Rick Stevens presented information about the Earth Microbiome Project (EMP), which aims to systematically characterize microbial life on Earth through a combination of extremely deep metagenomic sequencing and large-scale horizontal surveys. The EMP will establish common standards and coordinate independent projects proposed by the research community to advance large-scale microbial ecology research. It will generate over 1 petabase of sequencing data from around 1 million samples to map microbial habitats and discover new microbial diversity, genomes, and proteins.
Controversial Suggestion to Terraform Mars with Beneficial MicrobesMatt Kafker
A math- and science-focused university student, Mathew “Matt” Kafker has studied subjects such as electromagnetic physics and computer science. One area of current focus for Matt Kafker is microbial ecology, which involves the study of bacteria colonies in a number of settings and with various stimuli.
Dealing with heterogeneous data to improve our knowledge of biodiversity dynamics and ecosystem function: perspectives from synthesis projects: presented by Matthias Grenié for FREE (Causes and consequences of functional rarity from local to global scale) at the sfécologie conference 2018.
for more information on the group: http://www.cesab.org/index.php/fr/projets-en-cours/projets-2015/216-free
Controversial Suggestion to Terraform Mars with Beneficial MicrobesMatt Kafker
A math- and science-focused university student, Mathew “Matt” Kafker has studied subjects such as electromagnetic physics and computer science. One area of current focus for Matt Kafker is microbial ecology, which involves the study of bacteria colonies in a number of settings and with various stimuli.
Dealing with heterogeneous data to improve our knowledge of biodiversity dynamics and ecosystem function: perspectives from synthesis projects: presented by Matthias Grenié for FREE (Causes and consequences of functional rarity from local to global scale) at the sfécologie conference 2018.
for more information on the group: http://www.cesab.org/index.php/fr/projets-en-cours/projets-2015/216-free
Sleeping Beauty Transposon: Awakening a new approach to cancer treatmentJulie Kendrick
13 million years in the making, Perry Hackett’s Sleeping Beauty transposon has far-reaching implications for identifying causes of disease, use in gene therapy and more. His Sleeping Beauty (SB) transposon, reconstructed from a fish DNA sequence that went extinct 13 million years ago, proved to be a gamechanger in non-viral cancer gene therapy.
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
Sleeping Beauty Transposon: Awakening a new approach to cancer treatmentJulie Kendrick
13 million years in the making, Perry Hackett’s Sleeping Beauty transposon has far-reaching implications for identifying causes of disease, use in gene therapy and more. His Sleeping Beauty (SB) transposon, reconstructed from a fish DNA sequence that went extinct 13 million years ago, proved to be a gamechanger in non-viral cancer gene therapy.
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 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
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
IARU Global Challenges 2014 Cornell Tracking our declineSarah Cornell
There is growing attention to the global risks - not just local impacts - of present rates of biodiversity loss. It is worth keeping in mind that 'biodiversity loss' actually means the destruction (sometimes irreversible) – by us, people – of living organisms, Earth's 'genetic library', species, ecosystems and habitats. The fact that ecosystems are complex, adaptive, and locally specific means they can't be adequately represented in a single global measure. But without any overarching global perspective on losses, the locally contingent measures are 'untethered' to the real risks of systemic change. Scientists of many kinds are rising to the transdisciplinary challenge of dealing with this complexity in the face of global drivers of change (climate change, development pressures), recognizing that it is a challenge for everyone, not just academia.
Similar to Rick Stevens: Prospects for a Systematic Exploration of Earths Microbial Diversity (20)
IDW2022: A decades experiences in transparent and interactive publication of ...GigaScience, BGI Hong Kong
Scott Edmunds at International Data Week 2022: A decades experiences in transparent and interactive publication of FAIR data and software via an end-to-end XML publishing platform. 21st June 2022
GigaByte Chief Editor Scott Edmunds presents on how to prepare a data paper for the TDR and WHO sponsored call for data papers describing datasets on vectors of human diseases launched in Nov 2021. Presented at the GBIF webinar on 25th January 2022 and aimed at authors interested in submitting a manuscript submitted to the series.
STM Week: Demonstrating bringing publications to life via an End-to-end XML p...GigaScience, BGI Hong Kong
Scott Edmunds at the STM Week 2020 Digital Publishing seminar on Demonstrating bringing publications to life via an End-to-end XML publishing platform. 2nd December 2020
Scott Edmunds: A new publishing workflow for rapid dissemination of genomes u...GigaScience, BGI Hong Kong
Scott Edmunds on a new publishing workflow for rapid dissemination of genomes using GigaByte & GigaDB. Presented at Biodiversity 2020 in the Annotation & Databases track, 9th October 2020.
