Un update of the previous talk with the same title. A talk I gave at the Computational Life Science initiative (University of Oslo) about new High Throughput Sequencing instruments at the Norwegian Sequencing Centre. I also mentioned future upgrades, and the upcoming nanopore sequencing platform of Oxford nanopore.
New High Throughput Sequencing technologies at the Norwegian Sequencing Centr...Lex Nederbragt
A talk I gave at the Microbiology Research Group (University of Oslo) about new High Throughput Sequencing instruments at the Norwegian Sequencing Centre. I also mentioned future upgrades, and the upcoming nanopore sequencing platform of Oxford nanopore
In her recent publication “Fast isogenic mapping-by-sequencing of EMS-induced mutant bulks” in Plant Physiology, Dr. Franziska Turck and her team introduced deep candidate resequencing (dCARE) using the Ion PGM™ Sequencer to their Arabidopsis mutant identification pipeline.
These slides are from her Decmeber 5th live webinar presentation about the application of isogenic mapping approach for plant gene identification with fast and cost-effective barcoding using the Ion PGM™ system. She shared with the webinar attendees her experience with the ways that the Ion PGM™ system improves her deep sequencing workflow.
Learn more about the Ion Proton™ and Ion PGM™ here http://owl.li/g19ix
New High Throughput Sequencing technologies at the Norwegian Sequencing Centr...Lex Nederbragt
A talk I gave at the Microbiology Research Group (University of Oslo) about new High Throughput Sequencing instruments at the Norwegian Sequencing Centre. I also mentioned future upgrades, and the upcoming nanopore sequencing platform of Oxford nanopore
In her recent publication “Fast isogenic mapping-by-sequencing of EMS-induced mutant bulks” in Plant Physiology, Dr. Franziska Turck and her team introduced deep candidate resequencing (dCARE) using the Ion PGM™ Sequencer to their Arabidopsis mutant identification pipeline.
These slides are from her Decmeber 5th live webinar presentation about the application of isogenic mapping approach for plant gene identification with fast and cost-effective barcoding using the Ion PGM™ system. She shared with the webinar attendees her experience with the ways that the Ion PGM™ system improves her deep sequencing workflow.
Learn more about the Ion Proton™ and Ion PGM™ here http://owl.li/g19ix
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.1- Next Generation Sequencing. Technologies and Applications. Part I: NGS Introduction and Technology Overview.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Next-generation sequencing and quality control: An Introduction (2016)Sebastian Schmeier
This lecture is part is an introductory bioinformatics workshop. It gives a background to what sequencing is, what the results of a sequencing experiment are, how to assess the quality of a sequencing run, what error sources exist and how to deal with errors. The accompanying websites are available at http://sschmeier.com/bioinf-workshop/
Next-Generation Sequencing an Intro to Tech and Applications: NGS Tech Overvi...QIAGEN
This slidedeck provides a technical overview of DNA/RNA preprocessing, template preparation, sequencing and data analysis. It covers the applications for NGS technologies, including guidelines for how to select the technology that will best address your biological question.
How to cluster and sequence an ngs library (james hadfield160416)James Hadfield
A presentation for people intersted in understanding how Illumina adapter ligation, clustering ands SBS sequencing work. Follow core-genomics http://core-genomics.blogspot.co.uk/
my students use ideas from my class on business models to develop a business model for ion proton's DNA sequencer. This sequencer uses semiconductor technology to read an organism's DNA sequence and is faster and cheaper than existing sequencers. This presentation describes the value proposition, customer selection, method of value capture and other aspects of a business model for Ion Proton's DNA sequencer
Next-generation sequencing data format and visualization with ngs.plot 2015Li Shen
An introduction to the commonly used formats for the next-generation sequencing data. ngs.plot is a popular tool for the visualization and data mining of the NGS data.
This was presented on Mar 11, 2014 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/
Neuroscience core lecture given at the Icahn school of medicine at Mount Sinai. This is the version 2 of the same topic. I have made some modifications to give a more gentle introduction and add a new example for ngs.plot.
Thoughts on the recent announcements by Oxford Nanopore TechnologiesKeith Bradnam
Some notes I made for the weekly UC Davis 'Bits & Bites' sequence analysis discussion club.
This was a few days after the GridION and MinION technologies were announced at AGBT.
Next Gen Sequencing Technologies OverviewPatrick Merel
A presentation of the major nextgen sequencing technologies. Price indications were valid 1st quarter of 2009. Mac keynote file, half french half english. Hope this can help.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.1- Next Generation Sequencing. Technologies and Applications. Part I: NGS Introduction and Technology Overview.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Next-generation sequencing and quality control: An Introduction (2016)Sebastian Schmeier
This lecture is part is an introductory bioinformatics workshop. It gives a background to what sequencing is, what the results of a sequencing experiment are, how to assess the quality of a sequencing run, what error sources exist and how to deal with errors. The accompanying websites are available at http://sschmeier.com/bioinf-workshop/
Next-Generation Sequencing an Intro to Tech and Applications: NGS Tech Overvi...QIAGEN
This slidedeck provides a technical overview of DNA/RNA preprocessing, template preparation, sequencing and data analysis. It covers the applications for NGS technologies, including guidelines for how to select the technology that will best address your biological question.
