This document discusses developing apps and exposing data through Araport, an open platform for plant science data and tools. It provides an overview of why researchers should contribute to Araport, how to create web services and apps, commonly asked questions, and available resources. Key steps to creating a web service include implementing REST APIs, describing data sources in metadata, and testing and sharing the service. Developing a science app involves using app templates, consuming Araport APIs to build interactive tools, and publishing apps for others.
There is no doubt that Web APIs have become a fundamental aspect of modern architectures. However how to distinct a “good” API from an “evil” one is a topic for debate and one that often ends up in a “religious” debate. However, the one thing that is clear to most people, is that it all starts with a design, and getting that design right up-front will likely result in less headaches down the line.
So how to avoid “evil” APIs?
In this presentation, I will talk about the 7 most common pitfalls I’ve come across when doing API design in large implementations. With real-life examples, I will describe why such pitfalls deserved to be called “evil” and how to remediate them with “good" design practices.
The presentation will also touch upon how API-design first techniques can be applied to solve prevent some of the common issues.
It will be a highly interactive session with good balance of theory and practice.
GraphQL - The new "Lingua Franca" for API-Developmentjexp
Three years ago, with the release of the GraphQL specification, Facebook took a fresh stab at the topic of "API design between remote services and applications." The key aspects of GraphQL provide a common, schema-based, domain-specific language and flexible, dynamic queries at interface boundaries.
In the talk, I'd like to compare GraphQL and REST and showcase benefits for developers and architects using a concrete example in application and API development, data source and system integration.
GraphQL as an alternative approach to REST (as presented at Java2Days/CodeMon...luisw19
Originally designed by Facebook to allow its mobile clients to define exactly what data should be send back by an API and therefore avoid unnecessary roundtrips and data usage, GraphQL is a JSON based query language for Web APIs. Since it was open sourced by Facebook in 2015, it has undergone very rapid adoption and many companies have already switch to the GraphQL way of building APIs – see http://GraphQL.org/users.
However, with some many hundreds of thousands of REST APIs publicly available today (and many thousands others available internally), what are the implications of moving to GraphQL? Is it really worth the effort of replacing REST APIs specially if they’re successful and performing well in production? What are the pros/cons of using GraphQL? What tools / languages can be used for GraphQL? What about API Gateways? What about API design?
With a combination of rich content and hands-on demonstrations, attend this session for a point of view on how address these and many other questions, and most importantly get a better understanding and when/where/why/if GraphQL applies for your organisation or specific use case.
DEVOXX UK 2018 - GraphQL as an alternative approach to RESTluisw19
Originally designed by Facebook to allow its mobile clients to define exactly what data should be send back by an API and therefore avoid unnecessary roundtrips and data usage, GraphQL is a JSON based query language for Web APIs. Since it was open sourced by Facebook in 2015, it has undergone very rapid adoption and many companies have already switch to the GraphQL way of building APIs – see http://GraphQL.org/users.
However, with some many hundreds of thousands of REST APIs publicly available today (and many thousands others available internally), what are the implications of moving to GraphQL? Is it really worth the effort of replacing REST APIs specially if they’re successful and performing well in production? What are the pros/cons of using GraphQL? What tools / languages can be used for GraphQL? What about API Gateways? What about API design?
With a combination of rich content and hands-on demonstrations, attend this session for a point of view on how address these and many other questions, and most importantly get a better understanding and when/where/why/if GraphQL applies for your organisation or specific use case.
There is no doubt that Web APIs have become a fundamental aspect of modern architectures. However how to distinct a “good” API from an “evil” one is a topic for debate and one that often ends up in a “religious” debate. However, the one thing that is clear to most people, is that it all starts with a design, and getting that design right up-front will likely result in less headaches down the line.
So how to avoid “evil” APIs?
In this presentation, I will talk about the 7 most common pitfalls I’ve come across when doing API design in large implementations. With real-life examples, I will describe why such pitfalls deserved to be called “evil” and how to remediate them with “good" design practices.
The presentation will also touch upon how API-design first techniques can be applied to solve prevent some of the common issues.
