DNA sequence screening software that implements the best match method recommended by the federal government.
Publication: Adam L et al, Strengths and limitations of the federal guidance on synthetic DNA, Nature Biotechnology (2011) 29, 208–210 doi:10.1038/nbt.1802
US Department of Health and Human Services voluntary guidelines “Screening Framework Guidance for Synthetic Double-Stranded DNA Providers” November 2009.
Software: http://sourceforge.net/projects/genothreat/
I first describe the challenges associated to the rapid accumulation of HTS data; these issues are not trivial and may have a negative impact in terms of money, time and scientific quality/reproducibility. I then present recommendations for mitigating these issues and aiding in the management and analysis of HTS data.
Challenges of FFPE Sample Materials – Where Does Variation in Quantity of Pur...QIAGEN
In this slidedeck, we reveal how to get the most from your FFPE samples. We discuss variability in quantity and purity of DNA purified from FFPE samples manually or with automated procedures, assessed by different quantification and quality control methods. You can also learn more about the QIAxpert system and how it can help you gain reliable quantification of FFPE samples.
The QIAGEN Service Core provides a full service for genomic and expression analysis using cutting-edge tools. It accepts various sample types and performs experiments, such as pathway-focused analysis, whole genome analysis, and real-time PCR, using reagents and equipment. This allows customers to save costs by avoiding investing in their own resources and saves time by outsourcing experimental work. A variety of nucleic acid and data analysis services are available.
A Fully Automated POCKIT Central PCR System for Evaluation of the Infectious ...Simon Chung - genereach
This document discusses using PCR to evaluate the uniformity of infectious bronchitis vaccination in chickens. It finds:
1) A POCKIT Central PCR system can detect the IB vaccine virus in tracheal swabs up to 4 weeks after spraying vaccination at hatcheries.
2) Sequence analysis showed nucleic acids detected by the PCR system matched the vaccine used in the study.
3) A PCR positive rate of 40% or higher on day 7 after vaccination could be used as a cutoff for evaluating uniformity, with regular monitoring needed below that threshold.
The study demonstrates PCR is an effective quality control tool for checking IB vaccination uniformity. The portable POCKIT system makes this feasible for poultry grow
Ambion scientists Emily Zeringer and Marie Gonzalez presented the background, methods and what to expect when extracting nucleic acids from FFPE tissue samples. These are the slides from the presentation. The presentation can be viewed with audio here http://find.lifetechnologies.com/ambion/ffpewebinar/sldshr
Streamlined next generation sequencing assay development using a highly multi...Thermo Fisher Scientific
Next generation sequencing (NGS) assay development for solid tumor sequencing requires characterization of variant calling directly from formalin-fixed paraffin embedded (FFPE) tissue samples. However, cell line based FFPE and human FFPE samples only contain 2 to 20 variants, which require laboratories to invest significant resources in sample sourcing and preparation when developing assays to detect 100+ variants
This document summarizes various bioinformatics analyses performed on the pyruvate kinase gene sequence from Vibrio cholerae, including restriction mapping, finding the open reading frame, multiple sequence alignment, phylogenetic tree construction, and primer design. Restriction mapping identified several restriction enzyme cutting sites. The open reading frame encoding pyruvate kinase was identified. A phylogenetic tree grouped pyruvate kinase sequences into two clades. Four primer pairs were designed for PCR amplification.
I first describe the challenges associated to the rapid accumulation of HTS data; these issues are not trivial and may have a negative impact in terms of money, time and scientific quality/reproducibility. I then present recommendations for mitigating these issues and aiding in the management and analysis of HTS data.
Challenges of FFPE Sample Materials – Where Does Variation in Quantity of Pur...QIAGEN
In this slidedeck, we reveal how to get the most from your FFPE samples. We discuss variability in quantity and purity of DNA purified from FFPE samples manually or with automated procedures, assessed by different quantification and quality control methods. You can also learn more about the QIAxpert system and how it can help you gain reliable quantification of FFPE samples.
The QIAGEN Service Core provides a full service for genomic and expression analysis using cutting-edge tools. It accepts various sample types and performs experiments, such as pathway-focused analysis, whole genome analysis, and real-time PCR, using reagents and equipment. This allows customers to save costs by avoiding investing in their own resources and saves time by outsourcing experimental work. A variety of nucleic acid and data analysis services are available.
A Fully Automated POCKIT Central PCR System for Evaluation of the Infectious ...Simon Chung - genereach
This document discusses using PCR to evaluate the uniformity of infectious bronchitis vaccination in chickens. It finds:
1) A POCKIT Central PCR system can detect the IB vaccine virus in tracheal swabs up to 4 weeks after spraying vaccination at hatcheries.
2) Sequence analysis showed nucleic acids detected by the PCR system matched the vaccine used in the study.
3) A PCR positive rate of 40% or higher on day 7 after vaccination could be used as a cutoff for evaluating uniformity, with regular monitoring needed below that threshold.