Scott Edmunds: Quantifying how FAIR is Hong Kong: The Hong Kong Shareability ...GigaScience, BGI Hong Kong
Scot Edmunds talk at CODATA2019 on Quantifying how FAIR is Hong Kong: The Hong Kong Shareability of Hong Kong University Research Experiment. 19th September 2019 in Beijing
Scott Edmunds talk at IARC: How can we make science more trustworthy and FAIR...GigaScience, BGI Hong Kong
Scott Edmunds talk at IARC, Lyon. How can we make science more trustworthy and FAIR? Principled publishing for more evidence based research. 8th July 2019
PAGAsia19 - The Digitalization of Ruili Botanical Garden Project: Production...GigaScience, BGI Hong Kong
A 3 part talk presented at PAG Asia 2019 in Shenzhen- The Digitalization of Ruili Botanical Garden Project: Production, Curation and Re-Use. Presented by Huan Liu (CNGB), Scott Edmunds (GigaScience) & Stephen Tsui (CUHK). 8th June 2019
Democratising biodiversity and genomics research: open and citizen science to...GigaScience, BGI Hong Kong
Scott Edmunds at the China National GeneBank Youth Biodiversity MegaData Forum: Democratising biodiversity and genomics research: open and citizen science to build trust and fill the data gaps. 18th December 2018
Ricardo Wurmus at #ICG13: Reproducible genomics analysis pipelines with GNU Guix. Presented at the GigaScience Prize Track at the International Conference on Genomics, Shezhen 26th October 2018
Paul Pavlidis at #ICG13: Monitoring changes in the Gene Ontology and their im...GigaScience, BGI Hong Kong
Paul Pavlidis talk at the #ICG13 GigaScience Prize Track: Monitoring changes in the Gene Ontology and their impact on genomic data analysis (GOtrack). Shenzhen, 26th October 2018
Stefan Prost at #ICG13: Genome analyses show strong selection on coloration, ...GigaScience, BGI Hong Kong
Stefan Prost presentation for the #ICG13 GigaScience Prize Track: Genome analyses show strong selection on coloration, morphological and behavioral phenotypes in birds-of-paradise. Shenzhen, 26th October, 2018
Lisa Johnson at #ICG13: Re-assembly, quality evaluation, and annotation of 67...GigaScience, BGI Hong Kong
Lisa Johnson's talk at the #ICG13 GigaScience Prize Track: Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Shenzhen, 26th October 2018
Reproducible method and benchmarking publishing for the data (and evidence) d...GigaScience, BGI Hong Kong
Scott Edmunds presentation on: Reproducible method and benchmarking publishing for the data (and evidence) driven era. The Silk Road Forensics Conference, Yantai, 18th September 2018
Mary Ann Tuli: What MODs can learn from Journals – a GigaDB curator’s perspec...GigaScience, BGI Hong Kong
Mary Ann Tuli's talk at the International Society of Biocuration meeting : What MODs can learn from Journals – a GigaDB curator’s perspective. Shanghai 9th April 2018
Generating a custom Ruby SDK for your web service or Rails API using Smithyg2nightmarescribd
Have you ever wanted a Ruby client API to communicate with your web service? Smithy is a protocol-agnostic language for defining services and SDKs. Smithy Ruby is an implementation of Smithy that generates a Ruby SDK using a Smithy model. In this talk, we will explore Smithy and Smithy Ruby to learn how to generate custom feature-rich SDKs that can communicate with any web service, such as a Rails JSON API.
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
Today, after several years of existence, an extremely active community and an ultra-dynamic ecosystem, Kubernetes has established itself as the de facto standard in container orchestration. Thanks to a wide range of managed services, it has never been so easy to set up a ready-to-use Kubernetes cluster.
However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks.
In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
As AI technology is pushing into IT I was wondering myself, as an “infrastructure container kubernetes guy”, how get this fancy AI technology get managed from an infrastructure operational view? Is it possible to apply our lovely cloud native principals as well? What benefit’s both technologies could bring to each other?
Let me take this questions and provide you a short journey through existing deployment models and use cases for AI software. On practical examples, we discuss what cloud/on-premise strategy we may need for applying it to our own infrastructure to get it to work from an enterprise perspective. I want to give an overview about infrastructure requirements and technologies, what could be beneficial or limiting your AI use cases in an enterprise environment. An interactive Demo will give you some insides, what approaches I got already working for real.
