI inference-as-a-service to accelerate workflows for CMS, ProtoDUNE, LIGO, and other experiments.

Democratizing Science through Cyberinfrastructure - Manish Parashar

Larry Smarr

This document summarizes a presentation by Manish Parashar on democratizing science through cyberinfrastructure. The key points are: 1) Broad, fair, and equitable access to advanced cyberinfrastructure is essential for democratizing 21st century science, but there are significant barriers related to knowledge, technical issues, social factors, and balancing capabilities. 2) An advanced cyberinfrastructure ecosystem for all requires integrated portals, access to local and national resources through high-speed networks, diverse allocation modes, embedded expertise networks, and broad training. 3) Realizing this vision will require a scalable federated ecosystem with diverse capabilities and incentives for partnerships to meet growing needs for cyberinfrastructure and

Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;

Larry Smarr

This document summarizes a panel discussion on building the National Research Platform ecosystem with regional networks. The panelists discussed how their regional networks are connecting to and using the Nautilus nodes of the NRP. Examples included using NRP for deep learning and computer vision research at the University of Missouri, challenges of adoption in Nevada and potential solutions, and Georgia Tech's new involvement through the Southern Crossroads regional network. The regional networks see opportunities to expand NRP access and training to enable more researchers in their regions to take advantage of the platform.

Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...

Larry Smarr

The document discusses Open Force Field (OpenFF), an open-source project that enables rapid development of molecular force fields through automated infrastructure, open data and software, and an open science approach. OpenFF provides access to large quantum chemical datasets, runs quantum chemistry calculations on pre-emptible cloud resources with minimal human intervention, and facilitates easy iteration and testing of new force field hypotheses through an open development model.

Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...

Larry Smarr

The document discusses open infrastructure for an open society and the role of commercial clouds. It describes how the National Research Platform (NRP), Open Science Grid (OSG), and Open Science Data Federation (OSDF) provide open infrastructure through open source components that anyone can contribute to and use. It then discusses how Southwestern Oklahoma State University leveraged NRP resources on their campus and engaged students and local teachers. Finally, it outlines the pros and cons of commercial clouds, when they may be suitable to use, and how tools like CloudBank and Kubernetes can help facilitate science users' access to cloud resources.

Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...

Larry Smarr

The document discusses open infrastructure for an open society and the role of commercial clouds. It describes how the National Research Platform (NRP), Open Science Grid (OSG), and Open Science Data Federation (OSDF) provide open infrastructure through open source components that anyone can contribute to and use. It then discusses how Southwestern Oklahoma State University leveraged NRP resources on their campus and engaged students and local teachers. Finally, it outlines the pros and cons of commercial clouds, noting they provide huge capacity and variety but are very expensive for regular use. Facilitating science users on clouds requires services like CloudBank and Kubernetes federation.

Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...

Larry Smarr

The document discusses open infrastructure for an open society and the role of commercial clouds. It describes how the National Research Platform (NRP), Open Science Grid (OSG), and Open Science Data Federation (OSDF) provide open infrastructure through open source components that anyone can contribute to and use. It then discusses how Southwestern Oklahoma State University leveraged NRP resources on their campus and engaged students and local teachers. Finally, it outlines the pros and cons of commercial clouds, noting they provide huge capacity and variety but are very expensive for regular use. Facilitating science users on clouds requires tools for account management, documentation, and integrating cloud resources through HTCondor and Kubernetes.

Frank Würthwein - NRP and the Path forward

Larry Smarr

NRP will replace PRP and aims to democratize access to national research cyberinfrastructure. The long term vision is to create an open national cyberinfrastructure by federating resources across research institutions. Key innovations include an innovative network fabric, application libraries for FPGAs, a "bring your own resource" model, and innovative scheduling and data infrastructure. The NSF has funded the Prototype National Research Platform project to support NRP for the next 5 years. NRP aims to grow resources, introduce new capabilities, and be driven by the research community.

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An English 🇬🇧 translation of a presentation to the speech I gave about the main changes brought by CCS TSI 2023 at the biggest Czech conference on Communications and signalling systems on Railways, which was held in Clarion Hotel Olomouc from 7th to 9th November 2023 (konferenceszt.cz). Attended by around 500 participants and 200 on-line followers. The original Czech 🇨🇿 version of the presentation can be found here: https://www.slideshare.net/slideshow/hlavni-novinky-souvisejici-s-ccs-tsi-2023-2023-1695/269688092 . The videorecording (in Czech) from the presentation is available here: https://youtu.be/WzjJWm4IyPk?si=SImb06tuXGb30BEH .

