The presentation provides a perspective on how distributed computing has been instrumental to make ground breaking scientific discoveries possible, and how the opening of computing infrastructures at international level has been effective in delivering unprecedented compute capacity and advance data analytics tools to international research collaborations.
The presentation provides examples of the enormous scientific impact produced by the international collaboration of cyber infrastructures in Europe, Africa and other continents, and will explain the federated organizational model adopted by European countries to leverage national ICT investments and mobilize them.
The presentation offers an overview of the present and future technical and organisational challenges of data-driven research in various scientific domains. The European Open Science Cloud initiative of the European Commission will be explained and opportunities of collaboration will be discussed with the audience.
Conference website: http://www.eresearch-africa.uct.ac.za/
The ascent of scientific computing: the EGI role and contribution towards the...EGI Federation
The EGI Federation, delivering HTC, HPC and Cloud computing services for scientific communities in Europe and the world, for the first time in 2019 exceeded 71,500 users and delivered more that 5 Billion CPU hours in the last 12 months. Natural Sciences and Medical and Health sciences are the largest user communities.
Past, present and future of advanced computing for data-driven scienceEGI Federation
The EGI Federation celebrates 15 years of distributed computing in 2019. Many milestones were achieved to bring distributed computing from a vision to a real-life international production platform that today enables data-intensive processing at an unprecedented scale, supporting some of the greatest groundbreaking scientific discoveries of the XXI century.
The ascent of scientific computing: the EGI role and contribution towards the...EGI Federation
The EGI Federation, delivering HTC, HPC and Cloud computing services for scientific communities in Europe and the world, for the first time in 2019 exceeded 71,500 users and delivered more that 5 Billion CPU hours in the last 12 months. Natural Sciences and Medical and Health sciences are the largest user communities.
Past, present and future of advanced computing for data-driven scienceEGI Federation
The EGI Federation celebrates 15 years of distributed computing in 2019. Many milestones were achieved to bring distributed computing from a vision to a real-life international production platform that today enables data-intensive processing at an unprecedented scale, supporting some of the greatest groundbreaking scientific discoveries of the XXI century.
Europe today lacks a publicly funded cloud infrastructure for exploitation of research data. Data research infrastructures and e-Infrastructures should coordinate themselves to realize the International Data Commons.
Data management plans – EUDAT Best practices and case study | www.eudat.euEUDAT
| www.eudat.eu | Presentation given by Stéphane Coutin during the PRACE 2017 Spring School joint training event with the EU H2020 VI-SEEM project (https://vi-seem.eu/) organised by CaSToRC at The Cyprus Institute. Science and more specifically projects using HPC is facing a digital data explosion. Instruments and simulations are producing more and more volume; data can be shared, mined, cited, preserved… They are a great asset, but they are facing risks: we can miss storage, we can lose them, they can be misused,… To start this session, we will review why it is important to manage research data and how to do this by maintaining a Data Management Plan. This will be based on the best practices from EUDAT H2020 project and European Commission recommendation. During the second part we will interactively draft a DMP for a given use case.
Project Hub-laboratory Internet of things. The aim of project is to bring together local IOT stakeholders lay the groundwork for the development of innovative ecosystem in Lviv region through the establishment of an Regional Manufacturing innovative hub of Internet of Things which will be a centre of new information technologies and allows to increase the quality of regional ecosystem and straight digital manufacturing in the region. It will be a platform for business, production and education collaboration.
EDF2014: Christian Lindemann, Wolters Kluwer Germany & Christian Dirschl, Wol...European Data Forum
Invited Talk by Christian Lindemann, Wolters Kluwer Germany & Christian Dirschl, Wolters Kluwer Germany at the European Data Forum 2014, 20 March 2014 in Athens, Greece: Linked Data and Open Government Data as part of the business strategy of Wolters Kluwer Germany.
Integration data models, Learning Layers project meeting in BremenVladimir Tomberg
Report on process of building common semantic core for data from several Learning Layers applications for an integrated solution supported by Social Semantic Server
Shared Digital Twins: Collaboration in EcosystemsBoris Otto
This presentation introduces the concept of shared digital Twins from a cusiness perspective and outlines recent technological developments for shared digital twin management.
EUDAT Webinar "Organise, retrieve and aggregate data using annotations with B...EUDAT
| www.eudat.eu | Annotate your research data with B2NOTE:
A note in the margins of a book or a scientific paper, a comment on a manuscript: we are all using annotations to add information to existing physical documents. To offer a similar experience with digital content within the EUDAT Collaborative Data Infrastructure (CDI), we developed a service that allows associating additional information to a file, in a computer-readable format, without changing the file or the data record itself. These digital annotations can thus be searched to organize, retrieve and aggregate files, datasets and documents.