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
Essentials of Automations: Optimizing FME Workflows with ParametersSafe Software
Are you looking to streamline your workflows and boost your projects’ efficiency? Do you find yourself searching for ways to add flexibility and control over your FME workflows? If so, you’re in the right place.
Join us for an insightful dive into the world of FME parameters, a critical element in optimizing workflow efficiency. This webinar marks the beginning of our three-part “Essentials of Automation” series. This first webinar is designed to equip you with the knowledge and skills to utilize parameters effectively: enhancing the flexibility, maintainability, and user control of your FME projects.
Here’s what you’ll gain:
- Essentials of FME Parameters: Understand the pivotal role of parameters, including Reader/Writer, Transformer, User, and FME Flow categories. Discover how they are the key to unlocking automation and optimization within your workflows.
- Practical Applications in FME Form: Delve into key user parameter types including choice, connections, and file URLs. Allow users to control how a workflow runs, making your workflows more reusable. Learn to import values and deliver the best user experience for your workflows while enhancing accuracy.
- Optimization Strategies in FME Flow: Explore the creation and strategic deployment of parameters in FME Flow, including the use of deployment and geometry parameters, to maximize workflow efficiency.
- Pro Tips for Success: Gain insights on parameterizing connections and leveraging new features like Conditional Visibility for clarity and simplicity.
We’ll wrap up with a glimpse into future webinars, followed by a Q&A session to address your specific questions surrounding this topic.
Don’t miss this opportunity to elevate your FME expertise and drive your projects to new heights of efficiency.
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
Elevating Tactical DDD Patterns Through Object CalisthenicsDorra BARTAGUIZ
After immersing yourself in the blue book and its red counterpart, attending DDD-focused conferences, and applying tactical patterns, you're left with a crucial question: How do I ensure my design is effective? Tactical patterns within Domain-Driven Design (DDD) serve as guiding principles for creating clear and manageable domain models. However, achieving success with these patterns requires additional guidance. Interestingly, we've observed that a set of constraints initially designed for training purposes remarkably aligns with effective pattern implementation, offering a more ‘mechanical’ approach. Let's explore together how Object Calisthenics can elevate the design of your tactical DDD patterns, offering concrete help for those venturing into DDD for the first time!
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
Do you want to learn how to model and simulate an electrical network from scratch in under an hour?
Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)!
During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
- For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.
Encryption in Microsoft 365 - ExpertsLive Netherlands 2024Albert Hoitingh
In this session I delve into the encryption technology used in Microsoft 365 and Microsoft Purview. Including the concepts of Customer Key and Double Key Encryption.
Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf91mobiles
91mobiles recently conducted a Smart TV Buyer Insights Survey in which we asked over 3,000 respondents about the TV they own, aspects they look at on a new TV, and their TV buying preferences.
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
4. Institute for Computing in Science (ICiS)2010 Summer Session, Snowbird, Utah July 17-24|Computational Methods and Terabase Metagenomics | J. Gilbert, F. Meyer, R. Stevens Participants: 13 University, 9 Government and 3 Industry; 13 sessions These discussions became the first meeting of the Earth Microbiome Project and enabled the definition of a working committee, an implementation group, and a three-year plan. July 24-31| Future of the Field| F. Streitz and A. White Participants: 18 University, 4 Government and 6 Industry; 15 sessions Steering committee members and a select group of participants met to assess the state-of-the-art in scientific computing and identified areas for future programs. July 31-Aug. 7 |Optimization in Energy Systems | M. Anitescu and J. Meza Participants: 16 University, 10 Government and 3 Industry; 24 sessions Researchers from different areas discussed the major challenges facing the energy sector, and in particular, problems arising in optimization. Aug. 7-14 |Integrating, Representing, and Reasoning over Human Knowledge| J. Evans, I. Foster, A. Rzhetsky Participants: 18 University, 4 Government and 6 Industry; 16 sessions Participants were encouraged to think broadly about opportunities for transformative changes in knowledge that may become possible as data, computing, and collaboration are harnessed at exceptionally large scales.