It will be a highly interactive session with good balance of theory and practice.
GraphQL - The new "Lingua Franca" for API-Developmentjexp
Three years ago, with the release of the GraphQL specification, Facebook took a fresh stab at the topic of "API design between remote services and applications." The key aspects of GraphQL provide a common, schema-based, domain-specific language and flexible, dynamic queries at interface boundaries.
In the talk, I'd like to compare GraphQL and REST and showcase benefits for developers and architects using a concrete example in application and API development, data source and system integration.
GraphQL as an alternative approach to REST (as presented at Java2Days/CodeMon...luisw19
Originally designed by Facebook to allow its mobile clients to define exactly what data should be send back by an API and therefore avoid unnecessary roundtrips and data usage, GraphQL is a JSON based query language for Web APIs. Since it was open sourced by Facebook in 2015, it has undergone very rapid adoption and many companies have already switch to the GraphQL way of building APIs – see http://GraphQL.org/users.
However, with some many hundreds of thousands of REST APIs publicly available today (and many thousands others available internally), what are the implications of moving to GraphQL? Is it really worth the effort of replacing REST APIs specially if they’re successful and performing well in production? What are the pros/cons of using GraphQL? What tools / languages can be used for GraphQL? What about API Gateways? What about API design?
With a combination of rich content and hands-on demonstrations, attend this session for a point of view on how address these and many other questions, and most importantly get a better understanding and when/where/why/if GraphQL applies for your organisation or specific use case.
DEVOXX UK 2018 - GraphQL as an alternative approach to RESTluisw19
Originally designed by Facebook to allow its mobile clients to define exactly what data should be send back by an API and therefore avoid unnecessary roundtrips and data usage, GraphQL is a JSON based query language for Web APIs. Since it was open sourced by Facebook in 2015, it has undergone very rapid adoption and many companies have already switch to the GraphQL way of building APIs – see http://GraphQL.org/users.
However, with some many hundreds of thousands of REST APIs publicly available today (and many thousands others available internally), what are the implications of moving to GraphQL? Is it really worth the effort of replacing REST APIs specially if they’re successful and performing well in production? What are the pros/cons of using GraphQL? What tools / languages can be used for GraphQL? What about API Gateways? What about API design?
With a combination of rich content and hands-on demonstrations, attend this session for a point of view on how address these and many other questions, and most importantly get a better understanding and when/where/why/if GraphQL applies for your organisation or specific use case.
The Dynamic Action framework can make it easy to add dynamic behavior to your APEX applications without writing any JavaScript. But there are parts of the framework that aren’t so straight forward. JavaScript hooks, complex event bindings, debugging Ajax, and more – some might call these the hard parts of Dynamic Actions.
In this session, attendees will skip the introduction to Dynamic Actions and dive right into the hard parts. By the end, folks will leave with some new tools in their tool belt that will help them take the Dynamic Action framework further than they thought was possible.
Scaling Your Team With GraphQL: Why Relationships MatterJoel Bowen
Have you used GraphQL yet? If you haven't, you're likely to encounter the technology soon. If you have, you might have questions about how to scale your team and what best practices large and small companies are following. What principles should I be following when developing a new GraphQL API? What tooling is available to help me be more productive and spend less time writing boilerplate code? How can many teams with many apps across one company share one graph?
GraphQL Conf 2019 just wrapped up in Berlin where I was fortunate to hear meet thoughtful leaders on these and other subjects related to GraphQL. So, whether you're brand new to GraphQL or have an active project using GraphQL, I'd like to share some of what I have learned so you can be productive with GraphQL and your teams - while keeping relationships at the center of our work.
GraphQL is a query language for APIs and a runtime for fulfilling those queries. It gives clients the power to ask for exactly what they need, which makes it a great fit for modern web and mobile apps. In this talk, we explain why GraphQL was created, introduce you to the syntax and behavior, and then show how to use it to build powerful APIs for your data. We will also introduce you to AWS AppSync, a GraphQL-powered serverless backend for apps, which you can use to host GraphQL APIs and also add real-time and offline capabilities to your web and mobile apps. You can follow along if you have an AWS account – no GraphQL experience required!
