The document provides setup instructions for MateriApps LIVE!, a virtual machine containing materials science applications. It lists the required files, guides the user on installing VirtualBox and importing the virtual machine disk image, and describes configuring shared folders and booting the virtual machine to access pre-installed applications.
Pharo IoT Installation Improvements and Continuous IntegrationAllex Oliveira
Presented at Pharo Days 2019, Lille, France.
Now you can start with Pharo IoT runtime (PharoThings, TelePharo, ARM VM) in a Raspberry from scratch in less than 10 minutes or in less than 1 minute if your Raspberry Pi has Raspbian already installed. And in less than 1 minute you can run Pharo IoT IDE in your Linux, Window or Mac OSX.
How did we do this?? The answers are in this presentation :)
Take your Raspberry Pi and start now: get.pharoiot.org
EMC World 2016 - code.02 Introduction to Immutable Infrastructure{code}
No more artisanally hand-crafted infrastructures! Ban snowflake servers! Immutable means "unchanging over time or unable to be changed," which is great if you work in operations. Stable and predictable, but of course you will have to make changes every now and then. How do you handle changes to your infrastructure without impacting reliability, and how can you make sure the task is properly propagated over every part of the infrastructure that needs it? Handling immutable infrastructures has become much easier with modern tools. In this session we will show live demos of Vagrant, Terraform and Ansible.
TYPO3 CMS v8 in the cloud
This session will look into changes happening with TYPO3 CMS version 8 and how they relate to an improved integration with cloud infrastructure:
untangled file-handling for better support
untangled database abstraction layer to support different database backends
updated and now finely tuneable caching framework
composer changes for repeatable builds
possible pre-compilation for uid
Finally the session will also look into the practical example of deploying TYPO3 into the platform.sh cloud to kickstart the audience.
Inception: A reverse-engineer horror HistoryNelson Brito
Inception @ 2016 IBM Systems Technical University
Understanding reverse engineer using MS08-078. This presentation is an updated version of a previous series of presentations, which shows a practical methodology to perform a reverse engineering... The approach can be broader applied to any/most of the vulnerabilities targeting client-side applications.
For further details and informations, please, refer to:
- http://www.vimeo.com/nbrito
- https://www.slideshare.net/nbrito01/inception-support-slides
Learn how to use Linux, even if you’re a die-hard Windows user! There’s no question that Linux has taken over the enterprise, and paves the way for disruptive innovations in software. Join us for an informal breakout session where we’ll introduce you to the benefits of developing on a Linux platform and show you some basic usage fundamentals, so that you can get started with Linux today.
(Zendcon 2016 and Zendcon 2017 - Feedback here: https://joind.in/event/zendcon-2016/linux-101)
Pharo IoT Installation Improvements and Continuous IntegrationAllex Oliveira
Presented at Pharo Days 2019, Lille, France.
Now you can start with Pharo IoT runtime (PharoThings, TelePharo, ARM VM) in a Raspberry from scratch in less than 10 minutes or in less than 1 minute if your Raspberry Pi has Raspbian already installed. And in less than 1 minute you can run Pharo IoT IDE in your Linux, Window or Mac OSX.
How did we do this?? The answers are in this presentation :)
Take your Raspberry Pi and start now: get.pharoiot.org
EMC World 2016 - code.02 Introduction to Immutable Infrastructure{code}
No more artisanally hand-crafted infrastructures! Ban snowflake servers! Immutable means "unchanging over time or unable to be changed," which is great if you work in operations. Stable and predictable, but of course you will have to make changes every now and then. How do you handle changes to your infrastructure without impacting reliability, and how can you make sure the task is properly propagated over every part of the infrastructure that needs it? Handling immutable infrastructures has become much easier with modern tools. In this session we will show live demos of Vagrant, Terraform and Ansible.
TYPO3 CMS v8 in the cloud
This session will look into changes happening with TYPO3 CMS version 8 and how they relate to an improved integration with cloud infrastructure:
untangled file-handling for better support
untangled database abstraction layer to support different database backends
updated and now finely tuneable caching framework
composer changes for repeatable builds
possible pre-compilation for uid
Finally the session will also look into the practical example of deploying TYPO3 into the platform.sh cloud to kickstart the audience.
Inception: A reverse-engineer horror HistoryNelson Brito
Inception @ 2016 IBM Systems Technical University
Understanding reverse engineer using MS08-078. This presentation is an updated version of a previous series of presentations, which shows a practical methodology to perform a reverse engineering... The approach can be broader applied to any/most of the vulnerabilities targeting client-side applications.
