This document describes IPRStats, a visualization tool for InterProScan results. IPRStats allows users to view summaries and charts of protein domain annotations from InterProScan. It imports InterProScan XML files, generates statistics and taxonomy summaries, and exports results as HTML or Excel files. IPRStats uses a wxPython GUI, SQLite or PyTables for data storage, and generates pie charts, bar graphs and other visualizations of the annotation data.
Hiring and retaining legal staff in Asia-Pacific Businessesiohann Le Frapper
This article co-written by Randall Lewis and myself describes the importance of hiring and retaining the right staff that could be useful for GCs,HR heads and headhunters to read.
Hiring and retaining legal staff in Asia-Pacific Businessesiohann Le Frapper
This article co-written by Randall Lewis and myself describes the importance of hiring and retaining the right staff that could be useful for GCs,HR heads and headhunters to read.
Provenance for Data Munging EnvironmentsPaul Groth
Data munging is a crucial task across domains ranging from drug discovery and policy studies to data science. Indeed, it has been reported that data munging accounts for 60% of the time spent in data analysis. Because data munging involves a wide variety of tasks using data from multiple sources, it often becomes difficult to understand how a cleaned dataset was actually produced (i.e. its provenance). In this talk, I discuss our recent work on tracking data provenance within desktop systems, which addresses problems of efficient and fine grained capture. I also describe our work on scalable provence tracking within a triple store/graph database that supports messy web data. Finally, I briefly touch on whether we will move from adhoc data munging approaches to more declarative knowledge representation languages such as Probabilistic Soft Logic.
Presented at Information Sciences Institute - August 13, 2015
Provenance for Data Munging EnvironmentsPaul Groth
Data munging is a crucial task across domains ranging from drug discovery and policy studies to data science. Indeed, it has been reported that data munging accounts for 60% of the time spent in data analysis. Because data munging involves a wide variety of tasks using data from multiple sources, it often becomes difficult to understand how a cleaned dataset was actually produced (i.e. its provenance). In this talk, I discuss our recent work on tracking data provenance within desktop systems, which addresses problems of efficient and fine grained capture. I also describe our work on scalable provence tracking within a triple store/graph database that supports messy web data. Finally, I briefly touch on whether we will move from adhoc data munging approaches to more declarative knowledge representation languages such as Probabilistic Soft Logic.
Presented at Information Sciences Institute - August 13, 2015
Large Data Analyze with PyTables,
This presentation has been collected from several other presentations(PyTables presentation).
For more presentation in this field please refer to this link (http://pytables.org/moin/HowToUse#Presentations).
Jupyter Enterprise Gateway enables Jupyter Notebook to launch remote kernels in a distributed cluster, including Apache Spark managed by YARN, IBM Spectrum Conductor or Kubernetes.
It provides out of the box support for the following kernels:
Python using IPython kernel
R using IRkernel
Scala using Apache Toree kernel
Making your data work for you: Scratchpads, publishing & the biodiversity dat...Vince Smith
This is a derivative of a talk I gave at the Linnean society on 20th Sept. 2012. This version was given at the i4Life Environmental Genomics workshop on 25th Sept. and refocused to look at the dark taxa problem and developing published descriptions of molecular sequence clusters.
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
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.
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
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
Accelerate your Kubernetes clusters with Varnish CachingThijs Feryn
A presentation about the usage and availability of Varnish on Kubernetes. This talk explores the capabilities of Varnish caching and shows how to use the Varnish Helm chart to deploy it to Kubernetes.
This presentation was delivered at K8SUG Singapore. See https://feryn.eu/presentations/accelerate-your-kubernetes-clusters-with-varnish-caching-k8sug-singapore-28-2024 for more details.
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.
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.
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.
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.
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.
JMeter webinar - integration with InfluxDB and GrafanaRTTS
Watch this recorded webinar about real-time monitoring of application performance. See how to integrate Apache JMeter, the open-source leader in performance testing, with InfluxDB, the open-source time-series database, and Grafana, the open-source analytics and visualization application.
In this webinar, we will review the benefits of leveraging InfluxDB and Grafana when executing load tests and demonstrate how these tools are used to visualize performance metrics.
Length: 30 minutes
Session Overview
-------------------------------------------
During this webinar, we will cover the following topics while demonstrating the integrations of JMeter, InfluxDB and Grafana:
- What out-of-the-box solutions are available for real-time monitoring JMeter tests?