Level: Beginner
Speaker: Rohan Deshpande - Sr. Software Dev Engineer, AWS Mobile Applications
Slides from the workshop delivered at the Evolution of Technical Communication 2018 conference. The workshop features an introduction to REST APIs followed by hands-on activities in which the participants (technical communication professionals) put themselves in developers' shoes used and some APIs and API tools like developers.
Prospectus editing at the University of Bristol- an overview:TERMINALFOUR t44...Terminalfour
Prospectus Editing Tool at the University of Bristol. Mike Jones from the University of Bristol outlines how the University is improving the process of collating and editing content for the production of the 2015 undergraduate and postgraduate prospectuses. This session outlines the rationale, the approach, the technologies involved and it's experiences with the TERMINALFOUR Site Manager API.
This presentation was part of an internal training session at Jahia to make people aware of GraphQL, and also shared the lessons learned while working with it. It is intended for audiences that have no prior knowledge of GraphQL.
by Richard Threlkeld, Sr. Product Manager, AWS
Most applications are data-driven and our app is no exception to that. However, mobile development has some unique problems to be solved. In this session, we’ll introduce you to GraphQL – the latest in mobile-centric data access protocols – and show you how GraphQL can help with these problems.
Introduction to GraphQL (or How I Learned to Stop Worrying about REST APIs)Hafiz Ismail
Talk for FOSSASIA 2016 (http://2016.fossasia.org)
----
This talk will give a brief and enlightening look into how GraphQL can help you address common weaknesses that you, as a web / mobile developer, would normally face with using / building typical REST API systems.
Let's stop fighting about whether we should implement the strictest interpretation of REST or how pragmatic REST-ful design is the only way to go, or debate about what REST is or what it should be.
A couple of demos (In Golang! Yay!) will be shown that are guaranteed to open up your eyes and see that the dawn of liberation for product developers is finally here.
Background: GraphQL is a data query language and runtime designed and used at Facebook to request and deliver data to mobile and web apps since 2012.
Hafiz Ismail (@sogko) is a contributor to Go / Golang implementation of GraphQL server library (https://github.com/graphql-go/graphql) and is looking to encourage fellow developers to join in the collaborative effort.
Presentation to the workflow track of ISoLA 2010, Crete. Includes explanation of the SADI plug-in to Taverna, and how the SHARE client automatically constructs and semantic web service workflow to answer specific sparql queries.
With the rise of Microservice Architectures and rich mobile and web applications, APIs are more important than ever. Come learn how to tackle modern API design challenges with GraphQL, an open-source API query language used by Facebook, Amazon, Microsoft, Twitter, Virgin Trains, and more.
A presentation delivered to the Auckland Atlassian User Group on the 22nd February, 2012 - where we explore from a high level the Atlassian developer ecosystem, i.e. why you want to develop for it, how to develop for it etc.
This covered a number of things which are also landing in Jira 5 and above only i.e. activity streams and remote links.
http://www.meetup.com/Akl-AUG/events/47434772/
The world around us is full of connected information. Neo4j was originally developed to solve two complex "network" problems in a document management system, as it was too hard to manage rich connection information efficiently in traditional and new "NOSQL" databases.During this meetup, we will talk about the technology, and about the journey that a couple of technologists from Malmö took. You will learn* how Neo Technology grew from just the three founders in to a global database company with use-cases in every domain imaginable.* how focusing on customer and community feedback allows us to provide a solution for managing connected data to everyone, not just the large internet companies.
Of course we will also introduce the graph model, it's whiteboard friendlyness and how you get started with Neo4j and it's easy and powerful query language Cypher. We'll also compare the graph and relational data model to see how they differ in shape and capabilities. Finally we discuss the foundations that enable Graph databases to provide higher join performance, faster development processes and more inclusive software for all stakeholders. With use-cases from Gaming, Dating and Finance we'll see how to apply the graph capabilities to these domains to realize new functionality or opportunities that were not possible before.
Finally, if there's a question you've always wanted to ask/discuss, we'll have plenty of time for that at the end of Michael's presentation.
