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.
ChemOfice is an universal software package frm the CambridgeSoft Corporation. It is one of the most popular computer program in many chemical laboratories around the world.
CS Chem3D program is designed for visualization of chemical compounds, computer simulation and calculations.
The main elements of the user interface can be divided as follows:
Main menu;
Main panel;
Control panel.
In the center of the screen there is a working window, which displays the process of creating and editing three-dimensional models of molecules.
ChemOfice is an universal software package frm the CambridgeSoft Corporation. It is one of the most popular computer program in many chemical laboratories around the world.
CS Chem3D program is designed for visualization of chemical compounds, computer simulation and calculations.
The main elements of the user interface can be divided as follows:
Main menu;
Main panel;
Control panel.
In the center of the screen there is a working window, which displays the process of creating and editing three-dimensional models of molecules.
This lecture outlines the different strategies for finding a fragment hit and the subsequent elaboration strategies used in order to increase potency to develop a lead compound in drug discovery.
Presentation delivered at Lehigh University (Bethlehem, PA) on Friday, April 26, 2019.
This presentation begins with discussing the history of the cheminformatics field. In addition, it also discusses a question "what makes cheminformatics different from bioinformatics?" (by comparing the ways in which molecules are described and compared in the two fields).
A QSAR is a mathematical relationship between a biological activity of a molecular system and its geometric and chemical characteristics.
QSAR attempts to find consistent relationship between biological activity and molecular properties, so that these “rules” can be used to evaluate the activity of new compounds.
ADMET properties prediction using AI will accelerate the process of drug discovery.
This slide mostly focuses on using graph-based deep learning techniques to predict drug properties.
Mass spectrometry principle working inttumentation advantages diadvantages GC...sneha010196
Mass spectroscopy
History
What is mass number
Ms principle
Ms working
Instrumentation
Mass analysers
Fragmentation rules
Nitrogen rule
Types of peaks
Interpretation of spectra
Gc ms
Applications of ms
Advantages & disadvantages
Reference.
This lecture outlines the different strategies for finding a fragment hit and the subsequent elaboration strategies used in order to increase potency to develop a lead compound in drug discovery.
Presentation delivered at Lehigh University (Bethlehem, PA) on Friday, April 26, 2019.
This presentation begins with discussing the history of the cheminformatics field. In addition, it also discusses a question "what makes cheminformatics different from bioinformatics?" (by comparing the ways in which molecules are described and compared in the two fields).
A QSAR is a mathematical relationship between a biological activity of a molecular system and its geometric and chemical characteristics.
QSAR attempts to find consistent relationship between biological activity and molecular properties, so that these “rules” can be used to evaluate the activity of new compounds.
ADMET properties prediction using AI will accelerate the process of drug discovery.
This slide mostly focuses on using graph-based deep learning techniques to predict drug properties.
Mass spectrometry principle working inttumentation advantages diadvantages GC...sneha010196
Mass spectroscopy
History
What is mass number
Ms principle
Ms working
Instrumentation
Mass analysers
Fragmentation rules
Nitrogen rule
Types of peaks
Interpretation of spectra
Gc ms
Applications of ms
Advantages & disadvantages
Reference.
Project is from the chapter Electrochemistry . Project is based on the rusting of iron when coupled with different metals . One of the easiest projects in chemistry.
Please do like , share and comment if my work helped you ;)
chemistry project for class 12 on analysis of honeyRadha Gupta
this is a project for class 12 boards for chemistry subject on analysis of honey.it will be very helpful for students who are searching for chemistry project
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.
Docker & aPaaS: Enterprise Innovation and Trends for 2015WaveMaker, Inc.
WaveMaker Webinar: Cloud-based App Development and Docker: Trends to watch out for in 2015 - http://www.wavemaker.com/news/webinar-cloud-app-development-and-docker-trends/
CIOs, IT planners and developers at a growing number of organizations are taking advantage of the simplicity and productivity benefits of cloud application development. With Docker technology, cloud-based app development or aPaaS (Application Platform as a Service) is only becoming more disruptive − forcing organizations to rethink how they handle innovation, time-to-market pressures, and IT workloads.
Kitware is involved with Qt in two main areas. First, Kitware is the provider of the CMake (www.cmake.org) build tool which is used to build KDE, the flagship open source Qt project. In addition, Kitware has been using Qt for the ParaView (www.paraview.org) project. ParaView is an open-source, multi-platform data analysis and visualization application. With the recent change in Qt licensing Kitware is also starting to use Qt for many other open source scientific and medical projects. For cross platform C++ GUI development Qt now stands alone as really the only viable choice. This talk will cover the CMake build system, and the impact Qt and Qt derived projects are having on state of the art scientific computation.