The study demonstrates PCR is an effective quality control tool for checking IB vaccination uniformity. The portable POCKIT system makes this feasible for poultry grow
Ambion scientists Emily Zeringer and Marie Gonzalez presented the background, methods and what to expect when extracting nucleic acids from FFPE tissue samples. These are the slides from the presentation. The presentation can be viewed with audio here http://find.lifetechnologies.com/ambion/ffpewebinar/sldshr
Streamlined next generation sequencing assay development using a highly multi...Thermo Fisher Scientific
Next generation sequencing (NGS) assay development for solid tumor sequencing requires characterization of variant calling directly from formalin-fixed paraffin embedded (FFPE) tissue samples. However, cell line based FFPE and human FFPE samples only contain 2 to 20 variants, which require laboratories to invest significant resources in sample sourcing and preparation when developing assays to detect 100+ variants
This document summarizes various bioinformatics analyses performed on the pyruvate kinase gene sequence from Vibrio cholerae, including restriction mapping, finding the open reading frame, multiple sequence alignment, phylogenetic tree construction, and primer design. Restriction mapping identified several restriction enzyme cutting sites. The open reading frame encoding pyruvate kinase was identified. A phylogenetic tree grouped pyruvate kinase sequences into two clades. Four primer pairs were designed for PCR amplification.
171114 best practices for benchmarking variant calls justinGenomeInABottle
Benchmarking variant calls is challenging but important for evaluating sequencing and analysis methods. The GA4GH Benchmarking Team has developed standardized tools using Genome in a Bottle reference samples to robustly benchmark variant calls, including SNPs and indels. Their tools provide stratified performance metrics in different genomic contexts to better understand accuracy. Ongoing work focuses on more difficult variants like indels and structural variants. Standardized benchmarking allows fair comparison of methods and helps improve variant detection.
Following our latest publication, The Market for CRISPR/Cas9 Genome Editing Products, released in June 2015 on the Interactive Market Intelligence platform, a follow-up questionnaire was sent to The Science Advisory Board to quantify how the emergence of CRISPR/Cas9 technology is impacting the use of traditional tools and techniques. It was fielded between July 6-8, 2015.
To download, please go to: http://marketanalysts.lifescienceexecutive.com/blog/?p=1995
CellFree Sciences offers a cell-free protein expression platform using wheat germ extracts to rapidly produce proteins without cells. Their technology allows scalable and automated protein production from micrograms to grams, and expression of proteins difficult to produce in cell-based systems. They provide reagents, protein synthesizers, and contract research services to support protein research and production needs.
Bio-inspiring and evolutionary computation: Trends, applications and open issues workshop, 7 Nov. 2015 Faculty of Computers and Information, Cairo University
The document provides instructions for creating runs, defining protocols and graphs, viewing results, and performing background subtraction and quantification on the Smart Cycler system. It also discusses user administration, analysis settings, export options, melt analysis, and troubleshooting.
Presentation of the paper titled "Combining Global and Local Attention with Positional Encoding for Video Summarization", by E. Apostolidis, G. Balaouras, V. Mezaris, I. Patras, delivered at the IEEE Int. Symposium on Multimedia (ISM), Dec. 2021. The corresponding software is available at https://github.com/e-apostolidis/PGL-SUM.
The document presents a comparative analysis of different fault injection methods using on-chip debug (OCD) infrastructures. It describes experiments conducted using a Freescale MPC-565 microprocessor with enhanced OCD capabilities. The experiments compare basic, extended, and OCD-enhanced fault injection configurations across offline and real-time scenarios. Results show that the OCD-enhanced method enables higher fault detection rates with lower performance overhead compared to other approaches.
Search-Based Software Testing Tool Competition 2021 by Sebastiano Panichella,...Sebastiano Panichella
Sebastiano Panichella [1], Alessio Gambi [2], Fiorella Zampetti [3], Vincenzo Riccio [4]
ZURICH UNIVERSITY OF APPLIED SCIENCE (ZHAW), SWITZERLAND [1],
UNIVERSITY OF PASSAU, GERMANY [2],
UNIVERSITY OF SANNIO, ITALY [3],
UNIVERSITÀ DELLA SVIZZERA ITALIANA , SWITZERLAND [4]
The document proposes HUG, a hardware and software system to efficiently process large genomic data sets. HUG includes a hardware accelerator to speed up genomic analysis algorithms like Smith-Waterman and protein folding. It also accelerates genomic variant calling, which identifies DNA changes associated with diseases but requires comparing to large databases. The system implements regular expression matching for genomic data using a reconfigurable instruction set architecture circuit, achieving a 6x speedup over software. It aims to integrate algorithms and develop visualization tools to facilitate analysis of computed genomic data.
International Journal of Engineering Research and Applications (IJERA) is an open access online peer reviewed international journal that publishes research and review articles in the fields of Computer Science, Neural Networks, Electrical Engineering, Software Engineering, Information Technology, Mechanical Engineering, Chemical Engineering, Plastic Engineering, Food Technology, Textile Engineering, Nano Technology & science, Power Electronics, Electronics & Communication Engineering, Computational mathematics, Image processing, Civil Engineering, Structural Engineering, Environmental Engineering, VLSI Testing & Low Power VLSI Design etc.
Global Regulatory Issues: one BA method, one validation, one report ...Peter van Amsterdam
Comparison of the recent guidelines of the Brazilian, European, Japanese and US regualtory agencies on bioanalytical method validation in order to be able to validate a bioanalytical method in such a way that it would meet the requirements of these 4 agencies. Presented at the 2013 Land O'Lakes meeting
International Journal of Engineering Research and Applications (IJERA) is an open access online peer reviewed international journal that publishes research and review articles in the fields of Computer Science, Neural Networks, Electrical Engineering, Software Engineering, Information Technology, Mechanical Engineering, Chemical Engineering, Plastic Engineering, Food Technology, Textile Engineering, Nano Technology & science, Power Electronics, Electronics & Communication Engineering, Computational mathematics, Image processing, Civil Engineering, Structural Engineering, Environmental Engineering, VLSI Testing & Low Power VLSI Design etc.
