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
Genome assembly: then and now ā with notes āĀ v1.1Keith Bradnam
Ā
This was a talk given on 2014-06-19 for the Genome Centerās Bioinformatics Core as part of a 1 week workshop on using Galaxy. It concerns the Assemblathon projects as well as other aspects relating to genome assembly.
A version of this talk is also available on Slideshare without embedded notes.
Note, this is an evolving talk. There are older and newer versions of the talk also available on slideshare.
Thoughts on the feasibility of an Assemblathon 3 contestKeith Bradnam
Ā
A *draft* version of a talk presented at the 2015 Genome 10K meeting. These are slides I prepared for my PI (Ian Korf) to use. The final version of the talk may differ substantially to what is shown here.
This talk sets out some ideas as to what was bad about the Assemblathon 2 contest and how we could learn from this should there be an Assemblathon 3 contest.
What's in a name? Better vocabularies = better bioinformatics?Keith Bradnam
Ā
Most of the pain and suffering that occurs in bioinformatics happens when database identifier 'A' in file 1, doesn't quite match database identifier 'B' in file 2...even when they are supposed to be the same identifier.
Things don't always match up for a number of reasons, most of which *should* be under our control. This talk covers a few points relating to this and briefly discusses how we should all be using curated ontologies to describe our data.
Genome assembly: then and now ā with notes āĀ v1.1Keith Bradnam
Ā
This was a talk given on 2014-06-19 for the Genome Centerās Bioinformatics Core as part of a 1 week workshop on using Galaxy. It concerns the Assemblathon projects as well as other aspects relating to genome assembly.
A version of this talk is also available on Slideshare without embedded notes.
Note, this is an evolving talk. There are older and newer versions of the talk also available on slideshare.
Thoughts on the feasibility of an Assemblathon 3 contestKeith Bradnam
Ā
A *draft* version of a talk presented at the 2015 Genome 10K meeting. These are slides I prepared for my PI (Ian Korf) to use. The final version of the talk may differ substantially to what is shown here.
This talk sets out some ideas as to what was bad about the Assemblathon 2 contest and how we could learn from this should there be an Assemblathon 3 contest.
What's in a name? Better vocabularies = better bioinformatics?Keith Bradnam
Ā
Most of the pain and suffering that occurs in bioinformatics happens when database identifier 'A' in file 1, doesn't quite match database identifier 'B' in file 2...even when they are supposed to be the same identifier.
Things don't always match up for a number of reasons, most of which *should* be under our control. This talk covers a few points relating to this and briefly discusses how we should all be using curated ontologies to describe our data.
Snippy - Rapid bacterial variant calling - UK - tue 5 may 2015Torsten Seemann
Ā
Using Snippy to call variants in bacterial short read datasets via alignment to reference, and then using these alignments to produce core SNP alignments for phylogenomics.
Microarray as one of recent biomedical technologies produce high dimensional data. This makes statistical analysis become challenging. I presented an overview of microarray analysis specifically in the use of gene expression profiling in a discussion.
Lecture focuses on how to measure genetic distances, with emphasis on whole genome data.
Lecture held at the Nordic Working Group for Microbiology and Animal Health and Welfare (NMDD) meeting on Source attribution of Campylobacter in the Nordic countries.
K-mers in metagenomics
K-mers play a critical role in the exploration of metagenomic data. They have been widely used to assign taxonomic attributions to the short genomic fragments characteristic of shotgun (metagenomic) sequencing. These approaches provide an assembly-free method for profiling microbial communities, and have helped elucidate the factors driving microbial community composition across biogeochemical gradients. Advances in sequencing technology are now making it cost-effective to sequence microbial communities at sufficient depths to allow for the assembly of high-quality contigs. This has made it possible to adopt k-mer based approaches to enable reliable binning of contigs originating from a single microbial population within a community. In this session, I will present both an overview of how k-mers can be used to assign taxonomic attributions to short metagenomic reads, and discuss how these approaches have advanced to a point where population genomes can be recovered en masse from even complex microbial communities.
This PPT discusses the concept of Dynamic Linker as in Linux and its porting to Solaris ARM platform. It starts from the very basics of linking process
Snippy - Rapid bacterial variant calling - UK - tue 5 may 2015Torsten Seemann
Ā
Using Snippy to call variants in bacterial short read datasets via alignment to reference, and then using these alignments to produce core SNP alignments for phylogenomics.
Microarray as one of recent biomedical technologies produce high dimensional data. This makes statistical analysis become challenging. I presented an overview of microarray analysis specifically in the use of gene expression profiling in a discussion.
Lecture focuses on how to measure genetic distances, with emphasis on whole genome data.
Lecture held at the Nordic Working Group for Microbiology and Animal Health and Welfare (NMDD) meeting on Source attribution of Campylobacter in the Nordic countries.
K-mers in metagenomics
K-mers play a critical role in the exploration of metagenomic data. They have been widely used to assign taxonomic attributions to the short genomic fragments characteristic of shotgun (metagenomic) sequencing. These approaches provide an assembly-free method for profiling microbial communities, and have helped elucidate the factors driving microbial community composition across biogeochemical gradients. Advances in sequencing technology are now making it cost-effective to sequence microbial communities at sufficient depths to allow for the assembly of high-quality contigs. This has made it possible to adopt k-mer based approaches to enable reliable binning of contigs originating from a single microbial population within a community. In this session, I will present both an overview of how k-mers can be used to assign taxonomic attributions to short metagenomic reads, and discuss how these approaches have advanced to a point where population genomes can be recovered en masse from even complex microbial communities.