Presentation by BIll Hoffman held during Qt Developer Days 2009.
http://qt.nokia.com/developer/learning/elearning
UI Dev in Big data world using open sourceTech Triveni
He will be sharing his last 10 years of experience in UI Development for Big Data Analytics & ML world using available open-source plethora in the market. How 'UI dev' needs to target big data problems?
Key points to consider while choosing any open-source framework/library for the big data world.
Do you need to write a custom framework or use ready-made open source, when what to choose?
How dev can leverage open source frameworks like Angular, REACT to making big data apps faster?
How you can extend open-source BI tools like Kibana, superset graphana to make UI development tool?
How to show network big data using open source graph libraries?
How to deal with real-time data in Big data UI?
Why use & contribute to open source?
Design UI for future as in Big data world customer problems keep changing with time. Showcasing demo for our real customer's problems, how we achieved using these open source libraries.
Zero to ten million daily users in four weeks: sustainable speed is kingplumbee
A successful social game can achieve very rapid growth to large scale during a short period of time, with extreme cases (CityVille, The Sims Social, Gardens of Time) achieving millions of daily active users and tens of millions of monthly active users within a few weeks of launch. In this presentation I will argue that achieving the fastest possible sustainable speed of development is the most important technical factor in launching and operating a successful social game, or indeed any large-scale web business -- whether at startup phase, during rapid growth, or established and mature. I will propose some techniques, both technical and non-technical, to optimize rapid development at large scale. Finally, I will describe some of the typical architecture, processes, and tools used in the development of both the transactional and analytical systems of social games.
An Open Source Workbench for Prototyping Multimodal Interactions Based on Off...Jean Vanderdonckt
In this paper we present an extensible software workbench for supporting the effective and dynamic prototyping of multimodal interactive systems. We hypothesize the construction of such applications to be based on the assembly of several components, namely various and sometimes interchangeable modalities at the input, fusion-fission components, and also several modalities at the output. Successful realization of advanced interactions can benefit from early prototyping and the iterative implementation of design requires the easy integration, combination, replacement, or upgrade of components. We have designed and implemented a thin integration platform able to manage these key elements, and thus provide the research community a tool to bridge the gap of the current support for multimodal applications implementation. The platform is included within a workbench offering visual editors, non-intrusive tools, components and techniques to assemble various modalities provided in different implementation technologies, while keeping a high level of performance of the integrated system.
How static analysis supports quality over 50 million lines of C++ codecppfrug
Retour d’expérience sur l'utilisation d'outils d'analyse statique pour maintenir des activités Q&A dans le développement de logiciel scientifique de grande échelle au sein du CERN.
Abstract
The idea of this talk is to help development teams to make correct architectural decisions.
Andrei will highlight the basic architectural principles and show ways to achieve architecture that is good enough to cover the project requirements and evolve in the future.
He will also present several cases from real projects, where wrong, missing, or over-sophisticated architecture decisions really hurt the development teams:
- Painful sharing: do shared modules increase reusability or will be the source of problems?
- Microservices are the solution to every problem!
- Non-extensible extensibility: too sophisticated configuration hurts
- Over fine-grained: incorrect splitting to Microservices can make life even harder as with monolith
- Convey horizontal split: how organizational driven split can jeopardise the architecture
- Model-driven: central responsibility blocks and limits the team
- Cargo cult: blindly following patterns and rule can produce an unmaintainable system
- Freestyle architecture: what happens if teams completely ignore architecture
- Improve with less intelligence: smart endpoint and dumb pipes
Similar to Avogadro, Open Chemistry and Semantics (20)
Open Chemistry, JupyterLab and data: Reproducible quantum chemistryMarcus Hanwell
The Open Chemistry project is developing an ambitious platform to facilitate reproducible quantum chemistry workflows by integrating the best of breed open source projects currently available in a cohesive platform with extensions specific to the needs of quantum chemistry. The core of the project is a Python-based data server capable of storing metadata, executing quantum chemistry calculations, and processing the output. The platform exposes RESTful endpoints using programming language agnostic web endpoints, and uses Linux container technology to package quantum codes that are often difficult to build.
The Jupyter project has been leveraged as a web-based frontend offering reproducibility as a core principle. This has been coupled with the data server to initiate quantum chemistry calculations, cache results, make them searchable, and even visualize the results within a modern browser environment. The Avogadro libraries have been reused for visualization workflows, coupled with Open Babel for file translation, and examples of the use of NWChem and Psi4 will be demonstrated.