5. A Core Group Emerged Jack Gilbert Folker Meyer Rob Knight Jonathan Eisen Jed Fuhrman Janet Jansson Bin Hu Mark Bailey Rick Stevens
6. We need a new Idea Sequencing is getting cheap.. VERY cheap Terabase project becoming increasingly feasible Diversity studies are limited by sampling depth Need combination of breadth and depth Computing is scaling up to handle large data Supercomputing capabilities will keep scaling for a while Interest in range of metagenomics questions Thousands of uncoordinated studies Crowdsourcing of samples increasingly feasible But how to agree on protocols
7. EMP High-Level Concept Goal: A community approach to systematically approach the problem of characterizing microbial life on earth Strategy: combination of extremely deep metagenomics sequencing and very-large scale horizontal surveys to refine our understanding of: Global microbial diversity, dispersion and biogeography Microbial community structure and dynamics Microbial contributions to the global nutrient cycles
8. Big Science? Earth Microbiome Project Map % fraction of microbiological habitats Volume > 100x larger > 1 PB of data ~1M samples > 100K new genomes Millions of novel proteins Largest reference collection of metagenomics, field guide to the microbial universe used by scientists for decades to come Sloan Digital Sky Mapped ¼ sky Volume 100x larger 15 TB data Position/Brightness of > 100M objects Distance to 100K quasars New types of objects The SDSS will be a new reference point, a field guide to the universe that will be used by scientists for decades to come.
9. But its not a Complete Parallel EMP will have distributed sampling EMP will have distributed sequencing EMP will have distributed analysis EMP will have common protocols EMP will have common standards EMP might have centralized archive of data EMP might have repository of samples
10. What is the EMP model? A framework of standard practices that enables massively comparable meta-analyses of independent projects An network oriented organizational model to advance Large-scale Microbial Ecology research – establishing and coordinating projects proposed by the community which can be advanced using the EMP framework of standards and access to partner Centers
13. Common standards for: Sampling -> Methods tailored to environment Georeferenced metadata DNA Extraction -> MoBio kit Sequencing -> 515/806 for 16S, Illumina PE Analysis -> QIIME (16S), MG-RAST/IMG, etc. Concept: begin with defined, open (though imperfect) protocols, bless with “EMP seal of approval” new protocols that show equivalence
14. Why do we need the EMP? Microbial life is vast 1030 organisms on Earth 106 – 109 or more species, massive gene/protein diversity Requires a systematic approach with a common framework Reduce duplication, maximize coverage, improve comparability between studies Structures existing studies led by different PI’s into clusters of Driving Projects EMP standard protocols allow much better comparability between projects Leverage community structures and crowd sourcing
15. EMP Pilot Projects High-Impact science targets Large-scale survey projects to identify diversity hotspots and plan deeper studies Small number of very deep demonstrations Hypothesis driven programmatic problems Technical targets to debug the EMP approach Community sourcing with standard protocols High-levels of multiplexed sequencing Environmental parameter characterization Metadata and sample database Analysis pipelines
16. Earth Microbiome Project: Attacking Basic Science Questions Coordination of community efforts to address long standing issues in environmental microbiology How much diversity is there, what is driving it and where do we find it? Are there diversity hotspots? Does microbial biogeography exist, if so what patterns are present and can we predict the patterns? Are some taxa endemic and if so how unique are they? Does global dispersal happen, how much and between where and is there support for Baas Becking hypothesis? Are the long tails of community distributions covergent in taxa? Are rare taxa somewhere abundant? How many places do we have to look to capture X diversity? How do the patterns in microbial communities relate to macro ecological patterns?
17. Curtis and Sloan on Microbial Diversity Perhaps patterns in global microbial diversity affect community composition, stability and functionality at a local level. If, as we argue, diversity matters, then patterns in global diversity could have a substantial effect on studies that seek to link community function and structure, strategies for seeking new drugs, for probiotics, bioaugmentationor studies to determine the persistence of chemicals. Curtis and Sloan, Current Opinion in Microbiology 2004, 7:221-226
18. Curtis and Sloan Continued, To understand a microbial system at a local level we will have to understand something of the metacommunity from which it is drawn. Moreover, we will have to correctly understand the relationship between random factors and deterministic factors. Curtis and Sloan, Current Opinion in Microbiology 2004, 7:221-226
19. What can we learn from extremely Deep Sequencing? Latitude, Ph, Mineral Content, Rainfall, Mean Temperature, Insolation, etc.
