"Data Provenance: Principles and Why it matters for BioMedical Applications"Pinar Alper
Tutorial given at Informatics for HEalth 2017 COnference These slides are for the second part of the tutorial describing provenance capture and management tools.
"Data Provenance: Principles and Why it matters for BioMedical Applications"Pinar Alper
Tutorial given at Informatics for HEalth 2017 COnference These slides are for the second part of the tutorial describing provenance capture and management tools.
citation:
Missier, P., Soiland-Reyes, S., Owen, S., Tan, W., Nenadic, A., Dunlop, I., et al. (2010).
Taverna, reloaded. In M. Gertz, T. Hey, & B. Ludaescher (Eds.), Procs. SSDBM 2010. Heidelberg, Germany.
Paper available at: http://www.ssdbm2010.org/.
Metabolomic Data Analysis Workshop and Tutorials (2014)Dmitry Grapov
Get more information:
http://imdevsoftware.wordpress.com/2014/10/11/2014-metabolomic-data-analysis-and-visualization-workshop-and-tutorials/
Recently I had the pleasure of teaching statistical and multivariate data analysis and visualization at the annual Summer Sessions in Metabolomics 2014, organized by the NIH West Coast Metabolomics Center.
Similar to last year, I’ve posted all the content (lectures, labs and software) for any one to follow along with at their own pace. I also plan to release videos for all the lectures and labs.
[2017-05-29] DNASmartTagger : Development of DNA sequence tagging tools based on machine learning using public sequence annotation data, NIG International Symposium 2017.
Top Cited Articles International Journal of Computer Science, Engineering and...IJCSEA Journal
International Journal of Computer Science, Engineering and Applications (IJCSEA) is an open access peer-reviewed journal that publishes articles which contribute new results in all areas of the computer science, Engineering and Applications. The journal is devoted to the publication of high quality papers on theoretical and practical aspects of computer science, Engineering and Applications.
Best Practices for Validating a Next-Gen Sequencing WorkflowGolden Helix
Validating an NGS workflow is an iterative process that begins with collaboration with personnel and planning protocols for the entire workflow from sample preparation, sequencing and variant calling, all the way to data analysis and reporting. At Golden Helix, while we do not provide pre-validated black-box workflows, we provide our customers with support to validate workflows in a transparent manner, and assist them in reaching production deadlines. This webcast will be led by members of our Field Application Scientist team, and we will explore some of the best practices for NGS workflow validation that we have observed and helped to implement based on real-world examples from our customer base. Key topics for discussion will include:
Sample preparation and collection of adequate case/control data
Designing a robust workflow with special considerations for single versus family analyses and phenotypic considerations
Generating the desired output for clinical or other reports
Real world NGS workflow validation strategies
Tune in for tips and strategies that you can deploy when designing and validating your NGS workflow.
BioDec, based near Bologna, Italy, provides top-notch services, solutions, and consulting in the field of lab data management and in postgenomics "in silico" research. The presentation summarizes our main achievements and describes our commercial offer.
citation:
Missier, P., Soiland-Reyes, S., Owen, S., Tan, W., Nenadic, A., Dunlop, I., et al. (2010).
Taverna, reloaded. In M. Gertz, T. Hey, & B. Ludaescher (Eds.), Procs. SSDBM 2010. Heidelberg, Germany.
Paper available at: http://www.ssdbm2010.org/.
Metabolomic Data Analysis Workshop and Tutorials (2014)Dmitry Grapov
Get more information:
http://imdevsoftware.wordpress.com/2014/10/11/2014-metabolomic-data-analysis-and-visualization-workshop-and-tutorials/
Recently I had the pleasure of teaching statistical and multivariate data analysis and visualization at the annual Summer Sessions in Metabolomics 2014, organized by the NIH West Coast Metabolomics Center.
Similar to last year, I’ve posted all the content (lectures, labs and software) for any one to follow along with at their own pace. I also plan to release videos for all the lectures and labs.
