Musite is a tool for predicting protein phosphorylation sites. It uses machine learning models trained on features like amino acid frequencies, disorder scores, and KNN scores to classify sites as phosphorylated or not. Musite offers both general and kinase-specific phosphorylation site prediction. It is open source software that can perform predictions across entire proteomes more accurately than other tools, and it allows for customized model training.
Progenra Ubi Pro Drug Discovery Platform E3 Ligasemhixson
Progenra has developed the UbiProTM drug discovery platform for quantifying and characterizing the activity of ubiquitin ligase enzymes. This platform uses homogeneous assays that closely mimic physiological conditions and can be used to identify inhibitors of deubiquitylating enzymes and E3 ligases through high throughput screening. Progenra has accumulated a large collection of ubiquitin enzymes and substrates to enable drug discovery efforts. The platform provides advantages over traditional assays such as identifying compounds that may be missed by other assays and characterizing E3 ligase and substrate interactions.
This document outlines the key factors for success of a mobile offers app. It discusses how mobile is influencing retail sales and the coupons industry. The app will provide all major offer types in one place to offer value to both consumers and merchants. Success will rely on optimizing the user experience, effective targeting, distribution methods, and partnerships to source offers and content. The total addressable market for mobile offers is approximately $4 billion across various offer categories.
The document provides an architectural description of the reconstruction of Himeji Castle in Second Life. It summarizes the key defensive design features of the original Tenshukaku keep, including intricate internal paths to confuse invaders, hidden entrances, and extra concealed floors for important figures. The reconstruction aims to faithfully recreate these defensive characteristics at a 1:1 scale while also capturing the castle's aesthetic beauty and balance of textures between rooftops and smooth white plaster walls.
ONTO-Toolkit is a collection of tools within the Galaxy framework that enables bio-ontology engineering using OBO file format ontologies. It includes wrappers for functions from the ONTO-PERL API to retrieve ontology terms and substructures. Two use cases are demonstrated: 1) identifying common ancestor terms between two molecular functions, and 2) finding the intersection between sub-ontologies for two biological processes to investigate overlap. The toolkit provides rich ontology-driven solutions for biologists within Galaxy.
The document discusses different file formats and processing approaches for large SNP genotype datasets. It notes that processing 5 million data items with one CPU would take 2+ days, but distributing the work across eight CPUs could reduce it to 1-2 days. A new "matrix" file format where SNPs are columns and samples are rows allowed processing 12 million items on one CPU in about 30 minutes. The document recommends exploring solutions beyond just parallel processing, as file format changes can also simplify work, and dividing complex tasks between humans and computers.
C:\Users\The Andersens\Desktop\Karin\I Wanna Learn To Play Like The Dolphinskkindig
This document discusses different types of dolphins including bottle-nose dolphins, rough-toothed dolphins, spotted dolphins, and spinner dolphins. It provides information on their physical characteristics, habitat, and behavior. Bottle-nose, rough-toothed, spotted, and spinner dolphins can commonly be found in the waters surrounding Hawaii. Dolphins are highly social creatures that live in pods and communicate through clicks, whistles, and other vocalizations. They display playful and compassionate behaviors.
- Water is a major issue for manufacturing and exporting companies as two-thirds of the population will live in risky water conditions by 2025 and industries are extracting more water, especially in pulp/paper, oil, and metallurgy.
- Quebec holds over 3% of the world's water reserves but has unmatched daily consumption of 400 liters per person. There is a growing lobby to export water from Quebec.
- Cascades acknowledges water could generate revenue for the government but believes consumption in Quebec must reduce first through increased costs and incentives before exporting water saved. Cascades has significantly reduced its own water usage and wastewater.
Progenra Ubi Pro Drug Discovery Platform E3 Ligasemhixson
Progenra has developed the UbiProTM drug discovery platform for quantifying and characterizing the activity of ubiquitin ligase enzymes. This platform uses homogeneous assays that closely mimic physiological conditions and can be used to identify inhibitors of deubiquitylating enzymes and E3 ligases through high throughput screening. Progenra has accumulated a large collection of ubiquitin enzymes and substrates to enable drug discovery efforts. The platform provides advantages over traditional assays such as identifying compounds that may be missed by other assays and characterizing E3 ligase and substrate interactions.
This document outlines the key factors for success of a mobile offers app. It discusses how mobile is influencing retail sales and the coupons industry. The app will provide all major offer types in one place to offer value to both consumers and merchants. Success will rely on optimizing the user experience, effective targeting, distribution methods, and partnerships to source offers and content. The total addressable market for mobile offers is approximately $4 billion across various offer categories.
The document provides an architectural description of the reconstruction of Himeji Castle in Second Life. It summarizes the key defensive design features of the original Tenshukaku keep, including intricate internal paths to confuse invaders, hidden entrances, and extra concealed floors for important figures. The reconstruction aims to faithfully recreate these defensive characteristics at a 1:1 scale while also capturing the castle's aesthetic beauty and balance of textures between rooftops and smooth white plaster walls.
