In recent years smartphones and tablets have attained sufficient power and sophistication to replace conventional desktop and laptop computers for many tasks. Chemistry software is late to the party, but rapidly catching up. This webinar will explore some of the cheminformatics functionality that can currently be performed using mobile apps. A number of workflow scenarios will be discussed, such as: creating and maintaining chemical data (molecules, reactions, numbers & text); searching chemical databases and utilising the results; structure-aware lab notebooks; visualisation and structure-activity analysis; property calculation using remote webservices; and a multitude of ways to share data collaboratively, and integrate modular apps within distributed and heterogeneous workflows.
With audio: http://www.youtube.com/watch?v=_XU0FTP-j34
Reaction Lab Notebooks for Mobile Devices - Alex M. Clark - GDCh 2013Alex Clark
Presented at 2013 the German Chem[o]informatics Conference in Fulda, 2013: entitled "Putting together the pieces: building a reaction-centric electronic lab notebook for mobile devices".
FAIR Data and Model Management for Systems Biology(and SOPs too!)Carole Goble
MultiScale Biology Network Springboard meeting, Nottingham, UK, 1 June 2015
FAIR Data and model management for Systems Biology
Over the past 5 years we have seen a change in expectations for the management of all the outcomes of research – that is the “assets” of data, models, codes, SOPs and so forth. Don’t stop reading. Yes, data management isn’t likely to win anyone a Nobel prize. But publications should be supported and accompanied by data, methods, procedures, etc. to assure reproducibility of results. Funding agencies expect data (and increasingly software) management retention and access plans as part of the proposal process for projects to be funded. Journals are raising their expectations of the availability of data and codes for pre- and post- publication. And the multi-component, multi-disciplinary nature of Systems Biology demands the interlinking and exchange of assets and the systematic recording of metadata for their interpretation.
Data and model management for the Systems Biology community is a multi-faceted one including: the development and adoption appropriate community standards (and the navigation of the standards maze); the sustaining of international public archives capable of servicing quantitative biology; and the development of the necessary tools and know-how for researchers within their own institutes so that they can steward their assets in a sustainable, coherent and credited manner while minimizing burden and maximising personal benefit.
The FAIRDOM (Findable, Accessible, Interoperable, Reusable Data, Operations and Models) Initiative has grown out of several efforts in European programmes (SysMO and EraSysAPP ERANets and the ISBE ESRFI) and national initiatives (de.NBI, German Virtual Liver Network, SystemsX, UK SynBio centres). It aims to support Systems Biology researchers with data and model management, with an emphasis on standards smuggled in by stealth.
This talk will use the FAIRDOM Initiative to discuss the FAIR management of data, SOPs, and models for Sys Bio, highlighting the challenges multi-scale biology presents.
http://www.fair-dom.org
http://www.fairdomhub.org
http://www.seek4science.org
Презентация к докладу на SymfonyCampUA-2012.
В докладе рассмотрены основные вопросы работы с АОП в PHP, даны определения аспектов, срезов, советов, а также рассмотрено реальное использование библиотеки GO! для внедрения аспектно-ориентированной парадигмы в любое приложение.
Haiku Deck is a presentation tool that allows users to create Haiku style slideshows. The tool encourages users to get started making their own Haiku Deck presentations which can be shared on SlideShare. In just a few sentences, it pitches the idea of using Haiku Deck to easily create visual presentations.
Reaction Lab Notebooks for Mobile Devices - Alex M. Clark - GDCh 2013Alex Clark
Presented at 2013 the German Chem[o]informatics Conference in Fulda, 2013: entitled "Putting together the pieces: building a reaction-centric electronic lab notebook for mobile devices".
FAIR Data and Model Management for Systems Biology(and SOPs too!)Carole Goble
MultiScale Biology Network Springboard meeting, Nottingham, UK, 1 June 2015
FAIR Data and model management for Systems Biology
Over the past 5 years we have seen a change in expectations for the management of all the outcomes of research – that is the “assets” of data, models, codes, SOPs and so forth. Don’t stop reading. Yes, data management isn’t likely to win anyone a Nobel prize. But publications should be supported and accompanied by data, methods, procedures, etc. to assure reproducibility of results. Funding agencies expect data (and increasingly software) management retention and access plans as part of the proposal process for projects to be funded. Journals are raising their expectations of the availability of data and codes for pre- and post- publication. And the multi-component, multi-disciplinary nature of Systems Biology demands the interlinking and exchange of assets and the systematic recording of metadata for their interpretation.
Data and model management for the Systems Biology community is a multi-faceted one including: the development and adoption appropriate community standards (and the navigation of the standards maze); the sustaining of international public archives capable of servicing quantitative biology; and the development of the necessary tools and know-how for researchers within their own institutes so that they can steward their assets in a sustainable, coherent and credited manner while minimizing burden and maximising personal benefit.
The FAIRDOM (Findable, Accessible, Interoperable, Reusable Data, Operations and Models) Initiative has grown out of several efforts in European programmes (SysMO and EraSysAPP ERANets and the ISBE ESRFI) and national initiatives (de.NBI, German Virtual Liver Network, SystemsX, UK SynBio centres). It aims to support Systems Biology researchers with data and model management, with an emphasis on standards smuggled in by stealth.
This talk will use the FAIRDOM Initiative to discuss the FAIR management of data, SOPs, and models for Sys Bio, highlighting the challenges multi-scale biology presents.
http://www.fair-dom.org
http://www.fairdomhub.org
http://www.seek4science.org
Презентация к докладу на SymfonyCampUA-2012.
В докладе рассмотрены основные вопросы работы с АОП в PHP, даны определения аспектов, срезов, советов, а также рассмотрено реальное использование библиотеки GO! для внедрения аспектно-ориентированной парадигмы в любое приложение.
