The document describes Representative Proteomes (RPs), which provide a standardized, stable, and unbiased set of proteomes. RPs are generated computationally based on pair-wise comparisons of proteomes and are inspected by curators. RPs reduce the number of proteomes by over 90% while retaining over 95% of protein families and experimentally characterized proteins. RPs integrate with UniProt/UniRef and are released monthly. They allow mapping of proteomes to reference genomes and aid in sequence analysis and metagenomic sequence classification.
2013 Chevrolet Corvette Brochure | South Jersey Chevrolet DealerRK Chevrolet
Check out the 2013 Chevrolet Corvette brochure provided by RK Chevrolet in Vineland. Find the 2013 Chevrolet Corvette for sale in New Jersey. To learn more about our current sales and incentives give us a call at (856) 457-4040. http://www.myrkchevy.com/
2013 Chevrolet Corvette Brochure | South Jersey Chevrolet DealerRK Chevrolet
Check out the 2013 Chevrolet Corvette brochure provided by RK Chevrolet in Vineland. Find the 2013 Chevrolet Corvette for sale in New Jersey. To learn more about our current sales and incentives give us a call at (856) 457-4040. http://www.myrkchevy.com/
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdfPaige Cruz
Monitoring and observability aren’t traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current company’s observability stack.
While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
I, a former op, would like to extend an invitation to all application developers to join the observability party will share these foundational concepts to build on:
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
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
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Threats to mobile devices are more prevalent and increasing in scope and complexity. Users of mobile devices desire to take full advantage of the features
available on those devices, but many of the features provide convenience and capability but sacrifice security. This best practices guide outlines steps the users can take to better protect personal devices and information.
SAP Sapphire 2024 - ASUG301 building better apps with SAP Fiori.pdfPeter Spielvogel
Building better applications for business users with SAP Fiori.
• What is SAP Fiori and why it matters to you
• How a better user experience drives measurable business benefits
• How to get started with SAP Fiori today
• How SAP Fiori elements accelerates application development
• How SAP Build Code includes SAP Fiori tools and other generative artificial intelligence capabilities
• How SAP Fiori paves the way for using AI in SAP apps
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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.
UiPath Test Automation using UiPath Test Suite series, part 5DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 5. In this session, we will cover CI/CD with devops.
Topics covered:
CI/CD with in UiPath
End-to-end overview of CI/CD pipeline with Azure devops
Speaker:
Lyndsey Byblow, Test Suite Sales Engineer @ UiPath, Inc.
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdfPaige Cruz
Monitoring and observability aren’t traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current company’s observability stack.
While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
I, a former op, would like to extend an invitation to all application developers to join the observability party will share these foundational concepts to build on:
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
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
Threats to mobile devices are more prevalent and increasing in scope and complexity. Users of mobile devices desire to take full advantage of the features
available on those devices, but many of the features provide convenience and capability but sacrifice security. This best practices guide outlines steps the users can take to better protect personal devices and information.
SAP Sapphire 2024 - ASUG301 building better apps with SAP Fiori.pdfPeter Spielvogel
Building better applications for business users with SAP Fiori.
• What is SAP Fiori and why it matters to you
• How a better user experience drives measurable business benefits
• How to get started with SAP Fiori today
• How SAP Fiori elements accelerates application development
• How SAP Build Code includes SAP Fiori tools and other generative artificial intelligence capabilities
• How SAP Fiori paves the way for using AI in SAP apps
Dr. Sean Tan, Head of Data Science, Changi Airport Group
Discover how Changi Airport Group (CAG) leverages graph technologies and generative AI to revolutionize their search capabilities. This session delves into the unique search needs of CAG’s diverse passengers and customers, showcasing how graph data structures enhance the accuracy and relevance of AI-generated search results, mitigating the risk of “hallucinations” and improving the overall customer journey.
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.
UiPath Test Automation using UiPath Test Suite series, part 5DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 5. In this session, we will cover CI/CD with devops.