ONTO-Toolkit is a collection of tools within the Galaxy framework that enables bio-ontology engineering using OBO file format ontologies. It includes wrappers for functions from the ONTO-PERL API to retrieve ontology terms and substructures. Two use cases are demonstrated: 1) identifying common ancestor terms between two molecular functions, and 2) finding the intersection between sub-ontologies for two biological processes to investigate overlap. The toolkit provides rich ontology-driven solutions for biologists within Galaxy.
The document discusses different file formats and processing approaches for large SNP genotype datasets. It notes that processing 5 million data items with one CPU would take 2+ days, but distributing the work across eight CPUs could reduce it to 1-2 days. A new "matrix" file format where SNPs are columns and samples are rows allowed processing 12 million items on one CPU in about 30 minutes. The document recommends exploring solutions beyond just parallel processing, as file format changes can also simplify work, and dividing complex tasks between humans and computers.
C:\Users\The Andersens\Desktop\Karin\I Wanna Learn To Play Like The Dolphinskkindig
This document discusses different types of dolphins including bottle-nose dolphins, rough-toothed dolphins, spotted dolphins, and spinner dolphins. It provides information on their physical characteristics, habitat, and behavior. Bottle-nose, rough-toothed, spotted, and spinner dolphins can commonly be found in the waters surrounding Hawaii. Dolphins are highly social creatures that live in pods and communicate through clicks, whistles, and other vocalizations. They display playful and compassionate behaviors.
- Water is a major issue for manufacturing and exporting companies as two-thirds of the population will live in risky water conditions by 2025 and industries are extracting more water, especially in pulp/paper, oil, and metallurgy.
- Quebec holds over 3% of the world's water reserves but has unmatched daily consumption of 400 liters per person. There is a growing lobby to export water from Quebec.
- Cascades acknowledges water could generate revenue for the government but believes consumption in Quebec must reduce first through increased costs and incentives before exporting water saved. Cascades has significantly reduced its own water usage and wastewater.
The document discusses the benefits of implementing a sustainable workplace program called Enhancing Furniture's Environmental Culture (EFEC) at an upholstery company called C.R. Laine. After joining the EFEC program, C.R. Laine formed an environmental committee to evaluate its processes and impacts. In its first year in the program, C.R. Laine saved over $50,000 through initiatives like turning off lights and implementing recycling. The document emphasizes that sustainability programs require commitment from all levels of a company and that gradual improvements can lead to significant benefits over time.
This document provides tips for Nordic e-commerce companies to enter new markets. It discusses the importance of prioritizing foreign customers by understanding their needs, translating all text to the local language, and providing customer service in that language. The document outlines 10 easy steps companies can take, including using local payment options, phone numbers, addresses and logos to appear local. It also shares the story of CoolStuff, a Swedish company that successfully expanded to Denmark and Germany by following these best practices. Their sales in those foreign markets now make up 40% and 14% of total sales respectively.
Оптимизация интерактивного тестирования с использованием метрики Покрытие кодаSPB SQA Group
Доклад посвящен исследованию возможности оптимизации количества запускаемых интерактивных тестов базируясь на оценке покрытия. Как пример, приведены результаты, которых мы достигли в нашей компании — обоснованное уменьшение количества запускаемых тестов с ~900 до ~130. Также освещены некоторые аспекты работы с метрикой «покрытие кода».
This document summarizes a study that used interferometric synthetic aperture radar (InSAR) observations to analyze ground deformation from the 1995 eruption of Fogo volcano in Cape Verde. The key findings were:
1. InSAR data showed ground deformation due to intrusion of a two-segment feeder dike for the eruption, but no evidence of deformation from changes in a shallow magma reservoir.
2. Modeling suggests the dike intruded at a depth of around 2 km.
3. The lack of shallow reservoir involvement and modeling of eruption volumes indicates the magma source was deep, at least 16.5 km below the surface.
4. This supports the
RefWorks for DEPARTMENT OF FAMILY MEDICINE - Faculty Development Naz Torabi
This document provides an overview of how to use RefWorks, a bibliographic citation manager. It describes how to set up a RefWorks account, import references from various sources directly or indirectly, organize references into folders, share folders, create bibliographies, and access RefWorks off-campus. It also summarizes the features of RefWorks for saving citations, organizing research, and creating bibliographies from included citations in papers. Contact information is provided for getting help with RefWorks.
This document provides guidance on developing an effective marketing strategy. It stresses the importance of thorough research into the competition, brand, audience, and budget before creating a unique solution. Key aspects to consider include defining the product's positioning, identifying the target audience and how to communicate with them, and determining what feelings or benefits the product provides users. Measurement and getting feedback are also emphasized in order to continuously improve the strategy. The overall message is that planning, understanding the marketplace, and creating value for customers are essential for marketing success.