Although B2NOTE is a standalone service, it has been designed to be integrated with the existing EUDAT services. In the first pilot version, B2NOTE allows to annotate files located in B2SHARE. The service is called as a “widget” within the B2SHARE User Interface. B2NOTE allows you to easily and intuitively create three types of annotations: a semantic tag coming from identified ontology repositories (only Bioportal at the moment but we are working toward integrating more vocabularies), a free-text keyword that can be used when you do not find a semantic term in particular and a free-text comment.
Tiziana Ferrari presents EGI | OSFair2017 Workshop
Workshop title: National and European e-infrastructure cooparation for Open Science
Workshop overview:
This collaborative workshop comes in the context of coordinating EOSC related activities across large European infrastructures at European and national level. The workshop will offer an opportunity for cross-pollination on issues ranging from open scholarship to technical service provision, training, community engagement and support. OpenAIRE NOADs, EGI NGIs, GEANT NRENs and other national e-Infrastructure representatives will discuss gaps, synergies, coordination and service integration opportunities.
DAY 3 - PARALLEL SESSION 6 & 7
Europe today lacks a publicly funded cloud infrastructure for exploitation of research data. Data research infrastructures and e-Infrastructures should coordinate themselves to realize the International Data Commons.
Data management plans – EUDAT Best practices and case study | www.eudat.euEUDAT
| www.eudat.eu | Presentation given by Stéphane Coutin during the PRACE 2017 Spring School joint training event with the EU H2020 VI-SEEM project (https://vi-seem.eu/) organised by CaSToRC at The Cyprus Institute. Science and more specifically projects using HPC is facing a digital data explosion. Instruments and simulations are producing more and more volume; data can be shared, mined, cited, preserved… They are a great asset, but they are facing risks: we can miss storage, we can lose them, they can be misused,… To start this session, we will review why it is important to manage research data and how to do this by maintaining a Data Management Plan. This will be based on the best practices from EUDAT H2020 project and European Commission recommendation. During the second part we will interactively draft a DMP for a given use case.
Project Hub-laboratory Internet of things. The aim of project is to bring together local IOT stakeholders lay the groundwork for the development of innovative ecosystem in Lviv region through the establishment of an Regional Manufacturing innovative hub of Internet of Things which will be a centre of new information technologies and allows to increase the quality of regional ecosystem and straight digital manufacturing in the region. It will be a platform for business, production and education collaboration.
EDF2014: Christian Lindemann, Wolters Kluwer Germany & Christian Dirschl, Wol...European Data Forum
Invited Talk by Christian Lindemann, Wolters Kluwer Germany & Christian Dirschl, Wolters Kluwer Germany at the European Data Forum 2014, 20 March 2014 in Athens, Greece: Linked Data and Open Government Data as part of the business strategy of Wolters Kluwer Germany.
Integration data models, Learning Layers project meeting in BremenVladimir Tomberg
Report on process of building common semantic core for data from several Learning Layers applications for an integrated solution supported by Social Semantic Server
Shared Digital Twins: Collaboration in EcosystemsBoris Otto
This presentation introduces the concept of shared digital Twins from a cusiness perspective and outlines recent technological developments for shared digital twin management.
EUDAT Webinar "Organise, retrieve and aggregate data using annotations with B...EUDAT
| www.eudat.eu | Annotate your research data with B2NOTE:
A note in the margins of a book or a scientific paper, a comment on a manuscript: we are all using annotations to add information to existing physical documents. To offer a similar experience with digital content within the EUDAT Collaborative Data Infrastructure (CDI), we developed a service that allows associating additional information to a file, in a computer-readable format, without changing the file or the data record itself. These digital annotations can thus be searched to organize, retrieve and aggregate files, datasets and documents.
Although B2NOTE is a standalone service, it has been designed to be integrated with the existing EUDAT services. In the first pilot version, B2NOTE allows to annotate files located in B2SHARE. The service is called as a “widget” within the B2SHARE User Interface. B2NOTE allows you to easily and intuitively create three types of annotations: a semantic tag coming from identified ontology repositories (only Bioportal at the moment but we are working toward integrating more vocabularies), a free-text keyword that can be used when you do not find a semantic term in particular and a free-text comment.