- What are the benefits of integrating InfluxDB and Grafana into the load testing stack?
- Which features are provided by Grafana?
- Demonstration of InfluxDB and Grafana using a practice web application
To view the webinar recording, go to:
https://www.rttsweb.com/jmeter-integration-webinar
Unsubscribed: Combat Subscription Fatigue With a Membership Mentality by Head...
Friedberg bosc2010 iprstats
1. IPRStats: a Visualization Tool for
InterProScan
Iddo Friedberg
Microbiology and
Computer Science & Software Engineering
Miami University
http://github.com/devrkel/IPRStats.git
2. Microbes are Everywhere
●
1030 prokaryotic cells on Earth
(give or take a couple)
● Dominate the biosphere
● 90% of the cells in your body
are prokaryotic (1014)
● Found in the most hostile
environments
3. t
os
alm
Microbes do Everything
● Nutrient reservoir:
●
4x1010 tons carbon (rivaling
plants)
●
1x1010 tons Nitrogen
●
1x109 tons phosphorous
●
4. Of course there is health...
● Communicable
diseases
● Heart disease
● Gastric cancer
● Irritable Bowel
Syndrome
11. What is Metagenomics?
• Culture independent approach to study
microbial communities
– < 1% of microbes can be cultured
– DNA directly isolated from environmental sample
and sequenced
• Examining genomic content of organisms in
community/environment to better understand:
– Diversity of organisms
– Their roles and interactions in the ecosystem
13. Some things we can learn using Metagenomics
●Taxonomic content: Taxon diversity in a habitat (using taxonomic
markers)
• Functional content: biological functions, qualitative and quantitative
profiles
• Coping with the environment: differences in functional content
between habitats
• Decompose the biotic / abiotic elements in a habitat: metadata
analysis
16. A Metagenomic project
● Sequencing
● Assembly
● Annotation
● Gene finding
Population
● Function prediction analysis tools
● Diversity analysis
● Comparative
analysis
17. InterProScan
● Signature search against an
integrated resource of domains
and functional sites
● Easy to install, cluster-enabled
(pleasantly parallel)
● Maintained by EBI
● Can annotate whole genomes
● PIR, Pfam, TIGRFam, Panther,
Prodom, PRINTS,...
● Needs a visualization tool for
population / metagenomic
annotation
18. Open XML file Charting
Python SAX Parser
GUI: wxPython
Excel export: xlwt
Full Databases
IPRStats
File Help
PFAM
PIR
GENE3D
Aggregate
Queries
HAMAP
PANTHER
PRINTS
PRODOM
Resulting Tables PROFILE
PROSITE
SMART
SUPERFAMILY
TIGRFAMs
19. IPRStats Architecture
IPRStats standalone
importers (wx.Frame)
Menu
XML (wx.MenuBar)
PropertiesDlg
IPS (wx.Dialog)
Settings
Chart
(wx.StaticBitmap)
exporters
Table
(wx.PyGridTableBase)
HTML
StatsData
XLS
(using xlwt)
Results
(sqlite or pytables)
IPS
20. ?
What is PyTables?
- package for creating data structures that can handle large amounts of data
- uses NumPy (for in memory) and HDF5 (for disk storage) structures
- uses Numexpr (jit compiler) for evaluating expressions (like queries)
- in the context of IPRScan, it provides a way of accessing a huge table
of data without requiring that all the data be in memory
Pros Cons
- HDF5 provides very fast, compact and - Large memory overhead (particularly
efficient indexing in comparison to smaller datasets)
- NumPy provides efficient in-memory - Many large, complex dependencies
storage including HDF5, NumPy, Numexpr and
- Minimizes disk and memory usage Cython
- Very fast read times compared to - Slow write times (particularly important
SQLite and MySQL since IPRStats bottlenecks with writing)
24. Conclusions & Future
● A lightweight, machine-independent
visualization tool for InterProScan annotations
● License: AFL
● Todo:
● Comparative population analysis
● Large dataset handling
● More graphic options
● Anything else you like...
– http://github.com/devrkel/IPRStats.git
25. Thanks
● David Ream
● Han Wang
● Ian Fleming
● David Vincent
● Ryan Kelly
● EBI
● Miami University startup funding
● Miami University Undergraduate Summer Scholars
Program
26. The Friedberg Lab is Recruiting
● Graduate students
● Postdocs
● Catch me later, email me, or look at
iddo-friedberg.net to learn more