20. Estimates of Global Diversity NT/Nmax ~ 10 for soil NT/Nmax ~ 4 for aquatic Curtis, T.P. et al. (2002) Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. U. S. A. 99, 10494–10499
21. Pedros-Alio 2006 Are Most microbial taxa rare? Possibly Inactive?
22. Does a microbial biogeography exist? If yes can we map it? From Martiny et al 2006 “Microbial biogeography Review”
23. How Cosmopolitan are Mircrobes? From Martiny et al 2006 “Microbial biogeography Review”
24. Earth Microbiome Project: Attacking Programmatic Questions Improve understanding of microbial processes underlying the global carbon and nitrogen cycles Support process models development and uncertainty analysis for DOE mission critical environments (e.g. permafrost, oceans, subsurface) Discovery of novel microbial medicated global carbon pathways Improve our understanding of community structure/diversity/productivity/stability relationships Support community engineering and community design for targeting applications Search for novel biological functions relevant to bioprocessing, biofuels and bioremediation Targeting searching for organisms and communities containing DOE relevant to synthesis and degradation pathways Novel pathway discovery
25. The abundance of prokaryotic carbon and other elements may be compared with the statement of Kluyverthat about one-half of the ‘‘living protoplasm’’ on earth is microbial (2). Because most of the plant biomass is made up of extracellular material such as cell walls and structural polymers, the protoplasmic biomass of prokaryotes probably far exceeds that of plants, and Kluyver’s well-accepted estimate is probably much too conservative.
28. RMF returns a list of metabolites and whether those metabolites are more or less likely to be consumed or synthesized in one environment relative to another.
31. EMP at the Right Time Leverages the availability of continued advances in sequencing capacity Terabases to Petabases and beyond Evolution of sequencing center Models Push towards aggregation of projects (i.e. scale up) Community driven but coordinated Open, Real-time coordination, immediate data availability Novel approaches to address the scaling issues in sample collection and prep Crowd sourced samples, distributed prep? Targets both wide survey and deep sampling “Mapping” followed by targeted attacks
32. EMP Products and Deliverables Metagenomics datasets from many thousands of environments with standardized metadata Georeferenced inventory of global microbial 16s sequences Reference genomes recovered from the shotgun metagenomics datasets Community structure profiles for many thousands of communities Microbial protein catalog capturing global protein and gene diversity
36. Temperature – Antarctica, Brazil, North America, Arctic Tundra, Hydrothermal vents
37. Light availability – Water columns in the Pacific and Atlantic from surface to the abyssal plain.
38. pH – UK, North America, China biogeographic soils
39.
40. Projects request deep 16S rRNA sequencing of representative samples:
41. Globally distributed soil samples from China, Australia, India, Argentina, Peru, USA and Antarctica
42. Globally distributed time series samples from English Channel, Barrier Reef in Australia, Bermudan North Atlantic, Temperate Pacific and Tropical Pacific
43.
44. Projects using deep shotgun metagenomics to explore modeled metabolomics:
45. Temporal and spatial distributed samples from the gulf oil spill
46. Samples spanning the northern tundra belt from Canada, USA, Russia, Sweden
47.
48.
49. At the bottom individual or consortium led hypothesis driven proposals
52. Earth Microbiome Project Potential Dataflows Annotation & Statistical Analysis 16S/18S rRNA Metagenomics Metatranscriptomics Genome Assembly modelSEED & RMF Environmental Parameters Metagenome Datasets (1,000’s of Campaigns) Provision of targets for novel enzymes Model Metabolome Characterization of Novel Proteins Metametabolomics GC/MS & NMR Gap-filling for model
53. EMP needs new kinds of interfaces toSequencingworkflows Large-scale community projects will by necessity develop internal tracking systems Sampling, LIMS etc. Transacting with Seq Centers could be enhanced by interfacing between the internal/external tracking and LIMS systems Large-scaleEMPpilots could help develop this Services partners will also need this type of interfaces
54. What would change this strategy? Availability of “direct” interrogation of complex microbial environments Geochemical environmental mapping (nm->um) Environmental metabolomics and proteomics Roving cellular scale reporters and probes Dramatic improvements in microbial microcosm experimental capabilities Artificial community construction Time dependent high-resolution measurements
55. Phases of EMP Timeline 2011 Expert-Group consensus on EMP standards: sampling, extraction, sequencing, informatics Building the Global Environmental Sample Database (GESD) Pilot Project: 10,000 samples acquired, extracted, sequenced and analyzed by five core centers (ANL, LBNL, UC-Boulder, JGI, and BGI). 2012 and beyond- Ongoing EMP: Biological Driver Projects “collect” individual science driven sequencing proposals (e.g. JGI-CSP, BGI, ANL, etc.) EMP acts as a conceptual framework to allow comparative analysis within and between Driver Projects.
56. Thanks to the EMP Leadership Jack Gilbert Folker Meyer Rob Knight Jonathan Eisen Jed Fuhrman Janet Jansson Bin Hu Mark Bailey