The core of the platform is developed upon JSON data standards, and encouraging the wider adoption of JSON/HDF5 as the principle storage mediums. A single page web application using React at its core will be shown for sharing simple views of data output, and linking to the Jupyter notebooks that documents how they were made. Command line tools and links to the Avogadro graphical interface will be shown demonstrating capabilities from web through to desktop.
Presented at the first Avogadro User Meeting, and presents an overview of the history of Avogadro development. It discusses changes in the rewrite, and the broader Open Chemistry project.
Avogadro: Open Source Libraries and Application for Computational ChemistryMarcus Hanwell
In order to tackle upcoming molecular simulation and visualization challenges in key areas of materials science, chemistry and biology it is necessary to move beyond fixed software applications. The Avogadro project is in the final stages of an ambitious rewrite of its core data structures, algorithms and visualization capabilities. The project began as a grass roots effort to address deficiencies observed by many of the early contributors in existing commercial and open source solutions. Avogadro is now a robust, flexible solution that can tie in to and harness the power of VTK for additional analysis and visualization capabilities.
Science is not an exclusive realm limited to people in white lab coats with Ph.D.s, but rather a way of thinking applied to everything from advanced computational simulations on nuclear material to brewing an award-winning beer. However, current scientific practices are undermining the very progress and innovation they were designed to stimulate, bringing us to the brink of a crisis. The lack of openness, access to data and methods, and opaque review processes have created a system that threatens the very foundation of scientific reasoning.
However, there are many people and organizations working to prevent the collapse of the pillars science. The champions of the Open Science movement are passionately working to change the course of science and steer it back to its roots of reproducibility. In the process, the movement is also driving a new democratization of science that enables a much broader participation in scientific work and puts within the reach of the normal citizen the possibility of reproducing experiments and taking part in the scientific process. Science will fuel the future, if only we are all open to it.
http://tedxalbany.org/talks/2013/marcus-hanwell
Open Chemistry: Realizing Open Data, Open Standards, and Open SourceMarcus Hanwell
The Blue Obelisk has brought together the computational chemistry community and those who are passionate about Open Chemistry and realizing the promise of Open Data, Open Standards, and Open Software (ODOSOS); the three pillars the group promotes. We will present current work that has taken place over the past five years, which is inspired by these pillars, and present plans for future work.
The group is actively engaged in multiple open source projects that rely on and promote open standards and open data including: Avogadro (a powerful 3D molecular editor), OpenQube (a library for quantum mechanics), ChemData (a tool for large-scale chemical data analysis and visualization), Chemkit (a library for cheminformatics), MoleQueue (a HPC queue manager), and VTK (a library for scientific data visualization). The Open Chemistry project benefits greatly from the activities of the Blue Obelisk and makes use of several prominent open-source projects including Qt and MongoDB.
In his public lecture, Christian Timmerer provides insights into the fascinating history of video streaming, starting from its humble beginnings before YouTube to the groundbreaking technologies that now dominate platforms like Netflix and ORF ON. Timmerer also presents provocative contributions of his own that have significantly influenced the industry. He concludes by looking at future challenges and invites the audience to join in a discussion.
SAP Sapphire 2024 - ASUG301 building better apps with SAP Fiori.pdfPeter Spielvogel
Building better applications for business users with SAP Fiori.
• What is SAP Fiori and why it matters to you
• How a better user experience drives measurable business benefits
• How to get started with SAP Fiori today
• How SAP Fiori elements accelerates application development
• How SAP Build Code includes SAP Fiori tools and other generative artificial intelligence capabilities
• How SAP Fiori paves the way for using AI in SAP apps
Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. What’s changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
Guy Korland, CEO and Co-founder of FalkorDB, will review two articles on the integration of language models with knowledge graphs.
1. Unifying Large Language Models and Knowledge Graphs: A Roadmap.
https://arxiv.org/abs/2306.08302
2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs:
https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/
Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf91mobiles
91mobiles recently conducted a Smart TV Buyer Insights Survey in which we asked over 3,000 respondents about the TV they own, aspects they look at on a new TV, and their TV buying preferences.
Dev Dives: Train smarter, not harder – active learning and UiPath LLMs for do...UiPathCommunity
💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™:
See how to accelerate model training and optimize model performance with active learning
Learn about the latest enhancements to out-of-the-box document processing – with little to no training required
Get an exclusive demo of the new family of UiPath LLMs – GenAI models specialized for processing different types of documents and messages
This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath.