Haiku Deck is a presentation tool that allows users to create Haiku style slideshows. The tool encourages users to get started making their own Haiku Deck presentations which can be shared on SlideShare. In just a few sentences, it pitches the idea of using Haiku Deck to easily create visual presentations.
How to Teach Like an Award-winning InstructorJoel Gardner
This presentation illustrates some of the strategies and approaches used by award-winning instructors in higher education. Strategies include the us of Merrill's First Principles of Instruction. The presentation is based on a study done by Joel Gardner found at https://www.academia.edu/3538810/
This document provides advice for developing a business idea called BlogFollower, which would help bloggers make money through an automated service that follows blogs via RSS, email, Twitter, and Facebook. It discusses researching competitors, identifying the target audiences of bloggers and advertisers, determining how to make money through subscriptions or advertising cuts, creating an iterative development plan, and emphasizing continuous improvement and marketing. The core of the product would syndicate blogs across multiple platforms while facilitating self-serve advertising sales.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise boosts blood flow, releases endorphins, and promotes changes in the brain which help enhance one's emotional well-being and mental clarity.
Modern Architectural Masterpieces - design masterpiecesMakala D.
This document lists the names and locations of various uniquely designed buildings around the world, including dome-shaped houses in Florida and India, casinos in Macao and buildings shaped like pianos, violins, and elephants in China, Thailand, and various other countries.
The document discusses iterative design and provides examples of logo design projects. It describes iterative design as a step-by-step process that allows designers to start with initial ideas and refine them over multiple rounds of feedback and revisions. Examples show early sketches and concepts for two logo design projects that were refined over several iterations, receiving feedback at each stage from clients and other designers until a final design was selected. The process is described as reducing pressure to find a perfect solution immediately while allowing ideas to develop through iteration.
Get ready for 2014 planning by benchmarking the financial performance of your supply chain. Using a database of over 50 metrics with 20 years of data, the Supply Chain Insights team can help you better understand your supply chain potential. This analysis enables visualization of company performance on managing the trade-offs of growth, profitability, inventory/cash cycles and complexity.
We find that each company has a unique pattern in how they managed trade-offs. The analysis helps you benchmark against your peer group and make a conscious choice. Through a deeper understanding of industry averages and outliers, this type of study helps you to better understand your supply chain potential. While many companies have used this service to understand public performance, many leaders have taken it one step further to benchmark divisions or product groups within their companies.
This document discusses Finland's startup ecosystem and opportunities to support scalable startups. It notes that job growth will increasingly come from new companies, not existing ones, and outlines six types of startups. It argues that scalable startups offering unknown solutions will provide the most jobs but require a strong ecosystem. However, Finland currently lacks experienced entrepreneurs and policies that encourage risk-taking and startups. The document recommends Finland focus public funding on attracting private incubators and venture capital rather than directly funding companies to best support scalable startups and future job growth.
Este documento presenta varios programas de Google DevRel para Latinoamérica, incluyendo Academic Developer Technology Groups para formar grupos de I+D en universidades, University Class para dictar clases en línea, Lookthiscode para un blog técnico, y Developers Live para transmitir shows en vivo. También describe proyectos como GLabsPerú para formar laboratorios con facilitadores y hosting, y el reconocimiento Google Developer Expert.
Prosper Marketplace is an online peer-to-peer lending platform that connects borrowers and lenders. It leverages the power of community by allowing borrowers to get endorsements from friends and form groups to build reputation. This combines the best aspects of traditional lending markets like community support and diversification of online lending. The platform has over 400,000 users, facilitated over $87 million in loans, and made over 2.5 million payments to lenders.
Day 2 Recap from #CannesLions #OgilvyCannes Ogilvy
1. The document recaps day 2 of the 2015 Cannes Lions festival. It discusses the lack of diversity in Hollywood and initiatives to support more female filmmakers.
2. It also discusses the need for diversity beyond just gender, including ethnic and cultural diversity. Companies were urged to develop diverse teams and understand different cultural contexts.
3. The future of marketing was also discussed, with the perspective that consumers will have more information and seek more personal relationships with brands. Legacy brands will need to translate their power into these personal relationships.
This document discusses the importance of continuous product improvement through iterative experimentation and user validation. It emphasizes that teams often get stuck in "building traps" where they focus on building features without validating that they solve user needs. Instead, it promotes a scientific approach of planning small experiments, testing hypotheses with users, and using what is learned to continuously improve products and move toward goals. This helps ensure teams stay focused on user needs rather than arbitrary deadlines and helps products better retain, convert, and engage customers over time.
“Spikey Workloads”:
Emergency Management in the Cloud
One of the best use cases for the cloud involves websites with surges in computing needs. This session will feature organizations that have leveraged the cloud to handle their unique burst workloads without breaking the bank:
Speaker: , Solutions Architect, Amazon Web Services
An aspiring young professional with fine suits and fast cars, it’s fair to say that Henry has a slightly inflated ego. Recently, Henry was given a make-or-break career opportunity – to deliver a stunning presentation. So what did Mr. MBA do?
Within 24 hours he assembled a knockout PowerPoint, complete with a fancy company template and exquisite bullet points. Henry pulled out all the stops. He even made handouts of his slides. It was a recipe for success. So he thinks…
Meet Henry. He doesn’t know any better.
Today we live in a business culture that abuses the art and science of public speaking. It’s a culture where PowerPoint is the norm, reading from you slides is accepted, and wasting everyone’s time is a given. When you think about it, it’s really quite disturbing.
Now… meet Erica. Erica is changing the world.
A general futurist look at how linear, exponential and discontinuous growth is shaping the future of technology and what may be expected in key areas such as hardware, software, semiconductors, artificial intelligence, nanotechnology, biotechnology, life extension and virtual worlds.