This document discusses Purdue University's approach to academics for student-athletes. It explains that Purdue demands excellence from athletes both on and off the field. The Inter-collegiate Athletic Facility (IAF) aids student-athletes in their studies by providing tutoring sessions and space for extended work. If a student-athlete's GPA falls below 3.0, daily tutoring is mandatory. The IAF offers various study locations and plays a major role in Purdue's success in developing student-athletes.
This document provides an overview of Advanced Nutrients and what makes them different than other hydroponic nutrient companies. They view customers as clients and prioritize clients' long-term success. Advanced Nutrients is an industry innovator, having created more industry firsts than any other hydroponics company through extensive research and testing. They aim to provide clients with the best products, information, and results for their crops.
This is a power point presentation providing helpful info on different style\'s & common repair\'s of roof systems in the Southwest region of the United States.
Academic Honesty at Oxford College of Emory University: Fall 2011oxfordcollegelibrary
This document provides guidance on academic honesty and properly citing sources. It discusses citing direct quotes, paraphrases, and indirect citations from sources in writing. For a direct quote, the exact words from the source must be used along with a citation. A paraphrase restates the idea in your own words and still requires a citation. An indirect citation refers to an idea from a source but does not use a direct quote; the source must still be included in the citation. The document encourages asking for help on citations from professors, librarians, and writing centers to avoid plagiarism. No more than 10% of a paper should be direct quotes, and paraphrasing is important for properly citing sources without plagiarizing
The document discusses recommendations for a wireless carrier entering the mHealth industry. It provides an overview of trends in healthcare spending and delivery that are driving growth in mHealth. The mHealth market structure and service categories are described, showing remote monitoring as the largest segment. Partnerships with technology companies and healthcare providers are identified as key to success. Revenue models and the potential for incremental revenue are presented. The evolution of mHealth services from wellness to integrated solutions is depicted. Competitors and growth challenges are outlined. Recommendations focus on strategic partnerships, thought leadership, and executing a long-term vision to succeed in mHealth.
The document discusses social login and single sign-on (SSO) services. It describes how aggregators help publishers integrate social login and other functions by connecting them to identity providers. Gigya is highlighted as an aggregator that offers APIs and plugins allowing over 500,000 websites to offer social login through major identity providers like Facebook and Google. Users must consent to what personal data is shared during the social login process.
The document discusses an introduction to Drupal theming. It covers how Drupal's template system works, what Drupal theming is defined as, and the tools needed to get started with Drupal theming, including an understanding of HTML and CSS, a Drupal install, and a code editor. It also lists some Drupal projects that are useful for theming. The presentation plans to then move past slides and do a live theme building demonstration.
The Microsoft Biology Foundation (MBF) is an open-source library of bioinformatics algorithms and services built on .NET. MBF provides modular and reusable code for tasks like genomics, sequencing, and analysis. It leverages existing Microsoft technologies and allows distribution of computations across platforms from local to cloud. The first version was released in June 2010. MBF is developed openly on CodePlex and aims to benefit both commercial and non-commercial users.
The document discusses using cloud-scale computing for genomic analysis. It provides timing and cost estimates for running a genomic analysis pipeline called Myrna on Amazon EC2 using different numbers of compute nodes. The analysis of 1.1 billion reads would take 4 hours and 20 minutes on 1 master and 10 worker nodes at a cost of $44, or 1 hour and 38 minutes on 1 master and 40 workers at a cost of $66. It also discusses strategies for running genomic tools on cloud infrastructure or single computers.
The document discusses the benefits of implementing a sustainable workplace program called Enhancing Furniture's Environmental Culture (EFEC) at an upholstery company called C.R. Laine. After joining the EFEC program, C.R. Laine formed an environmental committee to evaluate its processes and impacts. In its first year in the program, C.R. Laine saved over $50,000 through initiatives like turning off lights and implementing recycling. The document emphasizes that sustainability programs require commitment from all levels of a company and that gradual improvements can lead to significant benefits over time.
This document provides tips for Nordic e-commerce companies to enter new markets. It discusses the importance of prioritizing foreign customers by understanding their needs, translating all text to the local language, and providing customer service in that language. The document outlines 10 easy steps companies can take, including using local payment options, phone numbers, addresses and logos to appear local. It also shares the story of CoolStuff, a Swedish company that successfully expanded to Denmark and Germany by following these best practices. Their sales in those foreign markets now make up 40% and 14% of total sales respectively.
Оптимизация интерактивного тестирования с использованием метрики Покрытие кодаSPB SQA Group
Доклад посвящен исследованию возможности оптимизации количества запускаемых интерактивных тестов базируясь на оценке покрытия. Как пример, приведены результаты, которых мы достигли в нашей компании — обоснованное уменьшение количества запускаемых тестов с ~900 до ~130. Также освещены некоторые аспекты работы с метрикой «покрытие кода».