Tiziana Ferrari presents EGI | OSFair2017 Workshop
Workshop title: National and European e-infrastructure cooparation for Open Science
Workshop overview:
This collaborative workshop comes in the context of coordinating EOSC related activities across large European infrastructures at European and national level. The workshop will offer an opportunity for cross-pollination on issues ranging from open scholarship to technical service provision, training, community engagement and support. OpenAIRE NOADs, EGI NGIs, GEANT NRENs and other national e-Infrastructure representatives will discuss gaps, synergies, coordination and service integration opportunities.
DAY 3 - PARALLEL SESSION 6 & 7
Presentation about EGI's Cloud Container Compute Service at the CompBioMed Containerisation Meeting (https://www.compbiomed.eu/events-2/compbiomed-containerisation-meeting/)
Cloud Computing Needs for Earth Observation Data Analysis: EGI and EOSC-hubBjörn Backeberg
This presentation was given during the Japan Geosciences Union 2019. Session details can be found at http://www.jpgu.org/meeting_e2019/SessionList_en/detail/M-GI31.htm
This presentation showcases the achievements and the scientific impact attained by European and Asian research data centres in big science in the past decade. We make a case about the need to increase current collaborations to address global societal challenges for health and environmental protection and to evolve scientific computing to deliver data and scientific software a service.
The EOSC Compute Platform with the EGI-ACE project EGI Federation
EGI-ACE’s main goal is to implement the compute platform of the European Open Science Cloud and contribute to the EOSC Data Commons by delivering integrated computing platforms, data spaces and tools as an integrated solution that is aligned with major European cloud federation projects and HPC initiatives.
This presentation introduces you to the architecture and composition of the EOSC Compute Platform, which delivers capabilities at the IaaS, PaaS and SaaS level.
Gergely Sipos (EGI): Exploiting scientific data in the international context ...Gergely Sipos
Keynote presentation given at "The Emerging Technology Forum – Data Creates Universe - Scientific Data Innovation Conference" of the "Pujiang Innovation Forum 2021" event.
The EGI Federated Cloud is experiencing a boost of demand of cloud services since 2018. More than 26 Million hours of CPU wall time were delivered and Natural Sciences are the most active scientific group.
EGI Cloud Services in a Federated Multi-Supply EnvirnmentEGI Federation
EGI Federated Cloud relies on a federated Service Management System based on the FitSM standard, and is ISO 20k compliant. Since 2018 we are facing an increasing demand of multi-supply cloud services to meet big data analytics performance requirements. The EGI Federated Cloud is one of the cloud pillars of the "European Open Science Cloud", an initiative aiming to federate data and digital infrastructures for research projects of European relevance.
European Open Science Cloud: Concept, status and opportunitiesEOSC-hub project
European Open Science Cloud: Concept, status and opportunities.
Presentation given by Gergely Sipos at the International Symposium on Grids and Clouds 2019 event in Taiwan.
The Ascent of Open Science and the European Open Science CloudTiziana Ferrari
Open science is becoming more and more part of the daily practice in conducting science. Around the world, researchers are increasingly aware of the value and importance of open science. As scientific research becomes highly data-driven and dependent on computing, scientists are conscious of the growing need to share data, software and infrastructure to reduce wasteful duplication and increase economies of scale. In an ideal world, every step of the research process would be public and transparent – the full methodology and all the tools used, as well as the data, would be accessible to the public and all groups without restriction, enabling reproducibility and refinement by other scientists.
This presentation will show case a number of success stories indicating how federated digital infrastructure, that have been sustained by the member states and the European Commission, have become an indispensable tool to enable collaboration ad sharing.
The European Open Science Cloud was launched by the European Commission in 2016 aiming to (1) increase the ability to exploit research data across scientific disciplines and between the public and private sector, (2) interconnect existing and new digital infrastructures in Europe and (3) support open science.
The presentation showcases how open data, open data analytics and open e-Infrastructures like EGI (https://www.egi.eu/) have been key enables of scientific discoveries from the discovery of gravitational waves with LIGO-VIRGO to drug design with the molecular modelling tools of WeNMR.
EOSC-hub (https://www.eosc-hub.eu/) - the first and the largest of the EOSC implementation projects of the H2020 funding programme, has succeeded in delivering some of the building blocks like the EOSC portal and Marketplace, tools and processes for federating data and services providers, harmonized policies, a federated AAI infrastructure, Competence Centres to support research infrastructures in their complex digital needs, interoperability guidelines and the Early Adopter Programme to provide expert support and service capacity to research projects.
Presentation on the European Open Science Cloud and work undertaken within the Research Data Alliance to coordinate global open science commons initiatives. The presentation was given to the G7 Open Science Working Group on behalf of the EOSC Executive Board.