Audio: http://feeds.feedburner.com/BroaderPerspectivePodcast
Alex M. Clark, Chemical Education, ACS 2012 PhiladelphiaAlex Clark
Presentation at the American Chemical Society meeting (Philadelphia, 2012) by Alex M. Clark from Molecular Materials Informatics, Inc. Use of mobile chemistry apps in education.
Novo Nordisk's journey in developing an open-source application on Neo4jNeo4j
This document discusses the development of an open-source application called OpenStudyBuilder that was built using Neo4j graph database. OpenStudyBuilder has three main components - a clinical metadata repository, a web application interface, and an API layer. It applies domain-driven design principles to model complex clinical study data. Some challenges discussed include performance issues with the Neo4j ORM library, how to present graph data in tables, changing data models over time which requires data migrations, and potential limitations for non-profit or smaller users due to reliance on Neo4j Enterprise features. In summary, the document outlines how a Neo4j database was used as the data store for an enterprise clinical study specification application to effectively model
Cheminformatics
workflows using the
mobile + cloud platform. Presentation by Dr. Alex M. Clark of Molecular Materials Informatics at the NETTAB 2013 meeting in Venice, Italy. The presentation introduces the significance of mobile apps in science, and the scope of their capabilities in chemical structure informatics. The bulk of the talk describes an account of a preliminary workflow using open science data to search for viable leads for a cure for tuberculosis. The workflow described makes use of a combination of mobile, cloud and conventional desktop-based technology, all stitched together by facile communication, sharing and collaboration features.
Utilising Cloud Computing for Research through Infrastructure, Software and D...David Wallom
This document discusses using cloud computing for research through Infrastructure as a Service (IaaS), Software as a Service (SaaS), and Desktop as a Service (DaaS). For IaaS, it describes the EGI Federated Cloud which provides cloud services from multiple public and private sector providers. For SaaS, it discusses Hub for managing the research lifecycle and data, and Chipster for bioinformatics analysis. For DaaS, it covers EOSCloud which provides virtual desktops for bioinformatics research through the JASMIN cloud. Overall it promotes cloud computing for enabling flexible infrastructure, services, and environments to support diverse research needs.
Alex M. Clark, CINF, ACS 2012 PhiladelphiaAlex Clark
Presentation at the American Chemical Society meeting (Philadelphia, 2012) by Alex M. Clark from Molecular Materials Informatics, Inc. Mobile apps participating in open science, both content creation and consumption.
How to Teach Like an Award-winning InstructorJoel Gardner
This presentation illustrates some of the strategies and approaches used by award-winning instructors in higher education. Strategies include the us of Merrill's First Principles of Instruction. The presentation is based on a study done by Joel Gardner found at https://www.academia.edu/3538810/
This document provides advice for developing a business idea called BlogFollower, which would help bloggers make money through an automated service that follows blogs via RSS, email, Twitter, and Facebook. It discusses researching competitors, identifying the target audiences of bloggers and advertisers, determining how to make money through subscriptions or advertising cuts, creating an iterative development plan, and emphasizing continuous improvement and marketing. The core of the product would syndicate blogs across multiple platforms while facilitating self-serve advertising sales.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise boosts blood flow, releases endorphins, and promotes changes in the brain which help enhance one's emotional well-being and mental clarity.
Modern Architectural Masterpieces - design masterpiecesMakala D.
This document lists the names and locations of various uniquely designed buildings around the world, including dome-shaped houses in Florida and India, casinos in Macao and buildings shaped like pianos, violins, and elephants in China, Thailand, and various other countries.
The document discusses iterative design and provides examples of logo design projects. It describes iterative design as a step-by-step process that allows designers to start with initial ideas and refine them over multiple rounds of feedback and revisions. Examples show early sketches and concepts for two logo design projects that were refined over several iterations, receiving feedback at each stage from clients and other designers until a final design was selected. The process is described as reducing pressure to find a perfect solution immediately while allowing ideas to develop through iteration.
Get ready for 2014 planning by benchmarking the financial performance of your supply chain. Using a database of over 50 metrics with 20 years of data, the Supply Chain Insights team can help you better understand your supply chain potential. This analysis enables visualization of company performance on managing the trade-offs of growth, profitability, inventory/cash cycles and complexity.
We find that each company has a unique pattern in how they managed trade-offs. The analysis helps you benchmark against your peer group and make a conscious choice. Through a deeper understanding of industry averages and outliers, this type of study helps you to better understand your supply chain potential. While many companies have used this service to understand public performance, many leaders have taken it one step further to benchmark divisions or product groups within their companies.
This document discusses Finland's startup ecosystem and opportunities to support scalable startups. It notes that job growth will increasingly come from new companies, not existing ones, and outlines six types of startups. It argues that scalable startups offering unknown solutions will provide the most jobs but require a strong ecosystem. However, Finland currently lacks experienced entrepreneurs and policies that encourage risk-taking and startups. The document recommends Finland focus public funding on attracting private incubators and venture capital rather than directly funding companies to best support scalable startups and future job growth.
Este documento presenta varios programas de Google DevRel para Latinoamérica, incluyendo Academic Developer Technology Groups para formar grupos de I+D en universidades, University Class para dictar clases en línea, Lookthiscode para un blog técnico, y Developers Live para transmitir shows en vivo. También describe proyectos como GLabsPerú para formar laboratorios con facilitadores y hosting, y el reconocimiento Google Developer Expert.
Prosper Marketplace is an online peer-to-peer lending platform that connects borrowers and lenders. It leverages the power of community by allowing borrowers to get endorsements from friends and form groups to build reputation. This combines the best aspects of traditional lending markets like community support and diversification of online lending. The platform has over 400,000 users, facilitated over $87 million in loans, and made over 2.5 million payments to lenders.