Topics covered:
CI/CD with in UiPath
End-to-end overview of CI/CD pipeline with Azure devops
Speaker:
Lyndsey Byblow, Test Suite Sales Engineer @ UiPath, Inc.
DevOps and Testing slides at DASA ConnectKari Kakkonen
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GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
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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/
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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/
Why You Should Replace Windows 11 with Nitrux Linux 3.5.0 for enhanced perfor...SOFTTECHHUB
The choice of an operating system plays a pivotal role in shaping our computing experience. For decades, Microsoft's Windows has dominated the market, offering a familiar and widely adopted platform for personal and professional use. However, as technological advancements continue to push the boundaries of innovation, alternative operating systems have emerged, challenging the status quo and offering users a fresh perspective on computing.
One such alternative that has garnered significant attention and acclaim is Nitrux Linux 3.5.0, a sleek, powerful, and user-friendly Linux distribution that promises to redefine the way we interact with our devices. With its focus on performance, security, and customization, Nitrux Linux presents a compelling case for those seeking to break free from the constraints of proprietary software and embrace the freedom and flexibility of open-source computing.
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
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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.
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.
Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. What’s changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
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Bc2012 submission 109a
1. Representative Proteomes
and Genomes
A standardized, stable and unbiased set of proteomes and
genomes
http://pir.georgetown.edu/rps/
Raja Mazumder (mazumder@gwu.edu)
4. Procedure to generate the RPs
Compute pair-wise co-membership value (X) in UniRef50 for all proteomes
For each proteome, compute the mean co-membership between
this proteome and the other proteomes
Create ranked proteome list based on the mean co-membership
RPG generation starts
For a given CMT, take the first proteome in the ranked list and
the ones with X ≥ CMT to form an RPG, and remove them from
ranked list
ranked
No
list
empty?
Yes
RPG generation ends
Select a Representative Proteome for each RPG (manually inspected by curator)
5. Proteome A Proteome B UniRef50
UniRef50
Sequence clusters (UniRef100, 90, 50)
From any organism
Part of UniProt production cycle
PMID: 17379688
6. RPs at Different CMTs
1000 100
900 90
3.02
800 80
700 2.69 70 # RPs
Million proteins
600 2.36 60
# RPs
% Reduction -
500 50 % 1
Proteomes
400 40
2.02 % Reduction -
300 30 Sequences
2
200 20
100 10
0 0
75 55 35 15
1
Based on 1144 complete genomes
CMT (%) 2
Based on 4.3 million sequences (complete genomes only)
UniProtKB total: 13.46 million sequences
7. • RP at higher level is used to cluster the lower levels
• RPGs are constructed based on co-membership, not
taxonomy
8. Manual mapping of UniProt and
NCBI genomes
The taxonomy ID of each proteome present
in UniProt is mapped to the NCBI
RefSeq/GenBank genome project IDs
When more than one genome is available
for the same taxonomy ID, the genomes are
ranked according to the availability of a
RefSeq genome, number of related
publications, number of citations for each
publication, and date of sequencing.
The highest ranking genome is mapped to
the UniProtKB proteome
9. RefSeq genomes and proteomes
Mapping allows us to retrieve genomes and
proteomes from RefSeq.
ftp://ftp.pir.georgetown.edu/databases/rps/rg
ftp://ftp.pir.georgetown.edu/databases/rps/rp_in_refseq_sequences/
11. Coverage Statistics – RP55
95% of all InterPro families contain at least
one protein from the RP set
InterPro covers ~75% of all proteins in
UniProtKB, and this number holds true as
well for RP55
93% of the experimentally-characterized
proteins are retained in the RP set
15. Visualizing all-against-all proteome
correlation matrix vs. the taxonomy
tree
Developed a method to graphically visualize NCBI's taxonomy
tree and overlay the proteome correlation tree (PCT) to illustrate
genomic similarity between organisms that may otherwise be
considered to have distant ancestry.