This document provides an overview of supply chain design and operations presented by Anqi Guo. It discusses where the presenter obtained their background from, including education and past clients. The content covers introductions to operations research and its applications in supply chain design. Case studies are presented on revitalizing a manufacturing company, designing a bike rental system, and improving a pharmacy supply chain for distributing antiviral drugs. Brief details are given on Amazon's use of algorithms to predict and stock popular products before customer orders.
Presentation of the paper titled "A Web Service for Video Smart-Cropping", by K. Apostolidis, V. Mezaris, delivered at the IEEE Int. Symposium on Multimedia (ISM), Dec. 2021. The corresponding software and dataset are available at https://github.com/bmezaris/RetargetVid.
The document discusses design verification and the Universal Verification Methodology (UVM). It describes how directed testing has drawbacks and coverage driven verification (CDV) using UVM is the recommended approach. UVM provides standard building blocks and methodologies for verification and is supported by major EDA vendors.
The document provides guidance on developing a protein purification strategy using a three phase approach - capture, intermediate purification, and polishing. It emphasizes defining objectives, understanding the target protein and contaminant properties, developing analytical assays, and limiting the number of purification steps. The goal is to purify the target protein efficiently and economically with a straightforward method.
The document provides guidance on developing a protein purification strategy using a three phase approach - capture, intermediate purification, and polishing. It emphasizes defining objectives, understanding the target protein and contaminant properties, developing analytical assays, and limiting the number of purification steps. The goal is to purify the protein efficiently and economically while maintaining activity.
The document provides guidance on developing a protein purification strategy using a three phase approach - capture, intermediate purification, and polishing. It emphasizes defining objectives, understanding the target protein and contaminant properties, developing analytical assays, and limiting the number of purification steps. The goal is to purify the target protein efficiently and economically with a straightforward method.
This document discusses using Microsoft Azure cloud computing resources to conduct genome-wide association studies (GWAS) and polygenic risk scoring (PRS) to predict COVID-19 mortality. Key steps include acquiring genotype and phenotype data, performing quality control, running GWAS and PRS analyses using HPC clusters on Azure, and downloading results. Azure provides scalable computing and storage for the large genomic datasets. Its HPC capabilities allow accelerating the analyses, which could otherwise take months to complete on-premises.
Need for Speed: Removing speed bumps from your Symfony projects ⚡️Łukasz Chruściel
No one wants their application to drag like a car stuck in the slow lane! Yet it’s all too common to encounter bumpy, pothole-filled solutions that slow the speed of any application. Symfony apps are not an exception.
In this talk, I will take you for a spin around the performance racetrack. We’ll explore common pitfalls - those hidden potholes on your application that can cause unexpected slowdowns. Learn how to spot these performance bumps early, and more importantly, how to navigate around them to keep your application running at top speed.
We will focus in particular on tuning your engine at the application level, making the right adjustments to ensure that your system responds like a well-oiled, high-performance race car.
171114 best practices for benchmarking variant calls justinGenomeInABottle
Benchmarking variant calls is challenging but important for evaluating sequencing and analysis methods. The GA4GH Benchmarking Team has developed standardized tools using Genome in a Bottle reference samples to robustly benchmark variant calls, including SNPs and indels. Their tools provide stratified performance metrics in different genomic contexts to better understand accuracy. Ongoing work focuses on more difficult variants like indels and structural variants. Standardized benchmarking allows fair comparison of methods and helps improve variant detection.
Following our latest publication, The Market for CRISPR/Cas9 Genome Editing Products, released in June 2015 on the Interactive Market Intelligence platform, a follow-up questionnaire was sent to The Science Advisory Board to quantify how the emergence of CRISPR/Cas9 technology is impacting the use of traditional tools and techniques. It was fielded between July 6-8, 2015.
To download, please go to: http://marketanalysts.lifescienceexecutive.com/blog/?p=1995
CellFree Sciences offers a cell-free protein expression platform using wheat germ extracts to rapidly produce proteins without cells. Their technology allows scalable and automated protein production from micrograms to grams, and expression of proteins difficult to produce in cell-based systems. They provide reagents, protein synthesizers, and contract research services to support protein research and production needs.
Bio-inspiring and evolutionary computation: Trends, applications and open issues workshop, 7 Nov. 2015 Faculty of Computers and Information, Cairo University
The document provides instructions for creating runs, defining protocols and graphs, viewing results, and performing background subtraction and quantification on the Smart Cycler system. It also discusses user administration, analysis settings, export options, melt analysis, and troubleshooting.
Presentation of the paper titled "Combining Global and Local Attention with Positional Encoding for Video Summarization", by E. Apostolidis, G. Balaouras, V. Mezaris, I. Patras, delivered at the IEEE Int. Symposium on Multimedia (ISM), Dec. 2021. The corresponding software is available at https://github.com/e-apostolidis/PGL-SUM.
The document presents a comparative analysis of different fault injection methods using on-chip debug (OCD) infrastructures. It describes experiments conducted using a Freescale MPC-565 microprocessor with enhanced OCD capabilities. The experiments compare basic, extended, and OCD-enhanced fault injection configurations across offline and real-time scenarios. Results show that the OCD-enhanced method enables higher fault detection rates with lower performance overhead compared to other approaches.