How to cluster and sequence an ngs library (james hadfield160416)James Hadfield
A presentation for people intersted in understanding how Illumina adapter ligation, clustering ands SBS sequencing work. Follow core-genomics http://core-genomics.blogspot.co.uk/
my students use ideas from my class on business models to develop a business model for ion proton's DNA sequencer. This sequencer uses semiconductor technology to read an organism's DNA sequence and is faster and cheaper than existing sequencers. This presentation describes the value proposition, customer selection, method of value capture and other aspects of a business model for Ion Proton's DNA sequencer
Next-generation sequencing data format and visualization with ngs.plot 2015Li Shen
An introduction to the commonly used formats for the next-generation sequencing data. ngs.plot is a popular tool for the visualization and data mining of the NGS data.
This was presented on Mar 11, 2014 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/
Neuroscience core lecture given at the Icahn school of medicine at Mount Sinai. This is the version 2 of the same topic. I have made some modifications to give a more gentle introduction and add a new example for ngs.plot.
Thoughts on the recent announcements by Oxford Nanopore TechnologiesKeith Bradnam
Some notes I made for the weekly UC Davis 'Bits & Bites' sequence analysis discussion club.
This was a few days after the GridION and MinION technologies were announced at AGBT.
Next Gen Sequencing Technologies OverviewPatrick Merel
A presentation of the major nextgen sequencing technologies. Price indications were valid 1st quarter of 2009. Mac keynote file, half french half english. Hope this can help.
The field of next-generation sequencing (NGS) has been experiencing explosive growth over the past several years and shows little sign of slowing down. The increasing capabilities and dramatically lowered costs have expanded NGS's reach beyond that of the human genome into nearly every corner of biological research. An overview of the platforms on the market today, including an assessment of their relative strengths and weaknesses, will be presented. The presentation will conclude with a peek into where the technology is going and what will be available in the future.
A class of DNA sequencing techniques currently in active development is third-generation sequencing, commonly referred to as long-read sequencing. In comparison to second generation sequencing, also referred to as next generation sequencing, third generation sequencing technologies have the capacity to create noticeably longer reads.
Next generation-sequencing.ppt-convertedShweta Tiwari
The advance version, sequences the whole genome efficiently with high speed and high throughput sequencing at reduce cost is termed as Next Generation Sequencing (NGS) or massively parallel sequencing (MPS).
Holographic memory came into existence to provide service of high data volume devices & increase their data transfer rate for processing by ultra speed microprocessor
A talk I gave at the Dec 2013 Assembly Masterclass at UC Davis. Really licensed under CC0. UPDATED May 2014, for the presentation I gave at the combined SeRC Nordic Assembly Workshop in Stockholm, Sweden, May 14th 2014
A talk I gave for my colleagues on how and why I use blogging and twitter for science, trying to convince them to start doing the same. DO check out the presenter notes! (see tab 'notes')
How to sequence a large eukaryotic genome - and how we sequenced the cod genome. A seminar I gave for the Computational Life Science (Univ. of Oslo) seminar series, September 28, 2011
Next generation sequencing: research opportunities and bioinformatic challenges. A seminar I gave for the Computational Life Science (Univ. of Oslo) seminar series, March 2, 2011
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/
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.
GridMate - End to end testing is a critical piece to ensure quality and avoid...ThomasParaiso2
End to end testing is a critical piece to ensure quality and avoid regressions. In this session, we share our journey building an E2E testing pipeline for GridMate components (LWC and Aura) using Cypress, JSForce, FakerJS…
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
Pushing the limits of ePRTC: 100ns holdover for 100 daysAdtran
At WSTS 2024, Alon Stern explored the topic of parametric holdover and explained how recent research findings can be implemented in real-world PNT networks to achieve 100 nanoseconds of accuracy for up to 100 days.
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.
Alt. GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using ...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.
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.
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.
The Art of the Pitch: WordPress Relationships and SalesLaura Byrne
Clients don’t know what they don’t know. What web solutions are right for them? How does WordPress come into the picture? How do you make sure you understand scope and timeline? What do you do if sometime changes?
All these questions and more will be explored as we talk about matching clients’ needs with what your agency offers without pulling teeth or pulling your hair out. Practical tips, and strategies for successful relationship building that leads to closing the deal.
A tale of scale & speed: How the US Navy is enabling software delivery from l...sonjaschweigert1
Rapid and secure feature delivery is a goal across every application team and every branch of the DoD. The Navy’s DevSecOps platform, Party Barge, has achieved:
- Reduction in onboarding time from 5 weeks to 1 day
- Improved developer experience and productivity through actionable findings and reduction of false positives
- Maintenance of superior security standards and inherent policy enforcement with Authorization to Operate (ATO)
Development teams can ship efficiently and ensure applications are cyber ready for Navy Authorizing Officials (AOs). In this webinar, Sigma Defense and Anchore will give attendees a look behind the scenes and demo secure pipeline automation and security artifacts that speed up application ATO and time to production.