Skybuffer SAM4U tool for SAP license adoption

Tatiana Kojar

Manage and optimize your license adoption and consumption with SAM4U, an SAP free customer software asset management tool. SAM4U, an SAP complimentary software asset management tool for customers, delivers a detailed and well-structured overview of license inventory and usage with a user-friendly interface. We offer a hosted, cost-effective, and performance-optimized SAM4U setup in the Skybuffer Cloud environment. You retain ownership of the system and data, while we manage the ABAP 7.58 infrastructure, ensuring fixed Total Cost of Ownership (TCO) and exceptional services through the SAP Fiori interface.

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Are you new to data warehouses (DWH)? Do you need to check whether your data warehouse follows the best practices for a good design? In both cases, this webinar is for you. A data warehouse is a central relational database that contains all measurements about a business or an organisation. This data comes from a variety of heterogeneous data sources, which includes databases of any type that back the applications used by the company, data files exported by some applications, or APIs provided by internal or external services. But designing a data warehouse correctly is a hard task, which requires gathering information about the business processes that need to be analysed in the first place. These processes must be translated into so-called star schemas, which means, denormalised databases where each table represents a dimension or facts. We will discuss these topics: - How to gather information about a business; - Understanding dictionaries and how to identify business entities; - Dimensions and facts; - Setting a table granularity; - Types of facts; - Types of dimensions; - Snowflakes and how to avoid them; - Expanding existing dimensions and facts.

HCL Notes und Domino Lizenzkostenreduzierung in der Welt von DLAU

panagenda

Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-und-domino-lizenzkostenreduzierung-in-der-welt-von-dlau/ DLAU und die Lizenzen nach dem CCB- und CCX-Modell sind für viele in der HCL-Community seit letztem Jahr ein heißes Thema. Als Notes- oder Domino-Kunde haben Sie vielleicht mit unerwartet hohen Benutzerzahlen und Lizenzgebühren zu kämpfen. Sie fragen sich vielleicht, wie diese neue Art der Lizenzierung funktioniert und welchen Nutzen sie Ihnen bringt. Vor allem wollen Sie sicherlich Ihr Budget einhalten und Kosten sparen, wo immer möglich. Das verstehen wir und wir möchten Ihnen dabei helfen! Wir erklären Ihnen, wie Sie häufige Konfigurationsprobleme lösen können, die dazu führen können, dass mehr Benutzer gezählt werden als nötig, und wie Sie überflüssige oder ungenutzte Konten identifizieren und entfernen können, um Geld zu sparen. Es gibt auch einige Ansätze, die zu unnötigen Ausgaben führen können, z. B. wenn ein Personendokument anstelle eines Mail-Ins für geteilte Mailboxen verwendet wird. Wir zeigen Ihnen solche Fälle und deren Lösungen. Und natürlich erklären wir Ihnen das neue Lizenzmodell. Nehmen Sie an diesem Webinar teil, bei dem HCL-Ambassador Marc Thomas und Gastredner Franz Walder Ihnen diese neue Welt näherbringen. Es vermittelt Ihnen die Tools und das Know-how, um den Überblick zu bewahren. Sie werden in der Lage sein, Ihre Kosten durch eine optimierte Domino-Konfiguration zu reduzieren und auch in Zukunft gering zu halten. Diese Themen werden behandelt - Reduzierung der Lizenzkosten durch Auffinden und Beheben von Fehlkonfigurationen und überflüssigen Konten - Wie funktionieren CCB- und CCX-Lizenzen wirklich? - Verstehen des DLAU-Tools und wie man es am besten nutzt - Tipps für häufige Problembereiche, wie z. B. Team-Postfächer, Funktions-/Testbenutzer usw. - Praxisbeispiele und Best Practices zum sofortigen Umsetzen

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June Patch Tuesday

Ivanti

Ivanti’s Patch Tuesday breakdown goes beyond patching your applications and brings you the intelligence and guidance needed to prioritize where to focus your attention first. Catch early analysis on our Ivanti blog, then join industry expert Chris Goettl for the Patch Tuesday Webinar Event. There we’ll do a deep dive into each of the bulletins and give guidance on the risks associated with the newly-identified vulnerabilities.

“Building and Scaling AI Applications with the Nx AI Manager,” a Presentation...