Day 2 Recap from #CannesLions #OgilvyCannes Ogilvy
1. The document recaps day 2 of the 2015 Cannes Lions festival. It discusses the lack of diversity in Hollywood and initiatives to support more female filmmakers.
2. It also discusses the need for diversity beyond just gender, including ethnic and cultural diversity. Companies were urged to develop diverse teams and understand different cultural contexts.
3. The future of marketing was also discussed, with the perspective that consumers will have more information and seek more personal relationships with brands. Legacy brands will need to translate their power into these personal relationships.
This document discusses the importance of continuous product improvement through iterative experimentation and user validation. It emphasizes that teams often get stuck in "building traps" where they focus on building features without validating that they solve user needs. Instead, it promotes a scientific approach of planning small experiments, testing hypotheses with users, and using what is learned to continuously improve products and move toward goals. This helps ensure teams stay focused on user needs rather than arbitrary deadlines and helps products better retain, convert, and engage customers over time.
“Spikey Workloads”:
Emergency Management in the Cloud
One of the best use cases for the cloud involves websites with surges in computing needs. This session will feature organizations that have leveraged the cloud to handle their unique burst workloads without breaking the bank:
Speaker: , Solutions Architect, Amazon Web Services
An aspiring young professional with fine suits and fast cars, it’s fair to say that Henry has a slightly inflated ego. Recently, Henry was given a make-or-break career opportunity – to deliver a stunning presentation. So what did Mr. MBA do?
Within 24 hours he assembled a knockout PowerPoint, complete with a fancy company template and exquisite bullet points. Henry pulled out all the stops. He even made handouts of his slides. It was a recipe for success. So he thinks…
Meet Henry. He doesn’t know any better.
Today we live in a business culture that abuses the art and science of public speaking. It’s a culture where PowerPoint is the norm, reading from you slides is accepted, and wasting everyone’s time is a given. When you think about it, it’s really quite disturbing.
Now… meet Erica. Erica is changing the world.
A general futurist look at how linear, exponential and discontinuous growth is shaping the future of technology and what may be expected in key areas such as hardware, software, semiconductors, artificial intelligence, nanotechnology, biotechnology, life extension and virtual worlds.
Audio: http://feeds.feedburner.com/BroaderPerspectivePodcast
Alex M. Clark, Chemical Education, ACS 2012 PhiladelphiaAlex Clark
Presentation at the American Chemical Society meeting (Philadelphia, 2012) by Alex M. Clark from Molecular Materials Informatics, Inc. Use of mobile chemistry apps in education.
Novo Nordisk's journey in developing an open-source application on Neo4jNeo4j
This document discusses the development of an open-source application called OpenStudyBuilder that was built using Neo4j graph database. OpenStudyBuilder has three main components - a clinical metadata repository, a web application interface, and an API layer. It applies domain-driven design principles to model complex clinical study data. Some challenges discussed include performance issues with the Neo4j ORM library, how to present graph data in tables, changing data models over time which requires data migrations, and potential limitations for non-profit or smaller users due to reliance on Neo4j Enterprise features. In summary, the document outlines how a Neo4j database was used as the data store for an enterprise clinical study specification application to effectively model
Cheminformatics
workflows using the
mobile + cloud platform. Presentation by Dr. Alex M. Clark of Molecular Materials Informatics at the NETTAB 2013 meeting in Venice, Italy. The presentation introduces the significance of mobile apps in science, and the scope of their capabilities in chemical structure informatics. The bulk of the talk describes an account of a preliminary workflow using open science data to search for viable leads for a cure for tuberculosis. The workflow described makes use of a combination of mobile, cloud and conventional desktop-based technology, all stitched together by facile communication, sharing and collaboration features.
Utilising Cloud Computing for Research through Infrastructure, Software and D...David Wallom
This document discusses using cloud computing for research through Infrastructure as a Service (IaaS), Software as a Service (SaaS), and Desktop as a Service (DaaS). For IaaS, it describes the EGI Federated Cloud which provides cloud services from multiple public and private sector providers. For SaaS, it discusses Hub for managing the research lifecycle and data, and Chipster for bioinformatics analysis. For DaaS, it covers EOSCloud which provides virtual desktops for bioinformatics research through the JASMIN cloud. Overall it promotes cloud computing for enabling flexible infrastructure, services, and environments to support diverse research needs.
Alex M. Clark, CINF, ACS 2012 PhiladelphiaAlex Clark
Presentation at the American Chemical Society meeting (Philadelphia, 2012) by Alex M. Clark from Molecular Materials Informatics, Inc. Mobile apps participating in open science, both content creation and consumption.
Under the grid computing paradigm, large sets of heterogeneous resources can be aggregated and shared. Grid development and acceptance hinge on proving that grids reliably support real applications, and on creating adequate benchmarks to quantify this support. However, applications of grids (and clouds) are just beginning to emerge, and traditional benchmarks have yet to prove representative in grid environments. To address this chicken-and-egg problem, we propose a middle-way approach: create and run synthetic grid workloads comprised of applications representative for today's grids (and clouds). For this purpose, we have designed and implemented GrenchMark, a framework for synthetic workload generation and submission. The framework greatly facilitates synthetic workload modeling, comes with over 35 synthetic and real applications, and is extensible and flexible. We show how the framework can be used for grid system analysis, functionality testing in grid environments, and for comparing different grid settings, and present the results obtained with GrenchMark in our multi-cluster grid, the DAS.
Mobile Molecular DataSheet Product OverviewAlex Clark
The Mobile Molecular DataSheet is a chemical information app for iOS mobile devices that allows users to view and edit molecular structures, reactions, and associated data. It features a built-in chemical structure editor, reaction drawing tools, data organization capabilities, and the ability to communicate and share information. The app is available for download from the Apple App Store and provides a powerful yet intuitive mobile platform for working with chemical data.