Search-Based Software Testing Tool Competition 2021 by Sebastiano Panichella,...Sebastiano Panichella
Sebastiano Panichella [1], Alessio Gambi [2], Fiorella Zampetti [3], Vincenzo Riccio [4]
ZURICH UNIVERSITY OF APPLIED SCIENCE (ZHAW), SWITZERLAND [1],
UNIVERSITY OF PASSAU, GERMANY [2],
UNIVERSITY OF SANNIO, ITALY [3],
UNIVERSITÀ DELLA SVIZZERA ITALIANA , SWITZERLAND [4]
The document proposes HUG, a hardware and software system to efficiently process large genomic data sets. HUG includes a hardware accelerator to speed up genomic analysis algorithms like Smith-Waterman and protein folding. It also accelerates genomic variant calling, which identifies DNA changes associated with diseases but requires comparing to large databases. The system implements regular expression matching for genomic data using a reconfigurable instruction set architecture circuit, achieving a 6x speedup over software. It aims to integrate algorithms and develop visualization tools to facilitate analysis of computed genomic data.
International Journal of Engineering Research and Applications (IJERA) is an open access online peer reviewed international journal that publishes research and review articles in the fields of Computer Science, Neural Networks, Electrical Engineering, Software Engineering, Information Technology, Mechanical Engineering, Chemical Engineering, Plastic Engineering, Food Technology, Textile Engineering, Nano Technology & science, Power Electronics, Electronics & Communication Engineering, Computational mathematics, Image processing, Civil Engineering, Structural Engineering, Environmental Engineering, VLSI Testing & Low Power VLSI Design etc.
Global Regulatory Issues: one BA method, one validation, one report ...Peter van Amsterdam
Comparison of the recent guidelines of the Brazilian, European, Japanese and US regualtory agencies on bioanalytical method validation in order to be able to validate a bioanalytical method in such a way that it would meet the requirements of these 4 agencies. Presented at the 2013 Land O'Lakes meeting
International Journal of Engineering Research and Applications (IJERA) is an open access online peer reviewed international journal that publishes research and review articles in the fields of Computer Science, Neural Networks, Electrical Engineering, Software Engineering, Information Technology, Mechanical Engineering, Chemical Engineering, Plastic Engineering, Food Technology, Textile Engineering, Nano Technology & science, Power Electronics, Electronics & Communication Engineering, Computational mathematics, Image processing, Civil Engineering, Structural Engineering, Environmental Engineering, VLSI Testing & Low Power VLSI Design etc.
This document provides an overview of supply chain design and operations presented by Anqi Guo. It discusses where the presenter obtained their background from, including education and past clients. The content covers introductions to operations research and its applications in supply chain design. Case studies are presented on revitalizing a manufacturing company, designing a bike rental system, and improving a pharmacy supply chain for distributing antiviral drugs. Brief details are given on Amazon's use of algorithms to predict and stock popular products before customer orders.
Presentation of the paper titled "A Web Service for Video Smart-Cropping", by K. Apostolidis, V. Mezaris, delivered at the IEEE Int. Symposium on Multimedia (ISM), Dec. 2021. The corresponding software and dataset are available at https://github.com/bmezaris/RetargetVid.
The document discusses design verification and the Universal Verification Methodology (UVM). It describes how directed testing has drawbacks and coverage driven verification (CDV) using UVM is the recommended approach. UVM provides standard building blocks and methodologies for verification and is supported by major EDA vendors.
The document provides guidance on developing a protein purification strategy using a three phase approach - capture, intermediate purification, and polishing. It emphasizes defining objectives, understanding the target protein and contaminant properties, developing analytical assays, and limiting the number of purification steps. The goal is to purify the target protein efficiently and economically with a straightforward method.
The document provides guidance on developing a protein purification strategy using a three phase approach - capture, intermediate purification, and polishing. It emphasizes defining objectives, understanding the target protein and contaminant properties, developing analytical assays, and limiting the number of purification steps. The goal is to purify the protein efficiently and economically while maintaining activity.
The document provides guidance on developing a protein purification strategy using a three phase approach - capture, intermediate purification, and polishing. It emphasizes defining objectives, understanding the target protein and contaminant properties, developing analytical assays, and limiting the number of purification steps. The goal is to purify the target protein efficiently and economically with a straightforward method.
This document discusses using Microsoft Azure cloud computing resources to conduct genome-wide association studies (GWAS) and polygenic risk scoring (PRS) to predict COVID-19 mortality. Key steps include acquiring genotype and phenotype data, performing quality control, running GWAS and PRS analyses using HPC clusters on Azure, and downloading results. Azure provides scalable computing and storage for the large genomic datasets. Its HPC capabilities allow accelerating the analyses, which could otherwise take months to complete on-premises.
Similar to GenoThreat / GenoGUARD -- open source biosecurity solution for the gene synthesis industry and the synthetic biology community. (20)
Need for Speed: Removing speed bumps from your Symfony projects ⚡️Łukasz Chruściel
No one wants their application to drag like a car stuck in the slow lane! Yet it’s all too common to encounter bumpy, pothole-filled solutions that slow the speed of any application. Symfony apps are not an exception.
In this talk, I will take you for a spin around the performance racetrack. We’ll explore common pitfalls - those hidden potholes on your application that can cause unexpected slowdowns. Learn how to spot these performance bumps early, and more importantly, how to navigate around them to keep your application running at top speed.
We will focus in particular on tuning your engine at the application level, making the right adjustments to ensure that your system responds like a well-oiled, high-performance race car.