Reproducible Open Science with EGI Notebooks, Binder and ZenodoEGI Federation
Open science is the movement to make scientific research and its dissemination accessible to all levels of an inquiring society, amateur or professional. Open access and sharing of publications, data, physical samples, and software are central in open science to increase the reproducibility of research. Jupyter Notebooks, Virtualisation/containerisation, Open Access data repositories provide a new foundation for open science, and are key assets for the European Open Science Cloud.
You can put all of this in practice with EGI Notebooks, Binder and Zenodo. To learn how, see the tutorial slides: https://documents.egi.eu/document/3442
EGI Notebooks is a new service from the EGI e-infrastructure collaboration, providing a user-friendly and highly flexible Jupyter-based hosted environment for researchers to develop and share data analysis and visualisation ‘notebooks’. Notebooks can contain programming codes in various languages, HTML scripts, dynamic visualization and equations as well as images and explanatory text that provide guidance and context for the captured data analysis workflows.
Through the notebooks users can easily share concepts, ideas and working applications, containing the full analytical methodology, connections to data sources, visualizations, and descriptive text to interpret those data. With the Binder ‘extension’ of Jupyter one can turn a Github repository with Jupyter notebooks into an executable environment, making code, visualisation and documentation immediately reproducible and reusable by anyone, anywhere.
Jupyter and Binder are becoming pillars for Open Science.
The tutorial will introduce the open access EGI Notebooks service. The tutorial will go through the main features of the EGI Notebooks service and show how to use it with Binder for Open Science. Participants will experience the system through hands-on exercises written in Python based on real applications from the environmental sciences domain. The integrated use of Notebooks with EGI’s DataHub service will be also demonstrated. Communities or national e-infrastructures who would like to setup a similar service locally will be also informed about how to do this.
Enjoy the tutorial!
The EGI Federation of clusters and research clouds are components of the European Open Science Cloud, and they offer technical solutions and an infrastructure to support the EuroGEOSS pilots, GEOSS and EO data exploitation platforms.
Learn how, by looking at the collaboration of EGI with NextGEOSS, the production support of the Geohazards TEP of Terradue and the EOSC-hub collaboration with GEOSS.
EGI and EUDAT support to the PaNOSC projectEGI Federation
Data transfer & archivingm, and Jupyter on the EGI Federated Cloud at the core of EGI and EUDAT support to Photon and Neutron science in the PaNOSC project
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.
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.
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.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Distributed scientific computing for open science, eResearch Africa 2019
1. www.egi.eu
@EGI_eInfra
The work of the EGI Foundation
is partly funded by the European Commission
under H2020 Framework Programme
EGI: Advanced Computing for Research
eResearch Africa 2019
Distributed scientific
computing for open science
Technical Director, EGI Foundation
Tiziana Ferrari
5. @EGI_eInfrawww.egi.eu 17/04/2019 5
EGI Federation (April 2019)
• ZA-UCT-ICTS University of Cape Town - ICTS HPC site
• ZA-UFS (University of the Free State Computing
Centre)
HPC site of the University of Bloemfontein
• ZA-WITS-CORE (University of the Witwatersrand
CORE)
Core research cluster of the University of the
Witwatersrand
4.4 Billion
CPU core
wall time
(2018)
> 1 Million
computing
cores in 2019
> 740 PB disk
& tape
2,915 service
end-points
10. @EGI_eInfrawww.egi.eu 17/04/2019 10
• Leverages national e-Infrastructure investments
• Opens access to part of the nationally funded capacity
• Supports international user groups
• Integrates community, private and/or public infrastructures into a scalable
data/computing platform for research
• Uses federated identities, authentication and authorization
• Ensures interoperability of scientific applications and data across multiple
providers bringing distributed computing to data
Benefits of Federation
15. @EGI_eInfrawww.egi.eu 17/04/2019 15
Architecture and Interfaces
• Tools to deal with
heterogeneity:
IaaS orchestration tools
with support for multiple
APIs:
o Infrastructure Manager,
Terraform, OCCOPUS, …
o https://wiki.egi.eu/wiki/Fe
derated_Cloud_IaaS_Orch
estration
IaaS libraries with support
for multiple APIs:
o libcloud, jclouds,…
17. @EGI_eInfrawww.egi.eu 17/04/2019 17
• Identity and Access Management solution
Single sign-on to services through eduGAIN, social media and other institutional or
community-managed identity providers
Only one account needed for federated access to multiple heterogeneous (web and