Avogadro is being rewritten and architected to put semantic chemical meaning at the center of its internal data structures in order to fully support data-centric workflows. Computational and experimental chemistry both suffer when semantic meaning is lost; through the use of expressive formats such as CML, along with lightweight data-exchange formats such as JSON, workflows that previously demanded manual intervention to retain semantic meaning can be used. Integration with projects like JUMBO and Open Babel when conversion is required, coupled with codes such as NWChem where direct support for CML is being added, allow for much richer storage, analysis, and indexing of data. As web-based data sources add more semantic structure to their data, Avogadro will take advantage of those resources.
redpill Mobile Case Study (Salvation Army)Peter Presnell
Case study that summarizes key findings by Red Pill Development as they built a mobile interface for Notes applications at Salvation Army. Using asymmetric modernization a mobile interface can be delivered for an entire portfolio of applications in a few days.
Data repositories -- Xiamen University 2012 06-08Jian Qin
The document discusses data repositories and services. It begins by defining what a data repository is, noting that it is a logical and sometimes physical partitioning of data where multiple databases reside. It then outlines some key aspects of data repositories, including technical features like standards, software, and staffing requirements. The document also discusses functions of repositories like content management, archiving, dissemination and system maintenance. It provides examples of institutional repositories and data repositories, highlighting characteristics of each. Finally, it provides a case study on Dryad, an international repository for data and publications in biosciences.
Cloud hosted APIs for cheminformatics on mobile devices (ACS Dallas 2014)Alex Clark
Mobile apps for cheminformatics are quite powerful on their own, but can be significantly boosted by connecting them with cloud-hosted functionality. This talk explores the range of functionality that can be covered simply by making use of apps with stateless webservices, i.e. anonymous access without persistent data.
The document discusses how the Earth System Grid Federation (ESGF) leverages tools from Apache Solr and Apache Object Oriented Data Technology (OODT) to manage and distribute large amounts of climate science data. ESGF is an international collaboration that uses a distributed network of nodes running various software components to provide access to over 2.5 petabytes of climate model output and observational data. This infrastructure supports the research of the Intergovernmental Panel on Climate Change and projects like CMIP5, the largest coordinated climate modeling effort to date.
Advantages and Disadvantages of a Monolithic Repositorymustafa sarac
This document discusses a case study conducted at Google to investigate the advantages and disadvantages of using a monolithic source code repository compared to multiple per-project repositories. The study utilized a survey of Google engineers as well as an analysis of developer tool logs. The survey found that engineers strongly prefer Google's monolithic repository and cited visibility of the codebase and simple dependency management as primary benefits. Engineer logs confirmed that they frequently view and edit code from other teams, indicating they take advantage of increased visibility. However, multi-repo systems provide benefits like more stable dependencies and flexibility in tool selection that a monolithic repo cannot match. Overall, the study uncovered several tradeoffs between the two approaches and that preferred development tools also influence engineers' preferences.
Towards application development for the internet of things updatedPankesh Patel
The document discusses developing a domain model for Internet of Things (IoT) applications. It identifies common IoT behaviors like data collection, sense-compute-actuate, and intermittent sensing. An IoT domain model is presented that captures key concepts like entities, sensors, actuators, devices, and software components, as well as their relationships. The domain model provides benefits like a common understanding of IoT terminology, modeling invariant properties, and enabling modular application design.
In this talk I will review several real-world applications and tools developed at the University of Waikato over the past 15 years. The early applications focused on agricultural problems such as cow culling, venison bruising and grass grubs. Following this we looked at the use of near infrared spectroscopy coupled with data mining as an alternate laboratory technique for predicting compound concentrations in soil and plant samples. Our latest application is in the area of gas chromatography mass spectrometry (GCMS), a technique used to determine in environmental applications, for example, the petroleum content in soil and water samples.
Chemical Databases and Open Chemistry on the DesktopMarcus Hanwell
The modern chemist has access to large databases containing both experimental and calculated data. The power of HPC resources continues to increase, with more practitioners having routine access to powerful computational chemistry tools. This places an increasingly high burden on users to assimilate these resources into their workflow in order to effectively utilize resources. The creation of an open, extensible application framework that puts computational tools, data, and domain specific knowledge at the fingertips of chemists is increasingly important. A data-centric approach to chemistry, storing all data in a searchable database, will empower users to efficiently collaborate, innovate, and push the frontiers of research. Providing an open, user-friendly and extensible application will open up new tools to experimental chemists, while providing computational chemists the ability to address greater challenges. Additionally, by distributing experimental and computational data across the research community, incorporating cheminformatics analytics techniques, and providing visual search for chemical structures, the workflow of both groups can be significantly improved. This requires suitable data formats for data exchange, and databases with appropriate APIs for querying, and uploading data in order to effectively share. This talk will discuss recent progress made in developing a suite of open chemistry applications on the desktop. The applications can query online databases, such as the NIH structure resolver service, download and manipulate structures, and prepare input files for standalone computational chemistry codes. Another application developed to submit jobs, monitor and retrieve results from HPC resources will also be shown, and a desktop chemistry database browser. The Quixote project aims to establish standards for data exchange in computational chemistry, along with data repositories for organizations. Establishing these standards is important to promote open, reproducible chemistry, and their integration into user-friendly desktop applications will promote their integration in the standard workflow of researchers.
Similar to Practical cheminformatics workflows with mobile apps (20)
Mixtures QSAR: modelling collections of chemicalsAlex Clark
This document discusses representing and modeling chemical mixtures. It proposes a new data format called Mixfile or MInChI to hierarchically define mixtures and their components, including concentrations. This format aims to support cheminformatics applications like property prediction. Examples are given modeling theophylline solubility and gas absorption using mixture data. The document also describes applying similar methods to model polymer entropy of mixing using a spreadsheet dataset converted to the mixtures format. It concludes that defining mixtures in digital formats will enable greater analysis, modeling and use of mixture data.