This PPT discusses the concept of Dynamic Linker as in Linux and its porting to Solaris ARM platform. It starts from the very basics of linking process
Building tungsten-clusters-with-postgre sql-hot-standby-and-streaming-replica...Command Prompt., Inc
Ā
Alex Alexander & Linas Virbalas
Hot standby and streaming replication will move the needle forward for high availability and scaling for a wide number of applications. Tungsten already supports clustering using warm standby. In this talk we will describe how to build clusters using the new PostgreSQL features and give our report from the trenches.
This talk will cover how hot standby and streaming replication work from a user perspective, then dive into a description of how to use them, taking Tungsten as an example. We'll cover the following issues:
* Configuration of warm standby and streaming replication
* Provisioning new standby instances
* Strategies for balancing reads across primary and standby database
* Managing failover
* Troubleshooting and gotchas
Please join us for an enlightening discussion a set of PostgreSQL features that are interesting to a wide range of PostgreSQL users.
Use case of the usage of Apache Spark @Windward Ltd.
Video lecture on YouTube: https://www.youtube.com/watch?v=rPO6P5YIKUI
Showing the domain of the company,
A short introduction of Apache Spark,
And the Tool Box used @Windward Ltd to form a working production Spark Data Pipeline.
Creating Connector to Bridge the Worlds of Kafka and gRPC at Wework (Anoop Di...confluent
Ā
What do you do when you've two different technologies on the upstream and the downstream that are both rapidly being adopted industrywide? How do you bridge them scalably and robustly? At Wework, the upstream data was being brokered by Kafka and the downstream consumers were highly scalable gRPC services. While Kafka was capable of efficiently channeling incoming events in near real-time from a variety of sensors that were used in select Wework spaces, the downstream gRPC services that were user-facing were exceptionally good at serving requests in a concurrent and robust manner. This was a formidable combination, if only there was a way to effectively bridge these two in an optimized way. Luckily, sink Connectors came to the rescue. However, there weren't any for gRPC sinks! So we wrote one.
In this talk, we will briefly focus on the advantages of using Connectors, creating new Connectors, and specifically spend time on gRPC sink Connector and its impact on Wework's data pipeline.
vectorQC: 'A pipeline for assembling and annotation of vectors'Luca Cozzuto
Ā
DNA vectors are widely used in molecular cloning, gene engineering, studies of gene expression and other applications. Sequence validation of a vector DNA is a crucial quality control step before using the vector. With the cost of sequencing rapidly decreasing it becomes cost-effective to ensure the vectors quality using high-throughput sequencing and bioinformatics analysis. VectorQC is an automatic pipeline for quality control of a collection of sequenced DNA vectors. The pipeline is built using the NextFlow framework and is distributed with the Docker container, which makes the pipeline easy to install, modify, and re-use on any Unix-compatible OS on a computer, cluster or cloud
Updated: New High Throughput Sequencing technologies at the Norwegian Sequenc...Lex Nederbragt
Ā
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
Ā
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
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
Neuro-symbolic is not enough, we need neuro-*semantic*Frank van Harmelen
Ā
Neuro-symbolic (NeSy) AI is on the rise. However, simply machine learning on just any symbolic structure is not sufficient to really harvest the gains of NeSy. These will only be gained when the symbolic structures have an actual semantics. I give an operational definition of semantics as āpredictable inferenceā.
All of this illustrated with link prediction over knowledge graphs, but the argument is general.
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Ā
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.
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
Ā
As AI technology is pushing into IT I was wondering myself, as an āinfrastructure container kubernetes guyā, 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 benefitās 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
Ā
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 ā USA
Expansion of bot farms ā 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 ā 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/
Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf91mobiles
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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.
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Ā
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.
Slack (or Teams) Automation for Bonterra Impact Management (fka Social Soluti...Jeffrey Haguewood
Ā
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.
UiPath Test Automation using UiPath Test Suite series, part 3DianaGray10
Ā
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
"Impact of front-end architecture on development cost", Viktor TurskyiFwdays
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I have heard many times that architecture is not important for the front-end. Also, many times I have seen how developers implement features on the front-end just following the standard rules for a framework and think that this is enough to successfully launch the project, and then the project fails. How to prevent this and what approach to choose? I have launched dozens of complex projects and during the talk we will analyze which approaches have worked for me and which have not.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
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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.
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
Ā
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.
DevOps and Testing slides at DASA ConnectKari Kakkonen
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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.
PHP Frameworks: I want to break free (IPC Berlin 2024)Ralf Eggert
Ā
In this presentation, we examine the challenges and limitations of relying too heavily on PHP frameworks in web development. We discuss the history of PHP and its frameworks to understand how this dependence has evolved. The focus will be on providing concrete tips and strategies to reduce reliance on these frameworks, based on real-world examples and practical considerations. The goal is to equip developers with the skills and knowledge to create more flexible and future-proof web applications. We'll explore the importance of maintaining autonomy in a rapidly changing tech landscape and how to make informed decisions in PHP development.
This talk is aimed at encouraging a more independent approach to using PHP frameworks, moving towards a more flexible and future-proof approach to PHP development.
13. Mate pair splitting and orientation
Illumina paired end reads
Illumina mate pair reads
454 mate pair reads
linker
junctionjunction
+ +
paired end reads
ācontaminationā
14. Mate pair splitting and orientation
Illumina paired end reads
Illumina mate pair reads
454 mate pair reads
linker
junctionjunction
+ +
paired end reads
ācontaminationā
Check what orientation
your assembler expects
for the reads!
42. Comparative measures
Log Average Probability (LAP)
Assembly Likelihood Evaluation (ALE)
See also Howison, Zapata2 and Dunn (2013) Toward a
statistically explicit understanding of de novo sequence
assembly doi: 10.1093/bioinformatics/btt525