The document provides instructions for setting up MateriApps LIVE!, a virtual machine containing various materials science applications. It includes downloading required files like the virtual disk image and configuration scripts. The virtual machine can then be run in VirtualBox. MateriApps LIVE! contains over 250 pre-installed applications and is aimed at promoting open source software in computational materials science through hands-on tutorials and workshops.
SAS University Edition - Getting StartedCraig Trim
Get Started with SAS University Edition on your local machine using Virtual Box to host a pre-installed instance. Work through the initial setup and configuration and run SAS code from the training modules.
Slides of the presentation I gave at the Dutch Container Day (https://containerday.nl) about how containers were introduced at bol.com and what we're doing with them.
A virtual machine (VM) is a software program or operating system that not only exhibits the behavior of a separate computer but is also capable of performing tasks such as running applications and programs like a separate computer.
Seminar about docker and its containerization capabilities during the "Aggiornamento Agile" event of Club degli Sviluppatori in January 2015, in Bari (Italy)
SAS University Edition - Getting StartedCraig Trim
Get Started with SAS University Edition on your local machine using Virtual Box to host a pre-installed instance. Work through the initial setup and configuration and run SAS code from the training modules.
Slides of the presentation I gave at the Dutch Container Day (https://containerday.nl) about how containers were introduced at bol.com and what we're doing with them.
A virtual machine (VM) is a software program or operating system that not only exhibits the behavior of a separate computer but is also capable of performing tasks such as running applications and programs like a separate computer.
Seminar about docker and its containerization capabilities during the "Aggiornamento Agile" event of Club degli Sviluppatori in January 2015, in Bari (Italy)
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
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.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
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.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
insect taxonomy importance systematics and classification
How to setup MateriApps LIVE!
1. How to setup MateriApps LIVE!
2020/02/14 [version 2.5]
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, 2013-2020. All rights reserved.2
3. MateriApps — a Portal Site for Materials Science Simulation
• Aiming at the community formation through the promotion of application
MateriApps, 2013-2020. All rights reserved.3
• Introducing 271 materials science
applications and tools (as of 2020.2)
• 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
• 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, 2013-2020. 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, 2013-2020. 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 2.5 was published in February 2020
• 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 CASINO, GAMESS, and VMD
• Available from MateriApps LIVE! webpage
• c.a. 6600 copies distributed since July, 2013
MateriApps, 2013-2020. 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, SALMON,
CASINO, 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, 2013-2020. 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, 2013-2020. All rights reserved.9
10. Booting in VirtualBox
1. Choose “MateriAppsLive…”
2. Press “Start” button.
3. Wait until login window will
appear.
MateriApps, 2013-2020. All rights reserved.10
11. • 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
• CD-ROM button
Login to MateriApps LIVE!
MateriApps, 2013-2020. All rights reserved.11
12. Tips (1/2)
✓ Copy & Paste: 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
✓ Setting: using Japanese keyboard
• start menu “System Tools” “Switch to Japanese Keyboard Layout”
(or execute “setxkbmap -layout jp” in terminal window)
• check if “@” key works correctly
✓ Setting: 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
MateriApps, 2013-2020. All rights reserved.12
13. Tips (2/2)
✓ Settings: browsing contents of ISO image file (* .iso) from the virtual machine
• click CD-ROM icon at the bottom of the virtual machine window frame, select
"Choose disk image ...", and select the ISO image file
• contents of ISO image file are accessible via /media/cdrom0
✓ Setting: file sharing between host OS and virtual machine
• choose MateriAppsLive-* in VirtualBox Manager window, and press
“Settings”
• open “Shared Folders” tab and click “+” on the right
• 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
• check “Auto-mount” box and press “OK”. Then press “OK” again
• the folder specified above can be accessed as /media/sf_… after rebooting
the virtual machine
MateriApps, 2013-2020. 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, 2013-2020. 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 Development Team
• Kota Ido (ISSP), Shusuke Kasamatsu (Dept. of Phys., Yamagata Univ.),
Takeo Kato (ISSP), Naoki Kawashima (ISSP), Hikaru Kouta (ISSP),
Takahiro Misawa (ISSP), Yuichi Motoyama (ISSP),
Synge Todo (Dept. of Phys., Univ. 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, 2013-2020. All rights reserved.15