non-web) service providers using different technologies (SAML, OpenID Connect,
OAuth 2.0, X509)
Identity linking enables access to resources using different login credentials
(institutional/social)
Assurance information associated to each authenticated identity
Aggregation and harmonisation of authorisation information (VOs/groups, roles,
assurance) from multiple sources
Federated AAI: Check-in
18. @EGI_eInfrawww.egi.eu 17/04/2019 18
• Conforms to AARC blueprint architecture
• Registered in eduGAIN as an SP complying
with REFEDS Research & Scholarship and
Sirtfi
• All community SPs can have one statically
configured IdP
• No need to run an IdP Discovery Service
on each SP
• Connected SPs get consistent/harmonised
user identifiers and accompanying
attribute sets from different IdPs/AAs that
can be interpreted in a uniform way for
authorisation purposes
Check-in: Identity Provider and Service
Provider Proxy
25. @EGI_eInfrawww.egi.eu 17/04/2019 25
• Heterogeneous
backend storage
• Common interfaces
(Web, REST, POSIX,
CDMI)
• Common AAI with
Check-in
• Discovery of Datasets
in the EGI DataHub
Federation of Data Repositories
26. @EGI_eInfrawww.egi.eu 17/04/2019 26
• Clients uses one
ore more providers
to access data
• Data can be
accessed over
multiple protocols
Transparent Data Access
27. @EGI_eInfrawww.egi.eu 17/04/2019 27
Data Caching
• Cloud provider A hosts data
& computing resources
• Provider B only hosts data
Provider X can use data from A
and B
• Without pre-staging
• Via pre-staging using APIs
• Local data access “à la”
POSIX with FUSE
35. @EGI_eInfrawww.egi.eu 17/04/2019 35
• The computational tools to solve a problem
Python, R, Julia, and wide ecosystem of libraries and tools for science
• An interface to facilitate coding / creating Jupyter
• A way to communicate work Notebooks
• A way to share work GitHub other similar repositories
• A way to pack it all for replication Docker
• A way to persistently identify it DOIs (Digital Object Identifiers)
Reproducible Open Science with
EGI Notebooks, Binder, Zenodo
https://documents.egi.eu/document/3442
43. @EGI_eInfrawww.egi.eu 17/04/2019 43
Today’s scenario
• Difficult cross-border access due to different funding models, access and
provisioning policies
Data and service provisioning to international user communities possible only when supported by
sound business models or existing collaboration agreements. Today only a few structured int.
research groups have achieved this.
• Needs of large investments for the creation, processing, preservation, access
and reuse of research data will the funding match the anticipated needs of
future data-intensive science?
Opportunities for economies of scale and aggregation of demand can arise with joint provisioning
of infrastructure common components
• Major separation between data preservation and data exploitation
infrastructures in many disciplines
Ris and e-Infrastructures should collaborate to support the entire research workflow of an
experiment
44. @EGI_eInfrawww.egi.eu 17/04/2019 44
Tomorrow’s scenario
The International Data Commons
A federation of research data, computing, applications
and other open science resources, responding to the
problem of scalable access to research data through a
new data provisioning service approach that is
complementary to the traditional data download
model.
45. @EGI_eInfrawww.egi.eu 17/04/2019 45
The Data Commons Should…
Allow to discover, access and analyze major research
datasets and information for third-party exploitation
Provide access to the data & data products close to
processing facilities while avoiding duplication of
local data storage & compute infrastructures across
research performing organizations in Europe
46. @EGI_eInfrawww.egi.eu 17/04/2019 46
The Data Commons Should…
• Offer a hybrid distributed compute platform (HTC, HPC,
cloud) and integrated rich portfolio of scientific application
tools supporting self-service provisioning
• Offer tools for scalable data movement across data
preservation infrastructures and distributed interconnected
network of “data hubs”
• Provide integrated capabilities for publishing and sharing
scientific outputs from experiments to support open science
• Support federated authentication and authorization for use
of existing personal credentials and easy to use access
channels
47. @EGI_eInfrawww.egi.eu 17/04/2019 47
The federated infrastructure and supporting initiative
providing
all researchers, innovators, companies and citizens
with seamless access to an open-by-default, efficient and
cross-disciplinary environment
for storing, accessing, reusing data, tools, publications and
other scientific outputs for research, innovation and
educational purposes
About the European Open Science Cloud
48. This work by the EGI Foundation
is licensed under a Creative Commons
Attribution 4.0 International License.
Questions?
Thank you
for your attention.
www.egi.eu
@EGI_eInfra
EGI: Advanced Computing for Research
The work of the EGI Foundation
is partly funded by the European Commission
under H2020 Framework Programme