This document summarizes a study that used interferometric synthetic aperture radar (InSAR) observations to analyze ground deformation from the 1995 eruption of Fogo volcano in Cape Verde. The key findings were:
1. InSAR data showed ground deformation due to intrusion of a two-segment feeder dike for the eruption, but no evidence of deformation from changes in a shallow magma reservoir.
2. Modeling suggests the dike intruded at a depth of around 2 km.
3. The lack of shallow reservoir involvement and modeling of eruption volumes indicates the magma source was deep, at least 16.5 km below the surface.
4. This supports the
RefWorks for DEPARTMENT OF FAMILY MEDICINE - Faculty Development Naz Torabi
This document provides an overview of how to use RefWorks, a bibliographic citation manager. It describes how to set up a RefWorks account, import references from various sources directly or indirectly, organize references into folders, share folders, create bibliographies, and access RefWorks off-campus. It also summarizes the features of RefWorks for saving citations, organizing research, and creating bibliographies from included citations in papers. Contact information is provided for getting help with RefWorks.
This document provides guidance on developing an effective marketing strategy. It stresses the importance of thorough research into the competition, brand, audience, and budget before creating a unique solution. Key aspects to consider include defining the product's positioning, identifying the target audience and how to communicate with them, and determining what feelings or benefits the product provides users. Measurement and getting feedback are also emphasized in order to continuously improve the strategy. The overall message is that planning, understanding the marketplace, and creating value for customers are essential for marketing success.
This document discusses Purdue University's approach to academics for student-athletes. It explains that Purdue demands excellence from athletes both on and off the field. The Inter-collegiate Athletic Facility (IAF) aids student-athletes in their studies by providing tutoring sessions and space for extended work. If a student-athlete's GPA falls below 3.0, daily tutoring is mandatory. The IAF offers various study locations and plays a major role in Purdue's success in developing student-athletes.
This document provides an overview of Advanced Nutrients and what makes them different than other hydroponic nutrient companies. They view customers as clients and prioritize clients' long-term success. Advanced Nutrients is an industry innovator, having created more industry firsts than any other hydroponics company through extensive research and testing. They aim to provide clients with the best products, information, and results for their crops.
This is a power point presentation providing helpful info on different style\'s & common repair\'s of roof systems in the Southwest region of the United States.
Academic Honesty at Oxford College of Emory University: Fall 2011oxfordcollegelibrary
This document provides guidance on academic honesty and properly citing sources. It discusses citing direct quotes, paraphrases, and indirect citations from sources in writing. For a direct quote, the exact words from the source must be used along with a citation. A paraphrase restates the idea in your own words and still requires a citation. An indirect citation refers to an idea from a source but does not use a direct quote; the source must still be included in the citation. The document encourages asking for help on citations from professors, librarians, and writing centers to avoid plagiarism. No more than 10% of a paper should be direct quotes, and paraphrasing is important for properly citing sources without plagiarizing
The document discusses recommendations for a wireless carrier entering the mHealth industry. It provides an overview of trends in healthcare spending and delivery that are driving growth in mHealth. The mHealth market structure and service categories are described, showing remote monitoring as the largest segment. Partnerships with technology companies and healthcare providers are identified as key to success. Revenue models and the potential for incremental revenue are presented. The evolution of mHealth services from wellness to integrated solutions is depicted. Competitors and growth challenges are outlined. Recommendations focus on strategic partnerships, thought leadership, and executing a long-term vision to succeed in mHealth.
The document discusses social login and single sign-on (SSO) services. It describes how aggregators help publishers integrate social login and other functions by connecting them to identity providers. Gigya is highlighted as an aggregator that offers APIs and plugins allowing over 500,000 websites to offer social login through major identity providers like Facebook and Google. Users must consent to what personal data is shared during the social login process.
The document discusses an introduction to Drupal theming. It covers how Drupal's template system works, what Drupal theming is defined as, and the tools needed to get started with Drupal theming, including an understanding of HTML and CSS, a Drupal install, and a code editor. It also lists some Drupal projects that are useful for theming. The presentation plans to then move past slides and do a live theme building demonstration.
The Microsoft Biology Foundation (MBF) is an open-source library of bioinformatics algorithms and services built on .NET. MBF provides modular and reusable code for tasks like genomics, sequencing, and analysis. It leverages existing Microsoft technologies and allows distribution of computations across platforms from local to cloud. The first version was released in June 2010. MBF is developed openly on CodePlex and aims to benefit both commercial and non-commercial users.
The document discusses using cloud-scale computing for genomic analysis. It provides timing and cost estimates for running a genomic analysis pipeline called Myrna on Amazon EC2 using different numbers of compute nodes. The analysis of 1.1 billion reads would take 4 hours and 20 minutes on 1 master and 10 worker nodes at a cost of $44, or 1 hour and 38 minutes on 1 master and 40 workers at a cost of $66. It also discusses strategies for running genomic tools on cloud infrastructure or single computers.