Neo4j-Databridge: Enterprise-scale ETL for Neo4jNeo4j
Neo4j-Databridge is a fully-featured ETL tool specifically built for Neo4j, and designed for usability, expressive power and high performance. It has been created to help solve the most common problems faced by large enterprises when importing data into Neo4j - data locality, multiple data sources and formats, performance when loading very large data sets, bespoke data conversions, inclusion of non-tabular data, filtering, merging and de-duplication...
In this webinar, we’ll take a quick tour of the main features of Neo4j-Databridge and understand how it can to help to solve these problems and facilitate importing your data easily and quickly into Neo4j.
It is a basic presentation which can help you understand the basic concepts about Graphql and how it can be used to resolve the frontend integration of projects and help in reducing the data fetching time
This presentation also explains the core features of Graphql and why It is a great alternative for REST APIs along with the procedure with which we can integrate it into our projects
These are the slides from the 1st module in the "Introduction to JavaScript for APEX Developers" workshop. This module covers the following topics: 1) Why JavaScript? 2) Variables and data types 3) Operators 4) Conditionals and loops 5) Objects and functions 6) Developer tools
Learn how to build advanced GraphQL queries, how to work with filters and patches and how to embed GraphQL in languages like Python and Java. These slides are the second set in our webinar series on GraphQL.
Apps for SharePoint are easy-to-use, lightweight web applications.An app for SharePoint is a stand-alone, self-contained piece of functionality that extends the features and capabilities of a SharePoint site.App model is mainly designed for cloud hosting. It will not use server side code. It will use only client script like java script or jQuery, and will work on top of share point framework.
These slides are from my 2009 Fundamentals of Search workshop at KMWorld. Please contact me for information about search engines, consulting, workshops and training.
The Dynamic Action framework can make it easy to add dynamic behavior to your APEX applications without writing any JavaScript. But there are parts of the framework that aren’t so straight forward. JavaScript hooks, complex event bindings, debugging Ajax, and more – some might call these the hard parts of Dynamic Actions.
In this session, attendees will skip the introduction to Dynamic Actions and dive right into the hard parts. By the end, folks will leave with some new tools in their tool belt that will help them take the Dynamic Action framework further than they thought was possible.
Scaling Your Team With GraphQL: Why Relationships MatterJoel Bowen
Have you used GraphQL yet? If you haven't, you're likely to encounter the technology soon. If you have, you might have questions about how to scale your team and what best practices large and small companies are following. What principles should I be following when developing a new GraphQL API? What tooling is available to help me be more productive and spend less time writing boilerplate code? How can many teams with many apps across one company share one graph?
GraphQL Conf 2019 just wrapped up in Berlin where I was fortunate to hear meet thoughtful leaders on these and other subjects related to GraphQL. So, whether you're brand new to GraphQL or have an active project using GraphQL, I'd like to share some of what I have learned so you can be productive with GraphQL and your teams - while keeping relationships at the center of our work.
GraphQL is a query language for APIs and a runtime for fulfilling those queries. It gives clients the power to ask for exactly what they need, which makes it a great fit for modern web and mobile apps. In this talk, we explain why GraphQL was created, introduce you to the syntax and behavior, and then show how to use it to build powerful APIs for your data. We will also introduce you to AWS AppSync, a GraphQL-powered serverless backend for apps, which you can use to host GraphQL APIs and also add real-time and offline capabilities to your web and mobile apps. You can follow along if you have an AWS account – no GraphQL experience required!
Level: Beginner
Speaker: Rohan Deshpande - Sr. Software Dev Engineer, AWS Mobile Applications
Slides from the workshop delivered at the Evolution of Technical Communication 2018 conference. The workshop features an introduction to REST APIs followed by hands-on activities in which the participants (technical communication professionals) put themselves in developers' shoes used and some APIs and API tools like developers.
Prospectus editing at the University of Bristol- an overview:TERMINALFOUR t44...Terminalfour
Prospectus Editing Tool at the University of Bristol. Mike Jones from the University of Bristol outlines how the University is improving the process of collating and editing content for the production of the 2015 undergraduate and postgraduate prospectuses. This session outlines the rationale, the approach, the technologies involved and it's experiences with the TERMINALFOUR Site Manager API.