UI5con 2024 - Boost Your Development Experience with UI5 Tooling ExtensionsPeter Muessig
The UI5 tooling is the development and build tooling of UI5. It is built in a modular and extensible way so that it can be easily extended by your needs. This session will showcase various tooling extensions which can boost your development experience by far so that you can really work offline, transpile your code in your project to use even newer versions of EcmaScript (than 2022 which is supported right now by the UI5 tooling), consume any npm package of your choice in your project, using different kind of proxies, and even stitching UI5 projects during development together to mimic your target environment.
Measures in SQL (SIGMOD 2024, Santiago, Chile)Julian Hyde
SQL has attained widespread adoption, but Business Intelligence tools still use their own higher level languages based upon a multidimensional paradigm. Composable calculations are what is missing from SQL, and we propose a new kind of column, called a measure, that attaches a calculation to a table. Like regular tables, tables with measures are composable and closed when used in queries.
SQL-with-measures has the power, conciseness and reusability of multidimensional languages but retains SQL semantics. Measure invocations can be expanded in place to simple, clear SQL.
To define the evaluation semantics for measures, we introduce context-sensitive expressions (a way to evaluate multidimensional expressions that is consistent with existing SQL semantics), a concept called evaluation context, and several operations for setting and modifying the evaluation context.
A talk at SIGMOD, June 9–15, 2024, Santiago, Chile
Authors: Julian Hyde (Google) and John Fremlin (Google)
https://doi.org/10.1145/3626246.3653374
Neo4j - Product Vision and Knowledge Graphs - GraphSummit ParisNeo4j
Dr. Jesús Barrasa, Head of Solutions Architecture for EMEA, Neo4j
Découvrez les dernières innovations de Neo4j, et notamment les dernières intégrations cloud et les améliorations produits qui font de Neo4j un choix essentiel pour les développeurs qui créent des applications avec des données interconnectées et de l’IA générative.
SMS API Integration in Saudi Arabia| Best SMS API ServiceYara Milbes
Discover the benefits and implementation of SMS API integration in the UAE and Middle East. This comprehensive guide covers the importance of SMS messaging APIs, the advantages of bulk SMS APIs, and real-world case studies. Learn how CEQUENS, a leader in communication solutions, can help your business enhance customer engagement and streamline operations with innovative CPaaS, reliable SMS APIs, and omnichannel solutions, including WhatsApp Business. Perfect for businesses seeking to optimize their communication strategies in the digital age.
Artificia Intellicence and XPath Extension FunctionsOctavian Nadolu
The purpose of this presentation is to provide an overview of how you can use AI from XSLT, XQuery, Schematron, or XML Refactoring operations, the potential benefits of using AI, and some of the challenges we face.
E-Invoicing Implementation: A Step-by-Step Guide for Saudi Arabian CompaniesQuickdice ERP
Explore the seamless transition to e-invoicing with this comprehensive guide tailored for Saudi Arabian businesses. Navigate the process effortlessly with step-by-step instructions designed to streamline implementation and enhance efficiency.
Revolutionizing Visual Effects Mastering AI Face Swaps.pdfUndress Baby
The quest for the best AI face swap solution is marked by an amalgamation of technological prowess and artistic finesse, where cutting-edge algorithms seamlessly replace faces in images or videos with striking realism. Leveraging advanced deep learning techniques, the best AI face swap tools meticulously analyze facial features, lighting conditions, and expressions to execute flawless transformations, ensuring natural-looking results that blur the line between reality and illusion, captivating users with their ingenuity and sophistication.
Web:- https://undressbaby.com/
What is Augmented Reality Image Trackingpavan998932
Augmented Reality (AR) Image Tracking is a technology that enables AR applications to recognize and track images in the real world, overlaying digital content onto them. This enhances the user's interaction with their environment by providing additional information and interactive elements directly tied to physical images.
Introducing Crescat - Event Management Software for Venues, Festivals and Eve...Crescat
Crescat is industry-trusted event management software, built by event professionals for event professionals. Founded in 2017, we have three key products tailored for the live event industry.
Crescat Event for concert promoters and event agencies. Crescat Venue for music venues, conference centers, wedding venues, concert halls and more. And Crescat Festival for festivals, conferences and complex events.
With a wide range of popular features such as event scheduling, shift management, volunteer and crew coordination, artist booking and much more, Crescat is designed for customisation and ease-of-use.
Over 125,000 events have been planned in Crescat and with hundreds of customers of all shapes and sizes, from boutique event agencies through to international concert promoters, Crescat is rigged for success. What's more, we highly value feedback from our users and we are constantly improving our software with updates, new features and improvements.
If you plan events, run a venue or produce festivals and you're looking for ways to make your life easier, then we have a solution for you. Try our software for free or schedule a no-obligation demo with one of our product specialists today at crescat.io
Zoom is a comprehensive platform designed to connect individuals and teams efficiently. With its user-friendly interface and powerful features, Zoom has become a go-to solution for virtual communication and collaboration. It offers a range of tools, including virtual meetings, team chat, VoIP phone systems, online whiteboards, and AI companions, to streamline workflows and enhance productivity.
Do you want Software for your Business? Visit Deuglo
Deuglo has top Software Developers in India. They are experts in software development and help design and create custom Software solutions.
Deuglo follows seven steps methods for delivering their services to their customers. They called it the Software development life cycle process (SDLC).
Requirement — Collecting the Requirements is the first Phase in the SSLC process.
Feasibility Study — after completing the requirement process they move to the design phase.
Design — in this phase, they start designing the software.