This document summarizes a study on the persistence and availability of bioinformatics web services. The study analyzed over 900 web services listed in the Nucleic Acids Research journal between 2003-2009. It found that 17% of the original web addresses were no longer reachable. More recent services had higher quality standards but 24% of authors said their services would not be maintained long-term. The document provides recommendations for web service authors to improve long-term availability, such as using persistent URLs, releasing source code, and planning for the future maintenance of the service.
The document describes MOLGENIS, an open-source software system that allows users to define data models and generate full-featured web applications and databases from those models. Key features include a graphical user interface, database integration, support for common data formats, and the ability to rapidly develop applications by editing simple domain-specific models. The system has been applied to build several genomic and biomedical databases.
The document provides an update on the EMBOSS European Molecular Biology Open Software Suite project. It discusses new features added in the latest release including support for next-generation sequencing formats, additional data sources, and integration of ontologies. The EMBOSS team continues to work on improving interfaces and providing support to other projects.
The document discusses Evoker, a visualization tool for genotype intensity data from genome-wide association studies (GWAS). It provides background on GWAS and highlights the importance of rigorous quality control procedures for GWAS to eliminate sources of false positives like poor quality DNA, population structure, and genotyping artifacts. The document then discusses Evoker's implementation and software features for visualizing quality control metrics and genotype intensity data to assist with quality control checks.
This document contains 6 repeated links to the website http://www.g-language.org/PathwayProjector. The links all point to a pathway projection tool on the G-language website that can be used to visualize biological pathways.
This document discusses establishing a national repository for microarray gene expression data using MOLGENIS and MAGE-TAB. The objectives are to populate the repository with well-annotated microarray experiments from over 6,500 biobank samples, share the software as a microarray database solution for all biobanks, and combine gene expression data with GWAS studies to create novel eQTL datasets for complex diseases. The repository was created using MOLGENIS and populated with over 12,000 curated experiments from GEO and ArrayExpress for testing purposes. Future work includes populating with local data, integrating analysis tools, and enabling data and tool sharing between local installations while maintaining privacy.
This document discusses using Python to access libraries implemented in R through Bioconductor. It provides background on both Bioconductor and popular Python libraries for bioinformatics. As an example, it shows how to run an edgeR analysis from Python to identify differentially expressed genes from microarray data, accessing the R code and edgeR package from Python. This allows leveraging powerful statistical methods from R while taking advantage of Python's scripting abilities.
The document discusses the history and operations of the Apache Software Foundation. It began in 1995 with 8 developers working on the Apache HTTP Server. It is now a large organization with over 2,500 committers across 70+ projects. The ASF operates under an open governance model called "The Apache Way" which emphasizes merit-based consensus decision making. It also discusses how the ASF scales its operations through project oversight, incubating new projects, and community education programs like mentoring.
This document describes IPRStats, a visualization tool for InterProScan results. IPRStats allows users to view summaries and charts of protein domain annotations from InterProScan. It imports InterProScan XML files, generates statistics and taxonomy summaries, and exports results as HTML or Excel files. IPRStats uses a wxPython GUI, SQLite or PyTables for data storage, and generates pie charts, bar graphs and other visualizations of the annotation data.
The document summarizes updates to BioPerl, an open source Perl package for biological research. It discusses addressing new bioinformatics problems through collaborations, using modern Perl features to lower the barrier for new users, and potential approaches for BioPerl 2.0, including using Moose and preparing for Perl 6. The core of BioPerl provides classes for biological sequences, sequence I/O and features.
This document discusses the challenges of open source biological software projects including community engagement, integration with other tools, and increasing accessibility (democratization). It provides examples of how the Biopython project addresses these challenges such as through the Google Summer of Code program, improving documentation, and leveraging cloud computing resources to more easily distribute and access data and tools.
BioRuby is a bioinformatics library for the Ruby programming language. It provides object-oriented tools for tasks like sequence analysis, format conversion, running bioinformatics tools, and working with biological data. The latest version added features like improved support for phylogenetic XML (PhyloXML), next-generation sequencing FASTQ format reading/writing, and a REST API wrapper for the NCBI database. BioRuby development follows agile principles and its large developer community contributes new code frequently on GitHub. The project aims to improve integration with R and data visualization while maintaining a stable core.
This document discusses BioPython modules for handling RNA sequences containing modified nucleosides. There are 115 known post-transcriptionally modified nucleosides in RNA and several nomenclature schemes exist. The solution involves cloning a branch of the BioPython repository containing an RNA alphabet with modified nucleotides and using it to represent sequences containing modifications like 2-O-methyloadenosine. Example applications presented are ModeRNA for RNA structure modeling and CompaRNA for benchmarking RNA structure prediction methods, both of which use open source tools including BioPython.