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This document discusses the development of Mixtures InChI (MInChI), a standard for representing chemical mixtures in a machine-readable format. MInChI was developed to address the lack of standards for mixture informatics and interoperability. The document outlines the development of open source tools to generate and edit MInChI notation, as well as efforts to build a community and integrate MInChI into commercial products and databases to enable widespread use and generation of mixture data. Future work discussed includes finalizing the MInChI specification, extending it to additional chemical entities, developing associated properties and metadata, and implementing MInChI at large scale.
Mixtures as first class citizens in the realm of informaticsAlex Clark
Presented at Cambridge (UK) cheminformatics meeting, February 2021. Mixtures of chemicals are underutilised from an informatics point of view, and this presentation shows some of the work done by Collaborative Drug Discovery, IUPAC and InChI Trust to remedy this.
See recording: https://www.youtube.com/watch?v=0ILc0owuEzQ&list=PLfj_gc4RCduuwv9p8lh2xS1EhQ3p_Nd9S&index=1 ... my part starts at 1:05:00
Mixtures: informatics for formulations and consumer productsAlex Clark
The document proposes standards for representing mixtures in a machine-readable format. It introduces Mixfile and MInChI (Mixtures InChI) as hierarchical and concise formats for describing mixtures. Examples of formulations are provided to demonstrate how components, concentrations, and metadata can be encoded. Potential applications of the standards are discussed, such as enabling sophisticated searches of mixture data from publications and vendors to facilitate properties prediction and hazards assessment. Adoption of the standards could help ensure the longevity and sharing of mixture data.
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This document discusses representing chemical mixtures using an open format called Mixfile. It proposes Mixfile as a standard format for mixtures, analogous to Molfile for individual molecules. Tools were created to edit and manipulate Mixfiles. Over 5,600 real-world mixture examples were extracted from text and represented in the Mixfile format. A MInChI notation was also defined as a condensed representation of mixtures. Future work is proposed to integrate mixture definitions and lookups into electronic lab notebooks and improve automated extraction of mixture information from text.
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This document discusses bringing bioassay protocols into the world of informatics by using semantic annotations. It describes how measurements from bioassays contain many details that are usually only available as text, and outlines an approach using ontologies, natural language processing, and machine learning to extract this information and make it accessible for searching, comparing datasets, and identifying trends. The goal is to make all bioassay protocol data machine readable by developing common templates and annotation standards that can be applied to existing and new assay data sources.
Autonomous model building with a preponderance of well annotated assay protocolsAlex Clark
Combining large amounts of publicly available structure-activity data with assays that have carefully curated annotations opens the door to a number of ways to analyze the data behind the scenes. Combining fully machine readable input for a diverse variety of projects with modelling techniques that can be used without fussy parametrization allows models to be created and updated whenever new data arrives. Predictions from these models can be integrated into normal searching and visualization workflows, without any need for the user to opt-in or make extra decisions. This approach is novel and different from the way structure-activity models are normally deployed: useful predictions can be presented ubiquitously with literally zero additional work on behalf of the user. We will present our efforts to date regarding ways to both passively and actively draw attention to important drug discovery trends while exploring compounds and assays.
Representing molecules with minimalism: A solution to the entropy of informaticsAlex Clark
Cheminformatics as we know it is possible because so many molecular structures can be represented with datastructures and rules that are at first glance quite trivial. This first impression is highly misleading, since even within supposedly well behaved domains, edge cases arising from issues such as resonance, tautomerization, symmetry and stereochemistry - to name but a few - quickly add up. To supplement these genuine challenges, there is a whole additional class of problems caused by the mismatch between chemists' understanding of molecules and the datatypes that are necessary to capture a structure for informatics purposes. This line is blurred by the convenience of representing structures in a form that is very closely related to the diagram styles that have been in use since the dawn of chemistry. There are currently four major approaches to structure representation: connection tables (e.g. MDL Molfile), sketches (e.g. ChemDraw), canonical strings (e.g. SMILES and InChI) and atomic models (numerous 3D formats). Not only do all of these approaches have valid use cases, but they are deceptively incompatible with each other, even when addressing identical needs. Almost without exception, format conversions are not commutative, and every translation involves losing some amount of data. Given that recording chemical structures in machine readable form has become such a critical part of scientific research, it is essential to define a fundamental representation that captures the key structural definition asserted by the experimental chemist, for a broad and useful range of molecules, and ideally in a way that is closely related to visual drawing mnemonics. The number of data concepts needed to satisfy these conditions is quite small, and is mostly satisfied by the most commonly used subset of the venerable MDL Molfile format. This presentation will discuss how this subset, with a few minor corrections and clarifications, can and should be used as the reference standard for molecules, and how the informatics community can benefit from having well defined standards.
Presentation to the EPA (August 2016) about the BioAssay Express project, from Collaborative Drug Discovery. Describes the history and potential of the project, with the intention of opening a dialog about incorporating EPA toxicity data.
SLAS2016: Why have one model when you could have thousands?Alex Clark
Society for Laboratory Automation & Screening, San Diego, January 2016. Presented by Dr. Alex M. Clark. Describes the use of open data resources (ChEMBL) to build target-activity models for drug discovery and toxicity prediction, on a massive scale, using a fully automated process. Concludes with a demo of the PolyPharma app, which shows how these models can be used for prospective drug discovery.
The anatomy of a chemical reaction: Dissection by machine learning algorithmsAlex Clark
This document discusses using machine learning algorithms to analyze chemical reaction data. It describes how current reaction reporting formats are not well-suited for computational analysis. A more structured reporting format is proposed to fully describe reactions in a digitally friendly way, including specifying reactants, products, quantities, yields, and metrics like atom efficiency. This structured data would allow modeling of reaction substitutability and enable large-scale machine learning of chemical transformations.