For further details and informations, please, refer to:
- http://www.vimeo.com/nbrito
- https://www.slideshare.net/nbrito01/inception-support-slides
Learn how to use Linux, even if you’re a die-hard Windows user! There’s no question that Linux has taken over the enterprise, and paves the way for disruptive innovations in software. Join us for an informal breakout session where we’ll introduce you to the benefits of developing on a Linux platform and show you some basic usage fundamentals, so that you can get started with Linux today.
(Zendcon 2016 and Zendcon 2017 - Feedback here: https://joind.in/event/zendcon-2016/linux-101)
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
1. How to setup MateriApps LIVE!
2019/12/24 [version 2.4]
MateriApps LIVE! Development Team
2. • MateriApps LIVE! USB
• setup.pdf, setup-en.pdf
this document
• README.html, README-en.html
(copy from https://github.com/cmsi/MateriAppsLive/wiki/MateriAppsLive-ova)
• VirtualBox Installer: VirtualBox-*-OSX.dmg, VirtualBox-*-Win.exe
(available at https://www.virtualbox.org/wiki/Downloads)
• VirtualBox configuration scripts: vbconfig.*
(available at https://github.com/cmsi/MateriAppsLive/tree/master/ova)
• MateriApps LIVE! VitualBox Disk Image: MateriAppsLive-*-amd64.ova
(available at http://sourceforge.net/projects/materiappslive/files/)
What are included in USB Stick?
MateriApps, 2013-2019. All rights reserved.2
3. MateriApps — a Portal Site for Materials Science Simulation
• Aiming at the community formation through the promotion of application
MateriApps, 2013-2019. All rights reserved.3
• Introducing 268 materials science
applications and tools (as of 2019.12)
• Finding applications
• search tags: features, targets,
calculation methods/algorithms
• Information of applications
• brief introduction, link to official
pages, information installation,
usage, etc
• Information of hands-on sessions,
software update, etc
• New! - Glossary of keywords,
Concierge, Reviews
• 16000+ page views / month, 5500+
unique visitors / monthsince May 2013
5. Current status in computational materials science
• From developers’ viewpoint
• New algorithms should be implemented and used. Or, it will
be forgotten ever existed.
• It cost much to write and update documents
• Development of software itself is hardly considered as
scientific achievements
• From users’ viewpoint
• What kind of applications? Who develop them?
Which application should I use for my problem?
• Manual and documentation are not well prepared.
• How to evaluate the accuracy of results?
• Goal of MateriApps project
• Forming of community in the field of computational materials
science through the promotion of open source software
MateriApps, 2013-2019. All rights reserved.5
6. What MateriApps will provide
• To find and learn application software
• catalog of application/tool on MateriApps web
• To start using application software
• MateriApps LIVE!
• To active use application software
• pre-installation to the K computer, supercomputers, etc: MateriApps Installer
• Infrastructure for easily starting materials science simulations for theoreticians,
experimentalists, researchers in companies, students, and more…
MateriApps, 2013-2019. All rights reserved.6
Flagship system (K, post-K,...)
HPC infrastructure supercomputers in Japan
Supercomputers for shared-use in research fields
Cloud computing, on-premises PC clusters
Personal workstations, PCs
InstallerHands-on Cloud
7. What is MateriApps LIVE! ?
• Live Linux bootable on virtual machine
• run on Windows, Macintosh, etc
• just boot and get ready for materials science
simulations without installation
• Version 2.4 was published in December 2019
• Pre-installed applications and tools
• abinit, AkaiKKR, ALAMODE, ALPS, CP2K, Feram,
ERmod, DCore, DSQSS, HΦ, LAMMPS, mVMC,
OpenMX, Quantum ESPRESSO, SMASH, xTAPP, etc
• OVITO, ParaView, Tapioca, VESTA, VMD, XCrysDen…
• GUI installer for GAMESS and VMD
• Available from MateriApps LIVE! webpage
• c.a. 6400 copies distributed since July, 2013
MateriApps, 2013-2019. All rights reserved.7
8. MateriApps LIVE! is useful for ...
• Hands-on sessions using MateriApps LIVE!