This presentation was part of an internal training session at Jahia to make people aware of GraphQL, and also shared the lessons learned while working with it. It is intended for audiences that have no prior knowledge of GraphQL.
by Richard Threlkeld, Sr. Product Manager, AWS
Most applications are data-driven and our app is no exception to that. However, mobile development has some unique problems to be solved. In this session, we’ll introduce you to GraphQL – the latest in mobile-centric data access protocols – and show you how GraphQL can help with these problems.
Introduction to GraphQL (or How I Learned to Stop Worrying about REST APIs)Hafiz Ismail
Talk for FOSSASIA 2016 (http://2016.fossasia.org)
----
This talk will give a brief and enlightening look into how GraphQL can help you address common weaknesses that you, as a web / mobile developer, would normally face with using / building typical REST API systems.
Let's stop fighting about whether we should implement the strictest interpretation of REST or how pragmatic REST-ful design is the only way to go, or debate about what REST is or what it should be.
A couple of demos (In Golang! Yay!) will be shown that are guaranteed to open up your eyes and see that the dawn of liberation for product developers is finally here.
Background: GraphQL is a data query language and runtime designed and used at Facebook to request and deliver data to mobile and web apps since 2012.
Hafiz Ismail (@sogko) is a contributor to Go / Golang implementation of GraphQL server library (https://github.com/graphql-go/graphql) and is looking to encourage fellow developers to join in the collaborative effort.
Presentation to the workflow track of ISoLA 2010, Crete. Includes explanation of the SADI plug-in to Taverna, and how the SHARE client automatically constructs and semantic web service workflow to answer specific sparql queries.
With the rise of Microservice Architectures and rich mobile and web applications, APIs are more important than ever. Come learn how to tackle modern API design challenges with GraphQL, an open-source API query language used by Facebook, Amazon, Microsoft, Twitter, Virgin Trains, and more.
A presentation delivered to the Auckland Atlassian User Group on the 22nd February, 2012 - where we explore from a high level the Atlassian developer ecosystem, i.e. why you want to develop for it, how to develop for it etc.
This covered a number of things which are also landing in Jira 5 and above only i.e. activity streams and remote links.
http://www.meetup.com/Akl-AUG/events/47434772/
The world around us is full of connected information. Neo4j was originally developed to solve two complex "network" problems in a document management system, as it was too hard to manage rich connection information efficiently in traditional and new "NOSQL" databases.During this meetup, we will talk about the technology, and about the journey that a couple of technologists from Malmö took. You will learn* how Neo Technology grew from just the three founders in to a global database company with use-cases in every domain imaginable.* how focusing on customer and community feedback allows us to provide a solution for managing connected data to everyone, not just the large internet companies.
Of course we will also introduce the graph model, it's whiteboard friendlyness and how you get started with Neo4j and it's easy and powerful query language Cypher. We'll also compare the graph and relational data model to see how they differ in shape and capabilities. Finally we discuss the foundations that enable Graph databases to provide higher join performance, faster development processes and more inclusive software for all stakeholders. With use-cases from Gaming, Dating and Finance we'll see how to apply the graph capabilities to these domains to realize new functionality or opportunities that were not possible before.
Finally, if there's a question you've always wanted to ask/discuss, we'll have plenty of time for that at the end of Michael's presentation.
Neo4j-Databridge: Enterprise-scale ETL for Neo4jNeo4j
Neo4j-Databridge is a fully-featured ETL tool specifically built for Neo4j, and designed for usability, expressive power and high performance. It has been created to help solve the most common problems faced by large enterprises when importing data into Neo4j - data locality, multiple data sources and formats, performance when loading very large data sets, bespoke data conversions, inclusion of non-tabular data, filtering, merging and de-duplication...
In this webinar, we’ll take a quick tour of the main features of Neo4j-Databridge and understand how it can to help to solve these problems and facilitate importing your data easily and quickly into Neo4j.