Cytoscape Web is an interactive, web-based network browser that is a pared down version of Cytoscape, an open source software platform for visualizing and analyzing molecular interaction networks. It allows users to visualize networks, perform basic operations like filtering nodes and edges, and export images of the network. Performance depends on factors like the number of elements in the network, with networks over 2000 elements usually sluggish.
Bio.Phylo is a new phylogenetics library in Biopython for exploring, modifying, annotating, reading, writing, and visualizing trees and for connecting computational pipelines. It supports common file formats like Newick and Nexus and can read/write the XML-based PhyloXML format which allows for annotations. The demo shows how to read a Newick tree, inspect it, draw it, promote it to PhyloXML to add branch colors, and write it out.
Archaeopteryx is a tool for visualizing and analyzing evolutionary trees. It is based on ATV and built using the open source Forester framework. Archaeopteryx allows users to visualize large trees with over 20,000 nodes. It supports various file formats and can access online databases. Key features include zooming, duplication inference tools, and editing trees. An example biological study analyzed functional profiles of genomes using Forester, phyloXML, and Archaeopteryx.
The document discusses the transition from BioMoby to SADI as a framework for semantic web services. It provides statistics on BioMoby usage and describes demonstrations of complex queries being answered through SADI and SHARE without a centralized database. The demonstrations include finding pathways for a protein and lab results for transplant patients. It advocates for SADI to support the scientific method and personal hypotheses through distributed ontologies rather than centralized ones.
This document provides an overview of the Hadoop/MapReduce/HBase framework and its applications in bioinformatics. It discusses Hadoop and its components, how MapReduce programs work, HBase which enables random access to Hadoop data, related projects like Pig and Hive, and examples of applications in bioinformatics and benchmarking of these systems.
What is an RPA CoE? Session 1 – CoE VisionDianaGray10
In the first session, we will review the organization's vision and how this has an impact on the COE Structure.
Topics covered:
• The role of a steering committee
• How do the organization’s priorities determine CoE Structure?
Speaker:
Chris Bolin, Senior Intelligent Automation Architect Anika Systems
Driving Business Innovation: Latest Generative AI Advancements & Success StorySafe Software
Are you ready to revolutionize how you handle data? Join us for a webinar where we’ll bring you up to speed with the latest advancements in Generative AI technology and discover how leveraging FME with tools from giants like Google Gemini, Amazon, and Microsoft OpenAI can supercharge your workflow efficiency.
During the hour, we’ll take you through:
Guest Speaker Segment with Hannah Barrington: Dive into the world of dynamic real estate marketing with Hannah, the Marketing Manager at Workspace Group. Hear firsthand how their team generates engaging descriptions for thousands of office units by integrating diverse data sources—from PDF floorplans to web pages—using FME transformers, like OpenAIVisionConnector and AnthropicVisionConnector. This use case will show you how GenAI can streamline content creation for marketing across the board.
Ollama Use Case: Learn how Scenario Specialist Dmitri Bagh has utilized Ollama within FME to input data, create custom models, and enhance security protocols. This segment will include demos to illustrate the full capabilities of FME in AI-driven processes.
Custom AI Models: Discover how to leverage FME to build personalized AI models using your data. Whether it’s populating a model with local data for added security or integrating public AI tools, find out how FME facilitates a versatile and secure approach to AI.
We’ll wrap up with a live Q&A session where you can engage with our experts on your specific use cases, and learn more about optimizing your data workflows with AI.
This webinar is ideal for professionals seeking to harness the power of AI within their data management systems while ensuring high levels of customization and security. Whether you're a novice or an expert, gain actionable insights and strategies to elevate your data processes. Join us to see how FME and AI can revolutionize how you work with data!
HCL Notes and Domino License Cost Reduction in the World of DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-and-domino-license-cost-reduction-in-the-world-of-dlau/
The introduction of DLAU and the CCB & CCX licensing model caused quite a stir in the HCL community. As a Notes and Domino customer, you may have faced challenges with unexpected user counts and license costs. You probably have questions on how this new licensing approach works and how to benefit from it. Most importantly, you likely have budget constraints and want to save money where possible. Don’t worry, we can help with all of this!
We’ll show you how to fix common misconfigurations that cause higher-than-expected user counts, and how to identify accounts which you can deactivate to save money. There are also frequent patterns that can cause unnecessary cost, like using a person document instead of a mail-in for shared mailboxes. We’ll provide examples and solutions for those as well. And naturally we’ll explain the new licensing model.
Join HCL Ambassador Marc Thomas in this webinar with a special guest appearance from Franz Walder. It will give you the tools and know-how to stay on top of what is going on with Domino licensing. You will be able lower your cost through an optimized configuration and keep it low going forward.
These topics will be covered
- Reducing license cost by finding and fixing misconfigurations and superfluous accounts
- How do CCB and CCX licenses really work?