• MateriApps LIVE! Tutorials
• HΦ, xTAPP, ALPS, DCore, mVMC, ALAMODE, DDMRG, DSQSS, etc
• Practices in lectures
• Computational Physics
• Computer Experiments (UNIX + C, LaTeX, VCS)
• Used by experimentalists, researchers in private companies
• Used by researchers in the field of computer science
• Easy setup (c.a. 15min) without no troubles
• Useful for operation check, trouble shooting, user support
MateriApps, 2013-2019. All rights reserved.8
9. Booting in VirtualBox
✓ Copy files in USB stick memory to hard disk
• copy all the files to your PC, e.g. to desktop
✓ Install VirtualBox by double-clicking the installer
• For Windows: VirutalBox-5.*-Win.exe
• For Macintosh: VirtualBox-5.*-OSX.dmg
✓ Import MateriApps LIVE!
• double-click MateriAppsLive-*-amd64.ova
• VirtualBox will start automatically and import window will open. Then press
“import” button
• VirtualBox Manager window will appear in two or three minutes
• Host (host OS): operating system (Windows, Mac OS X, etc) on which VirtualBox is
running
• Virtual machine (guest OS): operating system (= MateriApps LIVE!) running on
VirtualBox
MateriApps, 2013-2019. All rights reserved.9
10. Setting up VirtualBox
✓ Setup: disabling unnecessary popup messages
• on Windows: double click “vbconfig.bat”.
• on Mac OS X: double click “vbconfig.command”, or run “sh vbconfig.command”
in terminal software.
✓ Setup: enabling access from virtual machine to hard disc on host OS
1. Choose MateriAppsLive-* in VirtualBox Manager window, and press
“Settings”.
2. Open “Shared Folders” tab and click “+” on the right.
3. Click “v” on the right of “Folder Path”, choose “Other…”, and select the
folder to which the files have been copied from the USB stick memory.
4. Check “Auto-mount” box and press “OK”. Then press “OK” again.
5. The folder specified in step 3 can be accessed as /media/sf_… after booting
the virtual machine (explained in the following pages).
MateriApps, 2013-2019. All rights reserved.10
11. Booting in VirtualBox
1. Choose “MateriAppsLive…”
2. Press “Start” button.
3. Wait until login window will
appear.
MateriApps, 2013-2019. All rights reserved.11
12. Login to MateriApps LIVE!
• Login window will appear in a few minutes
• Login by using
• User name (login): user
• Password: live
• Desktop (right) will appear
• Important buttons
• start menu
• logout
MateriApps, 2013-2019. All rights reserved.12
13. Copy & paste, Japanese keyboard
• How to paste strings copied from a PDF file on host OS?
• right click on terminal window “Paste”
• or press “V” with “shift” and “control” keys
• right click “Copy”, or “shift + control + C” to copy a string
• Setup for using Japanese keyboard
• start menu “System Tools” “LXTerminal”
• type “setxkbmap -layout jp” and “return” in terminal window
• check if “@” key works correctly
• (To revert to US keyboard: “setxkbmap -layout us”)
MateriApps, 2013-2019. All rights reserved.13
14. Materials Science Simulation by MateriApps LIVE!
• Introduction / Setup
• First-principles band calculation (OpenMX / Quantum ESPRESSO / xTAPP)
• Simulation of solution by molecular dynamics (LAMMPS / Gromacs)
• Lattice model simulation (ALPS / HΦ / mVMC)
• Quantum chemistry calculation (in preparation)
• Hands-on materials are available at https://github.com/cmsi/MateriAppsLive/wiki/
MaLiveTutorial (currently only in Japanese)
MateriApps, 2013-2019. All rights reserved.14
15. MateriApps planning & production
• Administration:
• Center for Computational Materials Science, Institute for Solid State Physics, University
of Tokyo (ISSP-CCMS)
• MateriApps Administration Team
• Kota Ido (ISSP), Shusuke Kasamatsu (ISSP), Takeo Kato (ISSP),
Naoki Kawashima (ISSP), Hikaru Kouta (ISSP), Takahiro Misawa (ISSP),
Yuichi Motoyama (ISSP), Synge Todo (Department of Physics, University of Tokyo/
ISSP), and Kanako Yoshizawa (RIST)
• Cooperation:
• Research Organization for Information Science and Technology (RIST)
• Materials research by Information Integration Initiative, NIMS (MI2I)
• Sponsor
• Post-K Priority Issue 7
• Elements Strategy Initiative
• Professional Development Consortium for Computational Materials Science (PCoMS)
• TIA “Kakehashi”
MateriApps, 2013-2019. All rights reserved.15