It is a basic presentation which can help you understand the basic concepts about Graphql and how it can be used to resolve the frontend integration of projects and help in reducing the data fetching time
This presentation also explains the core features of Graphql and why It is a great alternative for REST APIs along with the procedure with which we can integrate it into our projects
These are the slides from the 1st module in the "Introduction to JavaScript for APEX Developers" workshop. This module covers the following topics: 1) Why JavaScript? 2) Variables and data types 3) Operators 4) Conditionals and loops 5) Objects and functions 6) Developer tools
Learn how to build advanced GraphQL queries, how to work with filters and patches and how to embed GraphQL in languages like Python and Java. These slides are the second set in our webinar series on GraphQL.
Apps for SharePoint are easy-to-use, lightweight web applications.An app for SharePoint is a stand-alone, self-contained piece of functionality that extends the features and capabilities of a SharePoint site.App model is mainly designed for cloud hosting. It will not use server side code. It will use only client script like java script or jQuery, and will work on top of share point framework.
These slides are from my 2009 Fundamentals of Search workshop at KMWorld. Please contact me for information about search engines, consulting, workshops and training.
EcoMachines - Technology Dissemination in Practice - LESI Global Technology I...EcoMachines Ventures
21 January 2014 - EcoMachines' CEO, Ilian Iliev presented on 'Technology Dissemination in Practice' at the LESI Global Technology Impact Forum 2014 in Geneva. See the presentation here.
Ecosummit is the smart green business network and conference connecting startups, VCs and corporates to accelerate smart green innovation. Ecosummit London 2014 is our 8th conference and happens on 7-8 October 2014 at the Crystal, Siemens’ urban sustainability HQ in the Docklands.
Packaging computational biology tools for broad distribution and ease-of-reuseMatthew Vaughn
A typical instance of computational biology software is composed of interpreted code, compiled binaries, shared libraries, and shell scripts, sometimes mixed in with use of web services or databases, running in the context of a complex computer operating system, atop increasingly sophisticiated physical resources. How can we expect computations to be sharable and reproducible, and how can we hope to train people to use such resources? This talk will describe how the Texas Advanced Computing Center enables distribution and use scientific software via various approaches, including Jupyter notebooks, Github repositories, computation-oriented web service APIs, virtual machine images, and container technologies such as Docker, and how these approaches complement one another for training and education.
Clouds, Clusters, and Containers: Tools for responsible, collaborative computingMatthew Vaughn
Intro slides from AKES workshop at ISMB2016. This workshop addresses the challenges and requirements for working effectively on cloud computing and high performance computing resources, discusses the key principles that should guide responsible scientific computation and collaboration, and using hands-on sessions presents practical solutions using emergent software tools that are becoming widely adopted in the global scientific community. Specifically, we will look at using “containers” to bundle software applications and their full execution environment in a portable way. We will look at managing and sharing data across distributed resources. And finally, we will tackle how to orchestrate job execution across systems and capture metadata on the results (and the process) so that parameters and methodologies are not lost.
EcoMachines Incubator: Resource 2015 - Funding Options for StartupsEcoMachines Ventures
Presentation to accompany EcoMachines Incubator's workshop at Resource 2015 entitled 'Funding Innovation: Options for startups within the circular economy'.
Etude E-marketing : Email mobile - maelle urbanmaelleurban
Comment l’e-mail marketing peut-il être adapté au terminal mobile, afin de maintenir et renforcer la relation client ?
Avec l’expansion des téléphones pouvant se connecter à l’Internet mobile, il devient essentiel pour les entreprises d’adapter leur stratégie à ce nouveau canal. En effet, l’Internet mobile permet de consulter ses e-mails, première motivation de connexion via le téléphone mobile. Or, il existe une multitude de terminaux mobiles ayant tous des caractéristiques technologiques différentes. La lecture de l’e-mail sur téléphone mobile devient alors parfois laborieuse. Or, un e-mail non consulté est un client potentiellement perdu. L’e-mail doit donc s’adapter rapidement à ce nouveau canal.