- Understanding the DLAU tool and how to best utilize it
- Tips for common problem areas, like team mailboxes, functional/test users, etc
- Practical examples and best practices to implement right away
Your One-Stop Shop for Python Success: Top 10 US Python Development Providersakankshawande
Simplify your search for a reliable Python development partner! This list presents the top 10 trusted US providers offering comprehensive Python development services, ensuring your project's success from conception to completion.
Digital Marketing Trends in 2024 | Guide for Staying AheadWask
https://www.wask.co/ebooks/digital-marketing-trends-in-2024
Feeling lost in the digital marketing whirlwind of 2024? Technology is changing, consumer habits are evolving, and staying ahead of the curve feels like a never-ending pursuit. This e-book is your compass. Dive into actionable insights to handle the complexities of modern marketing. From hyper-personalization to the power of user-generated content, learn how to build long-term relationships with your audience and unlock the secrets to success in the ever-shifting digital landscape.
Dandelion Hashtable: beyond billion requests per second on a commodity serverAntonios Katsarakis
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Energy Efficient Video Encoding for Cloud and Edge Computing Instances
Gao bosc2010 musite
1. Musite: Prediction of Protein
Phosphorylation Sites
Jianjiong Gao
University of Missouri Columbia
Missouri,
http://musite.sourceforge.net/
2. Background:
Protein Phosphorylation
Protein phosphorylation is one of the most
important p
p post-translational modifications.
It was estimated that up to 50% of proteins are
phosphorylated in some cellular state
Abnormality in phosphorylation is a cause or
consequence of many diseases
Cancer
Diabete
Parkinson’s
Hepertitis B
…
3. Background:
Protein Phosphorylation
Phosphorylation-dephosphorylation is a
biochemical switch system regulating
y g g
various cellular processes.
Catalyzed by various specific protein
kinases.
Kinase
ON
OFF
Phosphatase
4. Phosphorylation Site Prediction
Problem Formulation
Phosphorylation site: a phosphorylated amino acid
in a protein (determined by protein sequence)
General phosphorylation site prediction: to predict
whether an amino acid can be phosphorylated
Kinase-specific p
p phosphorylation site p
p y prediction: to
predict whether an amino acid can be
p
phosphorylated by a specific kinase
p y y p
Based on protein sequence only
5. Limitations of Current Methods
Current prediction tools have
limitations when applying to whole
proteomes
Prediction accuracy could be improved
Most were released as web servers and have
restrictions for the uploaded data by users
Training data were out of date
Stringency adjustment was not fully
supported
6. Our tool Musite is unique
Novel method with better accuracy
First open source tool in the field that meet
open-source
OSI Open Standards Requirement
Standalone program designed for proteome-
scale prediction
p
Support both general and kinase-specific
phosphorylation site prediction
Support customized model training
Support continuous stringency adjustment
7. Phosphorylation Site Prediction
Flowchart
Data collection from high quality sources, Training data
such as Uniprot/Swiss-Prot,Phospho.ELM,
PhosphoPep,and PhosPhAt Bootstrap
Non-redundant datasets built by BLASTclust
Bootstrap
sample 1
... Bootstrap
sample m
Training
Phosphorylation it
Ph h l ti sites Non-phosphorylation it
N h h l ti sites
Feature extraction Classifier 1 ... Classifier m
KNN scores Disorder scores
Amino acid frequencies Aggregating
Specificity
Features from Features from estimation Phosphorylation
positive set negative set
prediction model
Control data Making predictions
on new data
8. Phosphorylation Site Prediction
Data Extraction
Data collection from high quality sources, Training data
such as Uniprot/Swiss-Prot,Phospho.ELM,
PhosphoPep,and PhosPhAt Bootstrap
Non-redundant datasets built by BLASTclust
Bootstrap
sample 1
... Bootstrap
sample m
Training
Phosphorylation it
Ph h l ti sites Non-phosphorylation it
N h h l ti sites
Feature extraction Classifier 1 ... Classifier m
KNN scores Disorder scores
Amino acid frequencies Aggregating
Specificity
Features from Features from estimation Phosphorylation
positive set negative set
prediction model
Control data Making predictions
on new data
9. Phosphorylation Site Prediction
Feature Extraction
Data collection from high quality sources, Training data
such as Uniprot/Swiss-Prot,Phospho.ELM,
PhosphoPep,and PhosPhAt Bootstrap
Non-redundant datasets built by BLASTclust
Bootstrap
sample 1
... Bootstrap
sample m
Training
Phosphorylation it
Ph h l ti sites Non-phosphorylation it
N h h l ti sites
Feature extraction Classifier 1 ... Classifier m
KNN scores Disorder scores
Amino acid frequencies Aggregating
Specificity
Features from Features from estimation Phosphorylation
positive set negative set
prediction model
Control data Making predictions
on new data
10. Phosphorylation Site Prediction
Feature Extraction
Data collection from high quality sources, Training data
such as Uniprot/Swiss-Prot,Phospho.ELM,
PhosphoPep,and PhosPhAt Bootstrap
Non-redundant datasets built by BLASTclust
Bootstrap
sample 1
... Bootstrap
sample m
Training
Phosphorylation it
Ph h l ti sites Non-phosphorylation it
N h h l ti sites
Feature extraction Classifier 1 ... Classifier m
KNN scores Disorder scores
Amino acid frequencies Aggregating
Specificity
Features from Features from estimation Phosphorylation
positive set negative set
prediction model
Control data Making predictions
on new data
11. KNN Features
Motivation
Rationale of using KNN features: local
sequence clusters exist around
phosphorylation sites, since
Each phosphorylation site is a substrate of a specific
protein kinase
Substrates of the same kinase or kinase family
usually shares similar patterns in local sequences
12. KNN Features
Result
(A)
Overall, phosphosites Phospho Nonphospho
have larger KNN scores 1
than non-phosphosites 0.8
core
KNN sc
0.6
Average KNN scores 0.4
0.7~0.8 for phosphosites 0.2
≈0.5 for non-phosphosites 0
0.25
0 25 0.5
05 1 2 4
Size of nearest neighbors (% of sample size)
Boxplot of KNN features
(Human S /Th )
(H Ser/Thr)
13. Disorder Features
Concept & Rationale
Disordered region (structure)
Some parts of a protein have a rigid structure,
such as α-helix and β-sheet.