Edge AI and Vision Alliance

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Tosin Akinosho

Monitoring and Managing Anomaly Detection on OpenShift Overview Dive into the world of anomaly detection on edge devices with our comprehensive hands-on tutorial. This SlideShare presentation will guide you through the entire process, from data collection and model training to edge deployment and real-time monitoring. Perfect for those looking to implement robust anomaly detection systems on resource-constrained IoT/edge devices. Key Topics Covered 1. Introduction to Anomaly Detection - Understand the fundamentals of anomaly detection and its importance in identifying unusual behavior or failures in systems. 2. Understanding Edge (IoT) - Learn about edge computing and IoT, and how they enable real-time data processing and decision-making at the source. 3. What is ArgoCD? - Discover ArgoCD, a declarative, GitOps continuous delivery tool for Kubernetes, and its role in deploying applications on edge devices. 4. Deployment Using ArgoCD for Edge Devices - Step-by-step guide on deploying anomaly detection models on edge devices using ArgoCD. 5. Introduction to Apache Kafka and S3 - Explore Apache Kafka for real-time data streaming and Amazon S3 for scalable storage solutions. 6. Viewing Kafka Messages in the Data Lake - Learn how to view and analyze Kafka messages stored in a data lake for better insights. 7. What is Prometheus? - Get to know Prometheus, an open-source monitoring and alerting toolkit, and its application in monitoring edge devices. 8. Monitoring Application Metrics with Prometheus - Detailed instructions on setting up Prometheus to monitor the performance and health of your anomaly detection system. 9. What is Camel K? - Introduction to Camel K, a lightweight integration framework built on Apache Camel, designed for Kubernetes. 10. Configuring Camel K Integrations for Data Pipelines - Learn how to configure Camel K for seamless data pipeline integrations in your anomaly detection workflow. 11. What is a Jupyter Notebook? - Overview of Jupyter Notebooks, an open-source web application for creating and sharing documents with live code, equations, visualizations, and narrative text. 12. Jupyter Notebooks with Code Examples - Hands-on examples and code snippets in Jupyter Notebooks to help you implement and test anomaly detection models.

Cosa hanno in comune un mattoncino Lego e la backdoor XZ?

Speck&Tech

ABSTRACT: A prima vista, un mattoncino Lego e la backdoor XZ potrebbero avere in comune il fatto di essere entrambi blocchi di costruzione, o dipendenze di progetti creativi e software. La realtà è che un mattoncino Lego e il caso della backdoor XZ hanno molto di più di tutto ciò in comune. Partecipate alla presentazione per immergervi in una storia di interoperabilità, standard e formati aperti, per poi discutere del ruolo importante che i contributori hanno in una comunità open source sostenibile. BIO: Sostenitrice del software libero e dei formati standard e aperti. È stata un membro attivo dei progetti Fedora e openSUSE e ha co-fondato l'Associazione LibreItalia dove è stata coinvolta in diversi eventi, migrazioni e formazione relativi a LibreOffice. In precedenza ha lavorato a migrazioni e corsi di formazione su LibreOffice per diverse amministrazioni pubbliche e privati. Da gennaio 2020 lavora in SUSE come Software Release Engineer per Uyuni e SUSE Manager e quando non segue la sua passione per i computer e per Geeko coltiva la sua curiosità per l'astronomia (da cui deriva il suo nickname deneb_alpha).

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1. Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)—Taking Metagenomics to Light Speed Invited Talk ONR Review Scripps Institution of Oceanography, UCSD June 27, 2006 Dr. Larry Smarr Director, California Institute for Telecommunications and Information Technologies Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD

4. OptIPuter Scalable Adaptive Graphics Environment (SAGE) Allows Integration of HD Streams Photo: David Lee, NCMIR, UCSD OptIPortal– Termination Device for the OptIPuter Global Backplane

5. PI Larry Smarr

7. Evolution is the Principle of Biological Systems: Most of Evolutionary Time Was in the Microbial World Source: Carl Woese, et al You Are Here Much of Genome Work Has Occurred in Animals

8. Marine Genome Sequencing Project Measuring the Genetic Diversity of Ocean Microbes CAMERA will include All Sorcerer II Metagenomic Data

9. Using the OptIPuter to Couple Data Assimilation Models to Remote Data Sources Including Biology Regional Ocean Modeling System (ROMS) http://ourocean.jpl.nasa.gov/ NASA MODIS Mean Primary Productivity for April 2001 in California Current System

10. Announced January 17, 2006

11.

12. The Future Home of the Moore Foundation Funded Marine Microbial Ecology Metagenomics Complex First Implementation of the CAMERA Complex Photo Courtesy Joe Keefe, Calit2 Major Buildout of Calit2 Server Room Underway

13.

14. Interactive Visualization of Thermatoga Proteins at Calit2 Source: John Wooley, Jurgen Schulze, Calit2

15. Calit2 and the Venter Institute Will Combine Telepresence with Remote Interactive Analysis Live Demonstration of 21st Century National-Scale Team Science OptIPuter Visualized Data HDTV Over Lambda 25 Miles Venter Institute

16. Countries are Aggressively Creating Gigabit Services: Interactive Access to CAMERA Data System www.glif.is Created in Reykjavik, Iceland 2003 Visualization courtesy of Bob Patterson, NCSA.

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