Arabidopsis Information Portal overview from Plant Biology Europe 2014Matthew Vaughn
An overview of the design, technical decisions, and implementation of the Arabidopsis Information Portal community-extensible data sharing and analytics platform.
SharePoint 2013 Apps and the App ModelJames Tramel
SharePoint 2013 Apps - deep dive. We'll look at they work, what they look like, what they do and how to us apps. Its all about the apps. Apps are good, very good.
Presentation on Presto (http://prestodb.io) basics, design and Teradata's open source involvement. Presented on Sept 24th 2015 by Wojciech Biela and Łukasz Osipiuk at the #20 Warsaw Hadoop User Group meetup http://www.meetup.com/warsaw-hug/events/224872317
Content Strategy and Developer Engagement for DevPortalsAxway
Slides from Write the Docs Ottawa Meet Up at Shopify HQ in Canada, June 24, 2019
We’ll walk through 5 scenarios and concrete ways of reaching a developer community for frictionless and increased engagement.
The Query Service is the new platform solution for querying a variety of data sources. The goal of Query Service is that administrators can configure a metadata description of the data source that can then be used by end users without detailed knowledge of the underlying data source. This session explains how to configure Query Service data sources and use them with the RESTful API or component collection.
Arabidopsis Information Portal: A Community-Extensible Platform for Open DataMatthew Vaughn
Araport is an innovative model organism database resource that offers users the ability to bring their own visualizations, data sets, algorithms, and genome browser tracks and share them with their colleagues.
Logic apps and PowerApps - Integrate across your APIsSriram Hariharan
We have a number of new feature in Logic apps and PowerApps that make it easier than ever to build workflows that orchetstrate across any RESTful API. We will cover some of the latest updates to Logic apps and PowerApps.
Araport Workshop Tutorial 2: Authentication and the Agave Profiles Servicestevemock
Araport Workshop Tutorial 2: Authentication and the Agave Profiles Service.
A tutorial for building a science application using the Araport.org platform, specifically the Agave API's Profiles RESTful endpoints from the araport app generator platform.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Developing Apps: Exposing Your Data Through Araport
1. araport.org
Developing Apps: Exposing Your
Data Through Araport
Matt Vaughn
Director, Life Sciences Computing
Texas Advanced Computing Center
vaughn@tacc.utexas.edu | @mattdotvaughn | www.slideshare.net/mattdotvaughn
2. araport.org
Overview
• Why contribute to Araport?
• How does one create a web service?
• How does one build a Science App?
• Commonly asked questions
• What resources are available?
3. araport.org
Why become an Araport contributor?
• Recognition
• Exposure
• Feedback
• Interoperability
• Professional presentation
• Reusability
4. araport.org
Araport: A Road Map
API.ARAPORT.ORG
CLI clients,
Scripts, 3rd party
applications
Core Resources
AGAVE
apps
meta
files
profile
jobssystems
ADAMA
manage
enroll
a b c d e f
Data Resources
API Types
• Query
• Map*
• Generic
• Pass-through
• Single-sign on
• Metering
• Unified logging
• API versioning
• Automatic HTTPS + CORS
REST*
CGI
SOAP
New Web
Services
InterMine
Chado &
Tripal
Computing
Storage
Database
APPS
APIs
6. araport.org
Araport Data and
Microservice API
• Implement REST-like web services
• Allow real-time integration with and transformation of
existing web-based services
• Promote interoperability
– Simple, extensible controlled vocabulary for queries
– Responses can conform to common schemas*
– GLOBAL SEARCH
• Solve some annoying problems
– Provide HTTPS + valid SSL certificate
– Enable Cross Origin Scripting Support (CORS)
– Implement authenticated access to services
• BE EASY TO ADOPT, USE, AND MAINTAIN
7. araport.org
Case Study: TIGR Gene Expression Database
• NSF Arabidopsis 2010
project (#0520022)
• How to make this
resource more broadly
usable and useful?