Compact models for compact devices: Visualisation of SAR using mobile appsAlex Clark
Presented at American Chemical Society meeting, Boston, 2015. Describes how cheminformatics algorithms and visualisation interfaces have advanced on mobile apps to cover a diverse variety of functionality, increasingly calculated on the device itself rather than deferring to a web service. Culminates in a demo of the PolyPharma app prototype (see http://cheminf20.org/2015/08/06/the-polypharma-app-a-mash-up-of-ideas-and-technology)
Green chemistry in chemical reactions: informatics by designAlex Clark
Chemical informatics technology can be of assistance to chemists for describing reactions in numerous ways, including calculating green chemistry metrics such as process mass intensity, E-factor and atom economy. To facilitate this, chemical reactions have to be described in more precise detail than is the norm for most chemists. There are also numerous practical ways to add more green chemistry functionality to lab notebooks, such as enumerating searchable reaction transforms for environmentally favourable reactions, automatically looking up toxicity and hazard information, and others which are mentioned in the slides.
This presentation was given at the Green Chemistry & Engineering conference in 2015 (Americal Chemical Society Green Chemistry Insititute).
Green chemistry is an important subject that needs to be a part of every chemist's education, as well as a part of the daily routine of the professional synthetic chemist. This talk describes how a new app can be used to bring green chemistry metrics to reaction descriptions, once they are captured in a proper cheminformatics format. It also describes some of the additional data resources that can be incorporated into the user experience, and how this helps both students and professionals.
Building a mobile reaction lab notebook (ACS Dallas 2014)Alex Clark
This document discusses building a mobile electronic lab notebook focused on chemical reactions called the Green Lab Notebook. It would allow users to draw chemical structures, balance reactions, and calculate quantities, yields, and green metrics. Key features include digitally capturing reaction data, prioritizing computer-friendly data structures and intuitive workflows, and linking to external databases for solvent data, sustainable feedstocks, and curated green reaction transforms. The goal is to facilitate recording, analyzing, and promoting the reuse of experimental reaction data in a sustainable chemistry context.
Open Drug Discovery Teams @ Hacking Health MontrealAlex Clark
Alex Clark of Molecular Materials Informatics (http://molmatinf.com) presents the Open Drug Discovery Teams project to the Hacking Health Montreal audience, April 2013.
Mobile+Cloud: a viable replacement for desktop cheminformatics?Alex Clark
Introduces the prospect of performing cheminformatics workflows using mobile devices for the UI and cloud resources for heavy duty computation. Describes a sample workflow using the SAR Table app to propose potential new drugs for eliminating malaria.
2. 2
Introduction
• Mobile apps in chemistry happening real fast: 3 years ago nothing
but the most trivial of apps...
• ... now there's a whole ecosystem
• For a detailed list of apps, see www.scimobileapps.com wiki
• Complex workflows can be executed using just mobile apps &
cloud-based infrastructure
• Molecular Materials Informatics founded with the goal of making
mobile + cloud solutions into a viable replacement for
cheminformatics infrastructure
info@molmatinf.com
3. 3
1. Information delivery
• Many apps designed for mainly one-way transmission of information,
i.e. content consumption
- Green Solvents
- Approved Drugs
- The Elements
- ACS Mobile, RSC Mobile
- Reagents, Organic Named Reactions,
• Typically a very simple user interface: close to zero learning curve
• Many for education, but some are relevant to professionals
• Mobile devices very well suited for these types of apps: quite easy to
produce, and can be very useful, despite their limited capacity
4. 4
2. Catalog lookup
• Apps designed to input a search query, submit the query to a server,
then display and utilise the results
• Examples include:
- ChemSpider Mobile
- SPRESImobile
- Mobile Reagents
- iKinase
- iProtein
• These apps are moderately difficult to produce; most of the action
takes place on remote servers, i.e. hosting the data and the search
algorithms
5. 5
3. Data visualisation
• Apps designed to visualise existing chemical data, e.g. PDB entries,
docking results, structure-activity relationships and collections of
molecules
• Examples include:
- Molecules
- PyMol
- iMolView
- iSpartan
- iMolecule Builder
- SAR Table
6. 6
4. Data creation
• Some of the most sophisticated apps provide the ability to assemble
chemical data within the app:
- molecular structures
- reactions
- scalar data
- higher order markup (SAR)
• Data can be created with the app UI, or pieces can be imported
from other sources. Examples:
- Mobile Molecular DataSheet (MMDS)
- MolPrime
- SAR Table
- Chirys, ChemDoodle Mobile, ChemJuice
7. 7
5. Lab notebooks
• Apps designed for entering information about experiments
• Ultimate objective is the paperless laboratory
• Mobile laboratory notebooks are mostly generic rather than
chemically aware, i.e. not specifically for synthesis
• Prototypical example is Yield101 (education focused)
• General purpose scientific lab notebook apps:
- LabGuru
- irisnote
• Many web-based lab notebooks that are vendor-endorsed for iPad
use
8. 8
6. Collaboration and sharing
• Apps have many options for sharing and importing data, e.g.
- Email (personal, bidirectional)
- Remote hosting (private, collaborative)
- Web sharing and tweeting (global, open)
• Examples:
- MMDS
- MolSync
- Reaction101
- ODDT
9. 9
Mobile app limitations
• Touchscreen is small, inaccurate: very different user interface
• Modern mobile processors are fast (Moore's law), but respecting
battery life requires careful conservation of CPU resources
• Limited memory and constricted multi-tasking: an app has a tightly
defined lifespan, and is expected to be lightweight, low-state
• Modular nature of apps makes large datasets hard to work with
• Functionality is often heavily network dependent
• Limited choice of development environments: native or web, stark
choice of quality vs. portability
• When these limitations can be overcome, the mobile + cloud
combination becomes a full replacement for desktop computing
10. 10
Workflow
• The following slides demonstrate a multipart workflow scenario
using:
- iOS apps (Apple iPhone/iPod/iPad)
- cloud-hosted webservices
• Each step is carried out using technology that is currently available...