We will cover:
- How to remove silos in DevSecOps
- How to build efficient development pipeline roles and component templates
- How to deliver security artifacts that matter for ATO’s (SBOMs, vulnerability reports, and policy evidence)
- How to streamline operations with automated policy checks on container images
5. High-throughput sequencing
Phase 1: more is better
2005 GS20 200 000 reads 100 bp
0.02 Gb/run
2011 GS FLX+ 1.2 million reads 750 bp
0.7 Gb/run
2006 GA 28 million reads 25 bp
0.7 Gb/run
2011 HiSeq 2000 3 billion reads 2x100 bp
600 Gb/run
6. High-throughput sequencing
Phase 2: smaller is better
GS Junior from Roche/454
0.04 GB/run
400 bp reads
0.7 GB/run
700 bp reads
MiSeq from Illumina
2 GB/run
2x150 bp reads
600 GB/run
2x100 bp reads
PGM from Ion Torrent/
Life Technologies
0.01, 0.1 or 1 GB/run
100 or 200 bp reads
7. High-throughput sequencing
Why benchtop sequencing instruments?
GS Junior from Roche/454
10 hours
23 hours
MiSeq from Illumina
27 hours
10 days
PGM from Ion Torrent/
Life Technologies
3 hours
8. High-throughput sequencing
Why benchtop sequencing instruments?
Diagnostics
Affordable price
per instrument Small projects
Fast turn around time
http://pennystockalerts.com/ http://www.highqualitylinkbuildingservice.com/
http://www.vetlearn.com/ http://vanillajava.blogspot.com
16. Announced upgrades
HiSeq 2000 HiSeq 2500 2x 250 bp reads
2x150 bp? Rapid run mode 27 hrs 8.5 Gbp
2x150 bp, 90 Gbp
750 bp reads?
400 bp reads
Proton from Ion Torrent
Fall 2012: 10 Gb on Proton I chip, 400 bp
2013: 4 x more wells on Proton II chip
21. High-throughput sequencing
Phase 3: single-molecule
C2 (current) chemistry:
Average read length 2500 bp
36 000 reads
90 MB per ‘run’
22. High-throughput sequencing
REVI EW S
Technology
Pacific Biosciences — Real-time sequencing
a Phospholinked hexaphosphate nucleotides
G A
b
1 nm
00
Zero-mode waveguide Limit of detection zone
Glass Fluorescence pulse
Intensity
Epifluorescence detection T
Figure 4 | Real-time sequencing. P acific Biosciences’ four-colour r
a | The zero-mode waveguide (ZMW) design reduces the observatio
fluorescently labelled molecules that enter the detection layer for a
the dilemma that DNA polymerases perform optimally when fluore
23. High-throughput sequencing
S
Technology
Real-time sequencing
Phospholinked hexaphosphate nucleotides
G A T C
b
Limit of detection zone
Fluorescence pulse
Intensity
e detection Time
Nature Reviews | Genetics
Figure 4 | Real-time sequencing. Pacific Biosciences’ four-colour real-time sequencing method is shown.
44. PacBio: first results
Raw reads
ZMWs Mean readlength
30,000 4,000
25,000 3,500
3,000
20,000
2,500
15,000 2,000
10,000 1,500
1,000
5,000
500
0 0
cod 4kb cod 17kb Fish X 4kbFish X 4kb Fish X Fish X cod 4kb cod 17kb Fish X 4kb Fish X 4kb Fish X Fish X
17kb 17kb 17kb 17kb
Longest read
25,000
20,000
15,000
10,000
5,000
0
cod 4kb cod 17kb Fish X 4kb Fish X 4kb Fish X 17kb Fish X 17kb
45. SMRTBell'template'
PacBio: first results
Length of longest subread for all raw reads
Standard'Sequencing'
Generates& pass& each&
one& on& molecule&
Large&
Insert&
Sizes&
sequenced&
Circular'Consensus'Sequencing'
Average length
16,000
Largest
Small&
Insert&
Sizes&
14,000
Generates&
mul8ple&
passes& each&
on& molecule&
12,000 sequenced&
10,000
8,000
6,000
4,000
2,000
0
cod 4kb cod 17kb Fish X 4kb Fish X 4kb Fish X 17kb Fish X 17kb
46. PacBio: first results
Length of longest subread for all raw reads
Per SMRTCell longest subread length density distribution
Fish X Salmon
Atlantic
Atlantic Cod
4kb libraries
Cod
3e−04
17kb libraries
2e−04
Density
1e−04
0e+00
0 2000 4000 6000 8000 10000
Maximum subread length
55. Oxford Nanopore
AGBT conference, February 2012
100 kbp reads
Currently at 4% error
1% error at release
GridION
2000 nanopores/node
tens of Gb data per 24 hour
Run until…
20 nodes 1 human genome in 15 minutes