Other parts, disordered regions, do not have
well defined
well-defined conformations
The conformational flexibility of disordered
regions may facilitate protein phosphorylation
[Dunker, 2008]: protein phosphorylation sites
are frequently located within disordered regions
14. Disorder Features
Result
For h
F phosphosites
h it (A) Phospho-S/T in H. sapiens
6
Occurrence increases exponentially 10000 5
when d so de sco e increases
e disorder score c eases 4
For non-phosphosites 5000 3
2
Significantly different distribution
occurrence
e
0 1
0 0.2 0.4 0.6 0.8 1
x 10
5
(B) Non-phospho-S/T in H. sapiens 0
Disorder score > 0.5 2.5
-1
2
Phosphosites: ~91% -2
1.5
Non-phosphosites: ~55% -3
1
Phosphosites are significantly 0.5
05
-4
over-represented in disordered 0
-5
-6
regions 0 0.2 0.4 0.6
Disorder Score
0.8 1
Histogram of disorder features
(Human Ser/Thr)
15. Amino Acid Frequencies
Result
quency) 1
0.5
0
Log2(Ratio of Freq
-0.5 H. sapiens (S/T)
M. musculus (S/T)
-1
1
D. melanogaster (S/T)
-1.5 C. elegans (S/T)
-2
2 S. cerevisiae (S/T)
( )
g
A. thaliana (S/T)
-2.5
P R D E S K G A Q N V T H L M I F Y W C
Amino Acid
A i A id
P, R, D, E, S, K, and G are enriched around
phosphosites
C, W, Y, F, I, M, L, H, T, and V are depleted
16. Phosphorylation Site Prediction
Classifier Training
Data collection from high quality sources, Training data
such as Uniprot/Swiss-Prot,Phospho.ELM,
PhosphoPep,and PhosPhAt Bootstrap
Non-redundant datasets built by BLASTclust
Bootstrap
sample 1
... Bootstrap
sample m
Training
Phosphorylation it
Ph h l ti sites Non-phosphorylation it
N h h l ti sites
Feature extraction Classifier 1 ... Classifier m
KNN scores Disorder scores
Amino acid frequencies Aggregating
Specificity
Features from Features from estimation Phosphorylation
positive set negative set
prediction model
Control data Making predictions
on new data
20. Phosphorylation Site Prediction
Software Implementation-Musite
Open Source
License: GNU General Public License (GPL)
http://musite.sourceforge.net/
http://musite sourceforge net/
Stand-alone application
Based on Java
Support Windows Linux and Mac OS X
Windows, Linux,
A web server is also being developed
g p
http://musite.net/
22. Implementation
Customized Model Training
A unique utility for users to train
prediction models f
di ti d l from th i own d t
their data
Take advantage of latest data
Train disease-specific models
Train organ-specific models
Integrate into experimental p
g p procedure in an
iterative way
23. Summary
Musite is for prediction of general and kinase-
specific phosphosites in a better accuracy
Musite is a open-source standalone program
capable of performing proteome-wide
proteome wide
predictions
24. Acknowledgements
Dr. Dong Xu (University of Missouri)
Dr. Jay Thelen (U e s ty o Missouri)
e e (University of ssou )
Dr. Keith Dunker (Indiana University)
Curtis Bollinger (University of Missouri)
Funding Visit us at
NSF [# DBI 0604439]
DBI-0604439] http://musite.sourceforge.net
p g
NIH [# R21/R33 GM078601] http://musite.net
Poster R09 at ISMB