Speakers:
👨🏫 Andras Palfi, Senior Product Manager, UiPath
👩🏫 Lenka Dulovicova, Product Program Manager, UiPath
DevOps and Testing slides at DASA ConnectKari Kakkonen
My and Rik Marselis slides at 30.5.2024 DASA Connect conference. We discuss about what is testing, then what is agile testing and finally what is Testing in DevOps. Finally we had lovely workshop with the participants trying to find out different ways to think about quality and testing in different parts of the DevOps infinity loop.
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024
https://alandix.com/academic/papers/synergy2024-epistemic/
As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.
Elevating Tactical DDD Patterns Through Object CalisthenicsDorra BARTAGUIZ
After immersing yourself in the blue book and its red counterpart, attending DDD-focused conferences, and applying tactical patterns, you're left with a crucial question: How do I ensure my design is effective? Tactical patterns within Domain-Driven Design (DDD) serve as guiding principles for creating clear and manageable domain models. However, achieving success with these patterns requires additional guidance. Interestingly, we've observed that a set of constraints initially designed for training purposes remarkably aligns with effective pattern implementation, offering a more ‘mechanical’ approach. Let's explore together how Object Calisthenics can elevate the design of your tactical DDD patterns, offering concrete help for those venturing into DDD for the first time!
Welcome to the first live UiPath Community Day Dubai! Join us for this unique occasion to meet our local and global UiPath Community and leaders. You will get a full view of the MEA region's automation landscape and the AI Powered automation technology capabilities of UiPath. Also, hosted by our local partners Marc Ellis, you will enjoy a half-day packed with industry insights and automation peers networking.
📕 Curious on our agenda? Wait no more!
10:00 Welcome note - UiPath Community in Dubai
Lovely Sinha, UiPath Community Chapter Leader, UiPath MVPx3, Hyper-automation Consultant, First Abu Dhabi Bank
10:20 A UiPath cross-region MEA overview
Ashraf El Zarka, VP and Managing Director MEA, UiPath
10:35: Customer Success Journey
Deepthi Deepak, Head of Intelligent Automation CoE, First Abu Dhabi Bank
11:15 The UiPath approach to GenAI with our three principles: improve accuracy, supercharge productivity, and automate more
Boris Krumrey, Global VP, Automation Innovation, UiPath
12:15 To discover how Marc Ellis leverages tech-driven solutions in recruitment and managed services.
Brendan Lingam, Director of Sales and Business Development, Marc Ellis
1. Avogadro, Open Chemistry and Semantics
August 21, 2012
Skolnik Symposium
Marcus D. Hanwell
Kyle Lutz
1
2. Introduction to Kitware
• Founded in 1998: 5 former GE Research employees
• 105 employees: more than 50 PhDs
• Privately held, profitable from creation, no debt
• Rapidly Growing: >30% in 2011, 7M web-visitors/quarter
• Offices
• 2011 Small Business
– Albany, NY Administration’s
– Carrboro, NC Tibbetts Award
– Santa Fe, NM • HPCWire Readers
and Editor’s Choice
– Lyon, France
• Inc’s 5000 List: 2008
– Bangalore, India to 2011
3. Avogadro
• Project began in 2006
• Split into library &
application (plugin-based)
• One of very few open source editors
• Designed to be extensible from the start
• Generates input & reads output from many
codes
• An active and growing community
• Chemistry needs a free, open framework
http://avogadro.openmolecules.net/
3
6. Vision for the Future
• Advancing the state-of-the-art
• Tight integration is needed
• Computational codes
• Clusters/supercomputers
• Data repositories
• Reduce, reuse, recycle!
• Facilitating sharing and
searching of data
• Embracing open data, cheminformatics
6
7. Opening Up Chemistry
• One of the most closed sciences
• Lots of black box proprietary codes
– Only a few have access to the code
– Publishing results from black box codes
– Many file formats in use, little agreement
• More papers should be including data
• Growing need for open standards
• Open tools needed to make that happen
7
8. Introduction to Open Chemistry
• User-friendly integration with
– Computational codes
– HPC/cloud resources
– Database/informatics resources
8
9. Introduction
• An open approach to chemistry software
Build, Test
– Open source frameworks & Package
Community
Review
– Developed openly
– Cross-platform
– Tested, verified
Software
– Contribution model Repository
– Supported by Kitware experts Developers
& Users
• BSD licensed to facilitate research/reuse
9
10. Open Chemistry Development Team
• Assembled an inter-disciplinary team
• Domain specialists: quantum chemistry,
biology, solid-state materials
• Computer scientists: build systems,
queuing, graphics, software process
• Marcus, Kyle, David L., Chris, David C.