Coding — when designing is completed, the developers start coding for the software.
Testing — in this phase when the coding of the software is done the testing team will start testing.
Installation — after completion of testing, the application opens to the live server and launches!
Maintenance — after completing the software development, customers start using the software.
Microservice Teams - How the cloud changes the way we workSven Peters
A lot of technical challenges and complexity come with building a cloud-native and distributed architecture. The way we develop backend software has fundamentally changed in the last ten years. Managing a microservices architecture demands a lot of us to ensure observability and operational resiliency. But did you also change the way you run your development teams?
Sven will talk about Atlassian’s journey from a monolith to a multi-tenanted architecture and how it affected the way the engineering teams work. You will learn how we shifted to service ownership, moved to more autonomous teams (and its challenges), and established platform and enablement teams.
Essentials of Automations: The Art of Triggers and Actions in FMESafe Software
In this second installment of our Essentials of Automations webinar series, we’ll explore the landscape of triggers and actions, guiding you through the nuances of authoring and adapting workspaces for seamless automations. Gain an understanding of the full spectrum of triggers and actions available in FME, empowering you to enhance your workspaces for efficient automation.
We’ll kick things off by showcasing the most commonly used event-based triggers, introducing you to various automation workflows like manual triggers, schedules, directory watchers, and more. Plus, see how these elements play out in real scenarios.
Whether you’re tweaking your current setup or building from the ground up, this session will arm you with the tools and insights needed to transform your FME usage into a powerhouse of productivity. Join us to discover effective strategies that simplify complex processes, enhancing your productivity and transforming your data management practices with FME. Let’s turn complexity into clarity and make your workspaces work wonders!
Transform Your Communication with Cloud-Based IVR SolutionsTheSMSPoint
Discover the power of Cloud-Based IVR Solutions to streamline communication processes. Embrace scalability and cost-efficiency while enhancing customer experiences with features like automated call routing and voice recognition. Accessible from anywhere, these solutions integrate seamlessly with existing systems, providing real-time analytics for continuous improvement. Revolutionize your communication strategy today with Cloud-Based IVR Solutions. Learn more at: https://thesmspoint.com/channel/cloud-telephony
8. Industry Response to Dual Use
• 5 members (all based in
Germany)
• Undersigned by:
► 6 German or
German/American
► 2 Chinese
• “Code of Conduct for Best
Practices in Gene Synthesis”
• 5 companies (American)
• 80% of worldwide synthesis
capacity
• “Harmonized Screening
Protocol”
7/10/2014 8GenoTHREAT
10. Our Primary Objectives
1. Interpret the (draft) guidance as an algorithm
2. Implement as a software: GenoTHREAT
3. Characterize screening efficacy
7/10/2014 10GenoTHREAT
11. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the
guidance
III. GenoTHREAT: implementation and
characterization
IV. Conclusions
7/10/2014 11GenoTHREAT
12. [Guidance] : Purpose
“[…] to minimize the risk that unauthorized individuals
or individuals with malicious intent will obtain “toxins
and agents of concern” through the use of nucleic
acid synthesis technologies, and to simultaneously
minimize any negative impacts on the conduct of
research and business operations.”
7/10/2014 12GenoTHREAT
13. [Guidance] : Goals of sequence screening
• Agent of concern?
• Select Agents and Toxins
• Sequences of concern?
• “dsDNA sequences derived from or encoding Select Agents and Toxins”
• Sequence unique to select agent
• No house-keeping genes
• Both DNA strands and the six-frames translation
• Detect any “sequence of concern”
• Embedded : as small as 200bps
Use Best match approach (at least)
7/10/2014 13GenoTHREAT
16. [Guidance] : Major Points
1. Perform Six Frame Translation
2. Divide the query sequences into
subsequences of 200bp or 66aa
3. For each subsequence
i. BLAST
ii. Best Matches
iii. Flag if SAT
4. Automatic decision
7/10/2014 16GenoTHREAT
17. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
1. Perform Six Frame Translation
2. Divide the query sequences into subsequences of 200bp or 66aa
3. For each subsequence
i. BLAST
ii. Best Matches
iii. Flag if SAT
4. Automatic decision
III. GenoTHREAT: implementation and characterization
IV. Conclusions
7/10/2014 17GenoTHREAT
20. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
1. Perform Six Frame Translation
2. Divide the query sequences into subsequences of 200bp or 66aa
3. For each subsequence
i. BLAST
ii. Best Matches
iii. Flag if SAT
4. Automatic decision
III. GenoTHREAT: implementation and characterization
IV. Conclusions
7/10/2014 20GenoTHREAT
22. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
1. Perform Six Frame Translation
2. Divide the query sequences into subsequences of 200bp or 66aa
3. For each subsequence
i. BLAST
ii. Best Matches
iii. Flag if SAT
4. Automatic decision
III. GenoTHREAT: implementation and characterization
IV. Conclusions
7/10/2014 22GenoTHREAT
23. [Algorithm] : What should we do with
subsequences?
7/10/2014 GenoTHREAT 23
24. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
1. Perform Six Frame Translation
2. Divide the query sequences into subsequences of 200bp or 66aa
3. For each subsequence
i. BLAST
ii. Best Matches
iii. Flag if SAT
4. Automatic decision
III. GenoTHREAT: implementation and characterization
IV. Conclusions
7/10/2014 24GenoTHREAT
26. Basic Local Alignment Search Tool (BLAST)
• Developed at the U.S. National Center for
Biotechnology Information
• One of the most widely used bioinformatics tools
• Aligns query sequences against sequences in the
GenBank sequence database
• Algorithm emphasizes speed over sensitivity
7/10/2014 26GenoTHREAT
28. BLAST Output
Percent Identity
► The percentage of identical nucleotides (or amino acid) in
the sequence aligned
Query Coverage
► The length of sequence aligned
7/10/2014 28GenoTHREAT
29. [Algorithm] : What should we do with all
those results of BLAST?