[2017-05-29] DNASmartTagger : Development of DNA sequence tagging tools based on machine learning using public sequence annotation data, NIG International Symposium 2017.
Top Cited Articles International Journal of Computer Science, Engineering and...IJCSEA Journal
International Journal of Computer Science, Engineering and Applications (IJCSEA) is an open access peer-reviewed journal that publishes articles which contribute new results in all areas of the computer science, Engineering and Applications. The journal is devoted to the publication of high quality papers on theoretical and practical aspects of computer science, Engineering and Applications.
Best Practices for Validating a Next-Gen Sequencing WorkflowGolden Helix
Validating an NGS workflow is an iterative process that begins with collaboration with personnel and planning protocols for the entire workflow from sample preparation, sequencing and variant calling, all the way to data analysis and reporting. At Golden Helix, while we do not provide pre-validated black-box workflows, we provide our customers with support to validate workflows in a transparent manner, and assist them in reaching production deadlines. This webcast will be led by members of our Field Application Scientist team, and we will explore some of the best practices for NGS workflow validation that we have observed and helped to implement based on real-world examples from our customer base. Key topics for discussion will include:
Sample preparation and collection of adequate case/control data
Designing a robust workflow with special considerations for single versus family analyses and phenotypic considerations
Generating the desired output for clinical or other reports
Real world NGS workflow validation strategies
Tune in for tips and strategies that you can deploy when designing and validating your NGS workflow.
BioDec, based near Bologna, Italy, provides top-notch services, solutions, and consulting in the field of lab data management and in postgenomics "in silico" research. The presentation summarizes our main achievements and describes our commercial offer.
Climate Science for a Sustainable Energy Future ProvenanceEric Stephan
Invited talk at the Earth System Grid Federation workshop
My web page: http://www.linkedin.com/in/ericstephan
My citations: http://scholar.google.com/citations?hl=en&user=f4bH2esAAAAJ
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.
Slack (or Teams) Automation for Bonterra Impact Management (fka Social Soluti...Jeffrey Haguewood
Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
We believe integration and automation are essential to user experience and the promise of efficient work through technology. Automation is the critical ingredient to realizing that full vision. We develop integration products and services for Bonterra Case Management software to support the deployment of automations for a variety of use cases.
This video focuses on the notifications, alerts, and approval requests using Slack for Bonterra Impact Management. The solutions covered in this webinar can also be deployed for Microsoft Teams.
Interested in deploying notification automations for Bonterra Impact Management? Contact us at sales@sidekicksolutionsllc.com to discuss next steps.
DevOps and Testing slides at DASA ConnectKari Kakkonen
My and Rik Marselis slides at 30.5.2024 DASA Connect conference. We discuss about what is testing, then what is agile testing and finally what is Testing in DevOps. Finally we had lovely workshop with the participants trying to find out different ways to think about quality and testing in different parts of the DevOps infinity loop.
UiPath Test Automation using UiPath Test Suite series, part 3DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 3. In this session, we will cover desktop automation along with UI automation.
Topics covered:
UI automation Introduction,
UI automation Sample
Desktop automation flow
Pradeep Chinnala, Senior Consultant Automation Developer @WonderBotz and UiPath MVP
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
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/
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.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
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!
Dev Dives: Train smarter, not harder – active learning and UiPath LLMs for do...UiPathCommunity
💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™:
See how to accelerate model training and optimize model performance with active learning
Learn about the latest enhancements to out-of-the-box document processing – with little to no training required
Get an exclusive demo of the new family of UiPath LLMs – GenAI models specialized for processing different types of documents and messages
This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath.
Speakers:
👨🏫 Andras Palfi, Senior Product Manager, UiPath
👩🏫 Lenka Dulovicova, Product Program Manager, UiPath
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.
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.
Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf
Leveraging The Open Provenance Model as a Multi-Tier Model for Global Climate Research
1. Leveraging The Open
Provenance Model as a Multi-
Tier Model for Global Climate
Research
Eric Stephan, Todd Halter, Brian Ermold
IPAW, 2010
2. Discussion Outline
! Background on Atmospheric Radiation
Measurement (ARM) program.
! Challenges without Provenance
! Requirements Analysis
! Multi-Tier Provenance Model
! Use of Open Provenance Model
! Impacts
3. Background
! Atmospheric Radiation Measurement Program
! Production system designed and developed in 1990
! Data is collected from over 300 remote sensors worldwide.
Expanding to over 400 sensors in 2010
! Data collection will reach over 500 GB/day of atmospheric
and satellite data by FY11
! Value added products (VAPs)
developed to correlate, aggregate
and support quality studies of raw
data into computational models
3
4. Challenges Facing Current VAP Development
! Causality, Lineage, Referential Knowledge Not
Formalized:
! Captured in multiple ways and stored in different media and
representation forms.
! Sample causality not directly accessible to scientists
! Inability to seamlessly analyze and visualize knowledge
! Provenance Required By Different Audiences
! Producers – Operations/VAP developers
! Consumers –scientist relying on VAPs
4
5. Requirements Analysis 1 of 2
Value Added Product Directed Graph
Lineage (Path)
Acyclic Graph and
Value Added Product
Common Properties
Workflow Causality (Hedge)
Ordered Autonomous
Sample Causality … Acyclic Graphs When
Processing Data
Product (Branch)
6. Requirements Analysis 2 of 2
Tier Purpose Resources Status Operations Developer Researcher
Path Lineage N/A Future Needed Needed Needed
Path Curation Sample Level QC Exists In Use Needed Needed
Path/Hedge Reference Metadata Repository Exists In Use In Use Needed
Hedge Reference Configuration files Exists In Use In Use Needed
Hedge/Branch Causality Log files Exists Needed In Use Needed
Hedge/Branch Derived Trends/Anomalies Future Needed Needed Needed
Branch Causality Sample Derivation Method Exists In Use Needed Needed
Branch Causality Sample Source Exists In Use Needed Needed
6
7. ARM Provenance Model
! Characteristics
! Knowledge required to depict interdependency, overall
processing, and discrete sample processing
! Multi-tier
! Each tier representing different granularity and purpose
! Each hedge in context of path, branch in context of hedge.
! Declared tiers make knowledge easier to perform cross
comparison
! Because sample provenance at branch tier is autonomous and
ordered, provenance can be processed in parallel or stored in
chunks.
! Leverage Standards and Community Efforts
7
10. Estimated Cost of Provenance
Sample
Quality
Control
Field
Origin
~30K for
each VAP
sample 2 bytes for
each VAP
~5-10K sample
< 5K graph
VAP Lineage VAP Sample
Path Hedge Branch
10 Low Granularity Medium Granularity High Granularity
11. Analysis Examples
! Timeline Inspection Anomaly and Trend Detection
! Aggregation
! Out of 43,200 potential samples (560K log entries)
! 15 distinct processes
! 60 distinct process results e.g.
! No AERO G data within minutes of x
! No RRTM_LW output for x
! No RRTM_SW output for x
! No clear sky longwave cloud forcing run for x
! No clear sky shortwave cloud forcing run for x
! No emissivities file RRTM_SW_sfcemissdata
! This can be used to help users know the kinds of questions they can ask.
11
12. Impacts
! Provenance articulates ARM data processing causality
and lineage in a formal and recognizable way.
! Adding provenance creates a data intensive computing
challenge due to the shear volume of provenance
represented as a large semantic graph.
! Use of a multi-tier model makes analysis and visualization
possible because the provenance graph can be broken
into chunks for distributed or parallel processing.
! Modeling the branch tier as autonomous acyclic graphs
makes quantitative analysis possible to look for trends or
anomalies within one data product, or between multiple
data products.