Computed all-against-all correlation values between all complete
proteomes
Comparison network can be browsed in Cytoscape network
software to easily identify nodes in the taxonomy tree that are not
supported by PCT data
Development tools: CytoscapeWeb, CytoscapeRPC, Perl
16. Family
Enterobacteriaceae Distance based on taxonomy tree
Shigella Escherichia Enterobacter Klebsiella Genus
Distance based on taxonomy tree
Species
ENT38 Distance based on correlation table
ECOLI
ESCF3 ECO24
ENTAK
ECOK1 KLEP7
SHIFL
SHIF8
18. Can easily identify genomic neighbors
The top 2 levels are family
and genus nodes arranged
according to taxonomic
position
The bottom nodes are
complete proteomes with a
heuristic force-directed
layout applied according to
all-against-all correlation
Although AGRT5 and
AGRVS share the same
genus, they are relatively
distant from each other
(~28%), compared to
AGRT5 and AGRSH
(~70%).
20. Conclusions
High quality RPs generated computationally and
inspected by curators
A standardized, stable and unbiased set of proteomes
and genomes
Completely integrated and into the UniProt/UniRef
production pipeline and has monthly releases
Automatically selects QFO/UniProt RF (if available in
RPG) as RP (provide feedback to QFO and others if
discrepancy)
Extended to RefSeq (
ftp://ftp.pir.georgetown.edu/databases/rps/rg;
ftp://ftp.pir.georgetown.edu/databases/rps/rp_in_refseq_s
equences/)
RGs can help placement of unknown metagenomic
sequences into the correct clusters
21. Acknowledgements
Chuming Chen (PIR)
Darren Natale (PIR)
Hongzhan Huang (PIR)
Jian Zhang (PIR)
Peter McGarvey (PIR)
Cathy Wu (PIR)
Mona Motwani (GWU)
Jamal Theodore (GWU)
Robert Finn (HHMI Janelia Farm/Pfam)
Eleanor Stanley (EBI)
Kim Pruitt (NCBI)
Yuri Wolf (NCBI)
UniProt Consortium
Editor's Notes
For the purpose of making the Representative Proteome Groups, we created a list of organisms ranked by mean co-membership, meaning that the average connectedness to all other organisms was computed. The list was then used to recruit organisms based on whether or not the co-membership score was greater than the CMT. We did some tests and found that varying the ranking system changed no more than 2% of the RPGs, and none of the RPs (meaning that in those cases, one organism “jumped ship” into another group).
In order to ensure that the RPs are hierarchical at different CMT’s we first calculate RP75, then take that set to generate RP55 and so on. Any RP in a smaller set (such as RP15) will be thus be found in all larger sets (such as RP75). The genus change for the Vibrio salmonicida to Aliivibrio illustrates why using taxonomy as the mechanism for determining RPGs is a bad idea: taxonomy can change, but the sequences won’t.
Stability of RPs is illustrated by a retrospective study. Using a UniProt release from 2004, there were 116 RPs. All 116 remained as RPs throughout the test period. Furthermore, any added RP (in 2005, 2006, etc) remained as RP in subsequent releases. The comparison of number of RP and number of complete proteomes illustrates that RPs are growing at a slower rate. The % reduction of sequence space is indicated by red and purple lines, which shows that there is a steady increase in the reduction rate. This rate is dependent upon the type of genomes being sequenced: if many related genomes (yet another E coli, for example) are added, then the reduction increases (see 2006_7).
The InterPro coverage stats indicate that the RP set covers most of the sequence space in terms of similarity families. They also indicate that there is not much significant over- or under-representation of sequences. The missing InterPro families tended to be viral (which are not yet included in RP) or lineage-specific. Experimentally-characterized proteins were determined using literature references in Swiss-Prot entries or GOA evidence codes. There are 30,000 such proteins in the examined set.