– Create modernized web
services
– Build an interactive
science app
8. araport.org
Creating a new data service in 5
easy steps
8
• Check out a
template
• Write and
debug service
locally
• Write docs
• Describe data
sources
Push to
GitHub*
Register new
service using
ADAMA
Test and
refine the
microservice
Share with
colleagues
or the public
Develop a
Science App
using APIs
Write
Code
Upload Enroll @
Araport
Use it Share Make a
Science
App
12. araport.org
Creating a new data service in 5
easy steps
12
• Check out a
template
• Write and
debug service
locally
• Write docs
• Describe data
sources
Push to
GitHub*
Register new
service using
ADAMA
Test and
refine the
microservice
Share with
colleagues
or the public
Develop a
Science App
using APIs
Write
Code
Upload Enroll @
Araport
Use it Share Make a
Science
App
13. araport.org
Using the new service (1)
• Use the Araport API Explorer
Home->Tools->Web Services-
>Community Data
• Use the Javascript console
embedded in your browser
• Manually via command line
tools like cURL or httpie
16. araport.org
Using the new service (4)
Every Araport web service is available via Javascript console
Data API namespace
Individual Data API
> Agave.api.adama.getNamespaces()
17. araport.org
Using the new service (5)
curl -X GET -sk -H "Authorization: Bearer
17f4700fb4ffa9ab32f1bf560e8a2b8" https://
api.araport.org/community/v0.3/jcvi/
image_by_id_v0.1/search?image_id=237 -O "237.png"
• Perform a GET using an Araport-issued
Oauth token to the image_by_id
community service; Save the result to a
file named 237.png
• Every Araport-hosted web service can be
used by scripts
• We offer Javascript and Python code
libraries available as well
18. araport.org
Using the new service (6)
BUILD A SCIENCE APP THAT CONSUMES IT
JCVI QPCR app
integrates half a
dozen web service
APIs
Some from the QPCR
service itself, some
from ThaleMine
Araport is a mash-up
engine for plant
science data
20. araport.org
5 Steps to Creating a Science App
Install tool
chain (just
once)
Launch a new
Science App (or
clone an existing
one)
Interactively
design and
build your
app
Push to
GitHub
Install @
Araport
then
Publish!
Setup Create New Write
Code
Upload Share
21. araport.org
Anatomy of a Science App
Your assets live inside /app
Static HTML content for
laying out the app
JavaScript functions
defined for the app
Cascading Style Sheets
(CSS) specific to the app
JavaScript dependencies
automatically managed
via Bower
https://github.com/Arabidopsis-Information-Portal/ATExpressionProfilingApp
24. araport.org
Science App Store
• Developers can share apps
privately during creation and
testing
• Request publication under My
Account->My Apps
• Araport staff will review the
app and either publish it or
make suggestions about how
to improve it
25. araport.org
Commonly Asked Questions
• How can I get credit or attribution if my app or data is
served through Araport?
• I have data type X - can I share it via Araport?
• Can I keep my work private or shared with only select
people?
• Can someone publish malicious code at Araport?
• What if my Science App needs to compute on data,
not just access a database?
• Can you help me learn to write web services and
Science Apps?
28. araport.org
The Road Ahead
Science Apps
• Improved create & publish workflow
• Tags, ratings, comments, & live previews
• “Compute applications”
• Automatic display of provenance information
• Dynamically resizable app display
• Communication between apps
Web Services
• Improved create & publish workflow
• Support for “native” web services
• Comprehensive logging and usage analytics
• Performance and reliability improvements
29. araport.org
Chris Town, PI
Lisa McDonald
Education and
Outreach Coordinator
Chris Nelson
Project ManagerJason Miller, Co-PI
JCVI Technical Lead
Erik Ferlanti
Software Engineer
Vivek Krishnakumar
Bioinf. Engineer
Svetlana Karamycheva
Bioinf Engineer
Eva Huala
Project lead, TAIR
Bob Muller
Technical lead, TAIR
Gos Micklem, co-PI Sergio Contrino
Software Engineer
Matt Vaughn
co-PI
Steve Mock
Portal Engineer
Rion Dooley,
API Engineer
Matt Hanlon,
Portal Engineer
Maria Kim
Bioinf Engineer
Ben Rosen
Bioinf Analyst
Joe Stubbs,
API Engineer
Walter Moreira,
API Engineer