The document provides instructions for setting up MateriApps LIVE!, a virtual machine containing various materials science simulation software. It describes downloading required files, installing VirtualBox, importing the virtual machine disk image, and configuring shared folders. Upon booting the virtual machine, users can access pre-installed applications and run materials science simulations without installing software locally. The goal is to promote open source simulation tools and form a community in computational materials science.
Apache Flink Crash Course by Slim Baltagi and Srini PalthepuSlim Baltagi
In this hands-on Apache Flink presentation, you will learn in a step-by-step tutorial style about:
• How to setup and configure your Apache Flink environment: Local/VM image (on a single machine), cluster (standalone), YARN, cloud (Google Compute Engine, Amazon EMR, ... )?
• How to get familiar with Flink tools (Command-Line Interface, Web Client, JobManager Web Interface, Interactive Scala Shell, Zeppelin notebook)?
• How to run some Apache Flink example programs?
• How to get familiar with Flink's APIs and libraries?
• How to write your Apache Flink code in the IDE (IntelliJ IDEA or Eclipse)?
• How to test and debug your Apache Flink code?
• How to deploy your Apache Flink code in local, in a cluster or in the cloud?
• How to tune your Apache Flink application (CPU, Memory, I/O)?
Apache Flink Crash Course by Slim Baltagi and Srini PalthepuSlim Baltagi
In this hands-on Apache Flink presentation, you will learn in a step-by-step tutorial style about:
• How to setup and configure your Apache Flink environment: Local/VM image (on a single machine), cluster (standalone), YARN, cloud (Google Compute Engine, Amazon EMR, ... )?
• How to get familiar with Flink tools (Command-Line Interface, Web Client, JobManager Web Interface, Interactive Scala Shell, Zeppelin notebook)?
• How to run some Apache Flink example programs?
• How to get familiar with Flink's APIs and libraries?
• How to write your Apache Flink code in the IDE (IntelliJ IDEA or Eclipse)?
• How to test and debug your Apache Flink code?
• How to deploy your Apache Flink code in local, in a cluster or in the cloud?
• How to tune your Apache Flink application (CPU, Memory, I/O)?
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.
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.
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
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.
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.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
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.
(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.
1. How to setup MateriApps LIVE!
2019/07/01 [version 2.3]
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 264 materials science
applications and tools (as of 2019.7)
• 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
• 19000+ 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 2.3 was published on May 14, 2019
• Pre-installed applications and tools
• abinit, AkaiKKR, ALAMODE, ALPS, CP2K, Feram,
ERmod, DCore, DSQSS, HΦ, LAMMPS, mVMC,
OpenMX, Quantum ESPRESSO, SMASH, xTAPP, etc
• ParaView, Tapioca, VESTA, VMD, XCrysDen…
• GUI installer for GAMESS and VMD
• Available from MateriApps LIVE! webpage
• c.a. 5000 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