10
11. OpenChemistry.org
• New website to promote open chemistry
• Hosts project-specific pages
• Provides an identity for related projects
• Promotes shared ownership of projects
– Website
– Code submission/review
– Testing infrastructure
– Wiki, mailing lists, news, galleries
11
13. Applications Being Developed
• Three independent applications
• Communication handled with local sockets
• Avogadro 2 – structure editing, input
generation, output viewing, and analysis
• MoleQueue – running local and remote
jobs in standalone programs, management
• ChemData – Storage of data, searching,
entry, annotation
13
14. Open Frameworks
• AvogadroLibs – core data structures and
algorithms shared across codes
• OpenQube – a collaboration platform for
quantum data ingestion and visualization
• Chemkit – file I/O, exploration and
chemoinformatics analysis
• VTK – specialized chemistry visualization/
data structures, use of above
14
19. Avogadro2
• Project began 2006
• Split into library &
application (plugin-based)
• One of very few open source editors
• Still using Qt, C++, Eigen, OpenGL
• Uses AvogadroLibs and OpenQube for core data
• Introduces client-server dataflow/patterns
• Includes new, efficient rendering code
• More liberally licensed – from GPL to BSD
19
20. Avogadro: Visualization
• GPU-accelerated rendering
• VTK for advanced visualization
• Support for 2D and 3D data plots
• Optimized data structures
– Large data
– Streaming
• Reworked interface
– Tighter database/workflow integration
20
21. MoleQueue: Job Management
• Tighter integration with remote queues
• Integration with databases
– Retains full log of computational jobs
– Triggers actions on completion
• Plugin-based system
– Easy addition of new codes
– Easy addition of new queuing systems
• Provides a client API for applications
21
23. New CML I/O
• Development of modular CML code
• Allows for multi-pass parsing of CML
• Keeps the CML closer to application
• Much faster, easier to extend and change
• Moving from simple CML to full semantic
documents that can be edited
• Learned from previous work in VTK and
Open Babel
23
24. File Format: CML & HDF5
• Leverages our experience with XDMF
• CML stores semantic data
– Name, formula, atoms, bonds
– Computational code, theory, basis set
• HDF5 used to store heavy data
– Basis set, intermediate data
– Eigenvectors, SCF matrix
– Volumetric data (MOs, electron density)
24
25. Rethinking Input File Generation
• Can we create a CML representation?
– Could be loaded directly by some codes
– Could be translated to input files for others
• Would allow search on input and output
• Could be stored and published
• Makes it easier to set up calculations
• Creates a more uniform experience
25
26. Advanced Impostor Rendering
• Using a scene, vertex buffer objects, and
OpenGL shading language
• Impostor techniques
– Sphere goes from 100s of triangles to 2!
– No artifacts from triangulation
– Scales to millions of spheres on modest GPU
26
28. Building Community
• Community around chemistry
Build, Test
projects & Package
Community
• Using Kitware’s software process Review
– Ensuring quality with continuous
testing
– Code contributions on the web
– Public mailing lists, bug trackers,
code review
• Promoting projects and Software
Repository
participation
– Publications
Developers
– Conferences & Users
– Workshops
28
29. Software Process
• Source code publicly hosted using Git
• Gerrit for code review
• CTest/CDash for testing/summary
– Gerrit can use CDash@Home
• Test proposed changes before merging
• CDash can now provide binaries
– Built nightly, available for direct download
• Wiki, mailing list, bug tracker
29
30. Conclusions
• Real opportunity to make an impact
• Improve research, industry and teaching
• Semantic data at the center of our work
– Storage
– Search
– Interaction with computational codes
– Comparison with experimental data
• Add support for iOS, Android and web
30
31. Acknowledgements
• Google Summer of Code for initial summer funding
• Avogadro developers: Geoffrey R. Hutchison, Donald E. Curtis,
David C. Lonie, Tim Vandermeersch and many more contributors,
users and supporters
• Kitware, Inc. for their unique business model & support
• The Engineer Research and Development Center’s Environmental
Laboratory for recent funding
• Open-source projects, standards and services we build on: Qt, Open
Babel, GLEW, CML, CACTUS Resolver, many, many more projects
• Support of many code developers including MOPAC, NWChem, Q-
Chem and others
• Support from Peter Murray-Rust and the Blue Obelisk
31