• ... and is representative of the state of the art
• The sequential tasks are based on a medicinal chemistry
exploration: investigating new tuberculosis drugs
• Any workflow with a similar level of technology is probably either
already possible, or could be made possible
11. 11
Step 1: Lookup
• Lookup a core scaffold for a series of known tuberculosis inhibitors
using the ChemSpider Mobile app:
12. 12
ChemSpider
• View ChemSpider record in mobile browser
• Structure can be downloaded as MDL Molfile
• Mofiles can be opened directly in apps
• Select Mobile Molecular DataSheet (MMDS)
13. 13
Step 2: Lookup a datasheet
• Imported molecular
structure into the scratch
sheet
• Open the Run WebService
feature...
14. 14
ChEBI Query
• Substructure search for the core scaffold produces a new datasheet
15. 15
Step 3: Assign scaffolds
• Open in SAR Table app...
• ... which represents a table of
compounds as scaffolds &
substituents
17. 17
Scaffolds + Substituents
• Structure-activity relationship is
aided by classifying scaffold and
substituents
• Assignment process is partly
manual, partly automated
• Structure fragments can be drawn
within the app, copied from other
cells, or computed by a webservice
18. 18
Step 4: Merge
• Have existing table, created from literature
data:
- V. Makarov et al., Benzothiazinones kill
Mycobacterium tuberculosis by
blocking arabinan synthesis, Science 324,
pp. 801-804 (2009)
• Activity values colour-coded by defining a
scheme
• Append the query data to the end...
19. 19
Appended rows
• Webservice builds a model based on existing
activity values
• Applies predictions to missing values
blank
activity
20. 20
Step 5: Examine SAR
matrix
view
• Predicted values suggest some promising R2 &
R3 substituents, based on known compounds
• These are from ChEBI, so can be looked up
21. 21
Step 6: Propose new lead
• Identify values for R2 and R3 by
examining current structure-
activity relationship
• Create a new row with the
proposed substituent moieties:
Scaffold R1 R2 R3 Molecule
22. 22
Step 7: Find a recipe
• Open the core structure in SPRESImobile app
• Search for similar structures, and search As Product to find a promising
synthesis that can be adapted
23. 23
Find reaction
• Found a promising synthesis
• Starting materials suitable for desired
functionalisation
• Link to literature provided within the app:
can be opened in Safari Mobile
24. 24
Step 8: Plan synthesis
• Can open the reaction with Yield101 app: scheme is transferred
• Need to customise the reaction components and add quantities
• Have the literature reference on hand
25. 25
Adapt synthesis
• Edit structure reactant and product to include functional groups
• Specify known quantities and expected yield: all implied quantities are
calculated, as is the process mass intensity
26. 26
Run the experiment
• Can use the mobile device in the
lab, and record the results directly
• OR:
• Create a PDF document, and print
it directly from the device or send
the file by email...
• ... then enter the results later.
27. 27
• Step 9: Sharing data
Many ways to share data: use Open-With to transfer to MMDS
• From there, can:
- send data by email
- export presentation quality graphics
- share on web & tweet
28. 28
Microsoft Office documents
• Outgoing emails can include many
attachments:
- machine-readable data
- graphics
• Graphics options include MS Word
and Excel documents with
embedded vector graphics
29. 29
Sharing with Dropbox
• Can link datasheets to Dropbox
using the MolSync app
• Storing data on Dropbox opens up
an entire landscape of
collaboration and sharing options
31. 31
Open Drug Discovery Teams
• Relevant tweets get picked up by the Open Drug Discovery Teams
project, and made available for browsing with a free app
• Chemical data is parsed and can be accessed with other apps
32. 32
Conclusion
• Gone from paper to idea to hypothesis to experiment to online
publication... all using mobile apps
• Multi-app workflows involve content creation, content consumption,
networked services and remote computation
• Realtime calculations are done by the apps, complex calculations are
offloaded to cloud servers
• Mobile apps are good for creating, visualising and sharing small
datasets
• Apps can access big datasets, but pipelining tools for manipulating
big data are underdeveloped
33. 33
Future work
• Evolution from proof-of-concept phase to apps designed to solve
specific workflows...
• ... expect more customised apps
• More integration with cloud services: apps cannot work with big
data without back-end support
• Pistoia Alliance is currently working on an AppStore, which provides
- an alternative storefront for mobile apps
- standardised service infrastructure, for big data & calculations
• Gradual replacement of all mainstream chemical information
software
34. 34
References
• Redefining Cheminformatics with Intuitive Collaborative Mobile
Apps, A.M. Clark, S. Ekins, A.J. Williams, Molecular Informatics, 31, 569-
584 (2012)
• Mobile apps for chemistry in the world of drug discovery, A.J.
Williams, S. Ekins, A.M. Clark, J.J. Jack, R.L. Apodaca, Drug Discovery
Today, 16, 928-939 (2011)
• Open Drug Discovery Teams: A Chemistry Mobile App for
Collaboration, S. Ekins, A.M. Clark, A.J. Williams, Molecular Informatics,
31, 585-597 (2012)
• Basic primitives for molecular diagram sketching, A.M. Clark, Journal
of Cheminformatics, 2:8 (2010)
35. Acknowledgments
• Antony Williams
• Sean Ekins
• Leah Rae McEwen, David Martinsen
• ACS CINF Division
http://molmatinf.com
http://molsync.com
• Inquiries to http://cheminf20.org
info@ molmatinf.co
m @aclarkxyz
35