7/10/2014 29GenoTHREAT
30. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
1. Perform Six Frame Translation
2. Divide the query sequences into subsequences of 200bp or 66aa
3. For each subsequence
i. BLAST
ii. Best Matches
iii. Flag if SAT
4. Automatic decision
III. GenoTHREAT: implementation and characterization
IV. Conclusions
7/10/2014 30GenoTHREAT
31. [Guidance] : The Best match approach
• Use local sequence alignment tool
• suggest Blast
• Best matches = greatest percent identity over
the entire fragment
• 66AA or 200bps fragments
7/10/2014 31GenoTHREAT
34. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
1. Perform Six Frame Translation
2. Divide the query sequences into subsequences of 200bp or 66aa
3. For each subsequence
i. BLAST
ii. Best Matches
iii. Flag if SAT
4. Automatic decision
III. GenoTHREAT: implementation and characterization
IV. Conclusions
7/10/2014 34GenoTHREAT
36. [Algorithm] : How can we know if a Best
Match is to a Select Agent or Toxin?
Problem: no suggestion in guidance
Solution:
keyword
and anti-keyword list
7/10/2014 36GenoTHREAT
37. BLAST
[Example] : Is this subsequence a
hit?
7/10/2014 GenoTHREAT 37
BLAST results PI QC (%)
Bacillus anthracis 100 100
Bacillus anthracis str. Sterne 100 100
Danio rerio 97 100
Danio rerio 43 80
Best matches
Bacillus anthracis
Bacillus anthracis str. Sterne
38. [Example] : Keyword vs. Anti-keyword
If a GenBank entry contains a keyword, then the
sequence is flagged
SA
7/10/2014 38GenoTHREAT
39. [Example] : Keyword vs. Anti-keyword
If a GenBank entry contains both a keyword and anti-
keyword, the order is not flagged
NSA
7/10/2014 39GenoTHREAT
45. [Algorithm] : Points of the Guidance left to
interpretation
How do you identify sequences of concern of 200bp or
greater which partially span two adjacent
subsequences?
Problem: no suggestion in guidance
Solution: extension method
7/10/2014 45GenoTHREAT
58. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
1. Perform Six Frame Translation
2. Divide the query sequences into subsequences of 200bp or 66aa
3. For each subsequence
i. BLAST
ii. Best Matches
iii. Flag if SAT
4. Automatic decision
III. GenoTHREAT: implementation and characterization
IV. Conclusions
7/10/2014 58GenoTHREAT
60. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
III. GenoTHREAT: implementation and characterization
1. Software implementation
2. Software Characterization
IV. Conclusions
7/10/2014 60GenoTHREAT
61. Using BLAST
Online BLAST
Performs BLAST via NCBI
website interface
► Faster per BLAST
► Computationally less
expensive
► Only sequential, due to NCBI
restrictions
► Lack of privacy
Local BLAST
Performs BLAST in parallel on
local machine
► User privacy
► Faster per sequence due to
parallelization
► Computational expensive
(Memory + CPU intensive )
7/10/2014 GenoTHREAT 61
62. Screening time & hardware
7/10/2014 GenoTHREAT 62
Online Desktop Business Class Server
Sequence length (bp) Screening time (min)*
2,000 2
10,000 12.5
*Screening performed using business class server
63. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
III. GenoTHREAT: implementation and characterization
1. Software implementation
2. Software Characterization
i. Database of test sequences
ii. Keyword list variation
iii. Detection of Potentially dangerous sequences
iv. BLAST parameters
v. Real world gene orders simulation
IV. Conclusions
7/10/2014 63GenoTHREAT
64. Database of Test Sequences
• Implementations must be compared to assess quality
• Standardized set of test sequences is needed
• Test Set contains 184 sequences:
• Select Agents
o Genes associated with toxins or pathogenicity
o Genes associated with normal function
• Model Organisms
64
7/10/2014 64GenoTHREAT
65. Database of Test Sequences
Contribute to the development of a standard test set
of sequences
65
7/10/2014 65GenoTHREAT
66. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
III. GenoTHREAT: implementation and characterization
1. Software implementation
2. Software Characterization
i. Database of test sequences
ii. Keyword list variation
iii. Detection of Potentially dangerous sequences
iv. BLAST parameters
v. Real world gene orders simulation
IV. Conclusions
7/10/2014 66GenoTHREAT
67. Keyword and Anti-Keyword list
• Test with the unmodified sequences (184 sequences)
• Two lists of keywords
• Limited
• extensive
• Plus
• anti-keyword list
• or not
7/10/2014 67GenoTHREAT
68. Keyword List Content Variation
7/10/2014 GenoTHREAT 68
0
20
40
60
80
100
120
Limited keywords Extensivekeywords
Correct SAT Correct NSAT
Keyword list method not mentioned in guidance
Limited keyword
list:
uniquely composed
of words in SAT List
Extensive keyword
list:
extension of limited
keyword list
containing words
uniquely related to
SAT.
70. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
III. GenoTHREAT: implementation and characterization
1. Software implementation
2. Software Characterization
i. Database of test sequences
ii. Keyword list variation
iii. Detection of potentially dangerous sequences
iv. BLAST parameters
v. Real world gene orders simulation
IV. Conclusions
7/10/2014 70GenoTHREAT
71. Modified Test Sequences
Modification performed on the initial unmodified
sequences
► Intervening sequences
► Degenerate sequences
► Mutated sequences (BLAST parameters)
7/10/2014 71GenoTHREAT
72. Degenerate Sequences
Potential Danger: Codon optimized nucleotide sequences
7/10/2014 GenoTHREAT 72
GATTTGGACACTCATTTCACC
DLDTHFT
Unmodified Nucleotide
Degenerate
NucleotideGATACGTCAACCTTTTAA
GC
Amino Acid
Sequence
Result: all codon optimized sequences detected due to screening of amino acid
sequences
73. Intervening sequences
Potential Danger: SAT sequences hidden within larger, benign sequences
300bps
NSAT
200bps
SAT
300bps
NSAT
300bps
NSAT
300bps
NSAT
250bps
SAT
7/10/2014 73GenoTHREAT
Result: All hidden sequences were detected
74. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
III. GenoTHREAT: implementation and characterization
1. Software implementation
2. Software Characterization
i. Database of test sequences
ii. Keyword list variation
iii. Detection of Potentially dangerous sequences
iv. BLAST parameters
v. Real world gene orders simulation
IV. Conclusions
7/10/2014 74GenoTHREAT
80. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
III. GenoTHREAT: implementation and characterization
1. Software implementation
2. Software Characterization
i. Database of test sequences
ii. Keyword list variation
iii. Detection of Potentially dangerous sequences
iv. BLAST parameters
v. Real world gene orders simulation
IV. Conclusions
7/10/2014 80GenoTHREAT
81. Real world gene orders simulation
Gene Synthesis company: low number of false hit
needed
1. iGEM registry
• Registry completed by iGEM teams each year
• Contains 10,000 sequences
2. GenoCAD database
• 1,258 sequences longer than 200 bp
7/10/2014 81GenoTHREAT
82. iGEM Registry
First step: screen registry sequences 1-->1724
Hit rate: 6.5%
Major causes of hits:
• 100% query coverage for Best Match too restrictive
• Some results have 100% query coverage but very low
Percent Identity
• Keyword list issues
7/10/2014 82GenoTHREAT
95%
60%
solved
2.9%
85. Real world gene orders simulation
Hits left are due to:
• Very often: 1 subsequence of 1 Protein frame leads
to a correct hit
Is it worth flagging the entire sequence?
• Sometimes: many subsequences leads to correct hits
Probably worth flagging
7/10/2014 85GenoTHREAT
86. Road Map
I. Current regulations
II. Sequence screening algorithm: interpreting the guidance
III. GenoTHREAT: implementation and characterization
IV. Conclusions
7/10/2014 86GenoTHREAT
87. GenoTHREAT
• “Best Match”
• Hardware and software parameters
• Keyword list
• BLAST parameters
• Certain types of sequence modifications
• High-resolution screen
7/10/2014 87GenoTHREAT
88. Guidance conclusion
Government Guidance potentially usable by
companies:
• Reasonable time
• Good detection of sequences of concern
• Number of false hits potentially low (manual review)
7/10/2014 88GenoTHREAT
94. 7/10/2014 GenoTHREAT 94
A T A A C T C C C T G G G T C G T T A A A C C G G
C G G C T G C G G C A G T C T T A G C A T A A T A
A T C G G A T A G C A C T T T A T G A C C T G T C
G T C G G G G C A C T A A A T G A A C T A G T G G
C A G T A A C T G T C A G G C A G C A T A T A C A
A C G T T C A A A T A A C T G C A T A G A A C C C
A G A A T A A C T A C C A C C A C C G A A T C T T
T A T C C A G A C G A C T G C A T G A C T C G C T
T C T A C G A C G G T G A A T G A C G T T G G G T
T G C G T C G C A T G G T A C C T A C T T A A C T
T C G G T C G C T C A A T G A T C T G C A A A A G
A A T C G G C T A T T G G A C T C C T A G G C G C
G T C T T A T A T A T G C G G C G C T T T T A C G
A T C C G G A C A T A A T C T A A G G T A T C G T
A C G C G C G G G A A C A C G A G G T T G T A A C
A C C G T A G C T A T C T C A T G C A T T C C G A
C C A G C G G T T A T A T A A T A C T C G T T T T
T T C C G C G T G C C A T C A T A C G A C G C T G
G C C G C C G C G T T A G T G T C G T G T G T A C
A C A C C G A G T T A C C C T C C T T C G T T C G
C A C C A G C G T T A C T G C G T G T A G A G G A
A A T T G G C T T G A G A G C T T T G C C C C A C
C G C A C G A G G T A A C T A T T G A G A T C A G
T C T A C A G A G T G C A A T A C A C C A A C G C
http://sourceforge.net/projects/genothreat/
95. Acknowledgeme
nts
Dr. Jean Peccoud
Mandy L. Wilson
The VT-ENSIMAG iGEM team (2010):
Michael Kozar
Gaelle Letort
Olivier Mirat
Arunima Srivastava
Tyler Stewart
My PhD committee:
Dr. Bevan
Dr. Garner
Dr. Peccoud
Dr. Ramakrishnan
Dr. Setubal
7/10/2014 GenoTHREAT 95