Pcaso is an interactive web tool for exploring point cloud data through multiple orthogonal views and smoothly zooming and highlighting points by metadata. It allows users to post datasets as shareable multiplot views, and smoothly switch between axes to track how points shift across dimensions. Future features will include zooming within plots, autocomplete search, and updating or deleting posts. Pcaso is intended to help interpret diverse complex datasets projected into multiple planes.
Présentation lors de la matinée "Linked Data et interopérabilité des images sur le Web" (Maison de l’Archéologie et de l’Ethnologie, Nanterre - 08/04/2016), par Stefanie Gehrke (Pool Biblissima)
Présentation lors de la matinée "Linked Data et interopérabilité des images sur le Web" (Maison de l’Archéologie et de l’Ethnologie, Nanterre - 08/04/2016), par Stefanie Gehrke (Pool Biblissima)
Talk at JISC Repositories conference intended for repository managers or research managers on some of the issues involved. Talk had to be originally given unaided because of a technology problem!
This presenations provides an outlook of what we anticipate with the structured data hub: to create linkable datasets, enhance the use of provenance, add quality flags to data, answer new questions and finally, borrow from and provide to public sources such as dbpedia
Spark Summit Europe: Share and analyse genomic data at scaleAndy Petrella
Share and analyse genomic data
at scale with Spark, Adam, Tachyon & the Spark Notebook
Sharp intro to Genomics data
What are the Challenges
Distributed Machine Learning to the rescue
Projects: Distributed teams
Research: Long process
Towards Maximum Share for efficiency
Data Communities - reusable data in and outside your organization.Paul Groth
Description
Data is a critical both to facilitate an organization and as a product. How can you make that data more usable for both internal and external stakeholders? There are a myriad of recommendations, advice, and strictures about what data providers should do to facilitate data (re)use. It can be overwhelming. Based on recent empirical work (analyzing data reuse proxies at scale, understanding data sensemaking and looking at how researchers search for data), I talk about what practices are a good place to start for helping others to reuse your data. I put this in the context of the notion data communities that organizations can use to help foster the use of data both within your organization and externally.
Building collaborative Machine Learning platform for Dataverse network. Lecture by Slava Tykhonov (DANS-KNAW, the Netherlands), DANS seminar series, 29.03.2022
Towards a rebirth of data science (by Data Fellas)Andy Petrella
Nowadays, Data Science is buzzing all over the place.
But what is a, so-called, Data Scientist?
Some will argue that a Data Scientist is a person able to report and present insights in a data set. Others will say that a Data Scientist can handle a high throughput of values and expose them in services. Yet another definition includes the capacity to create meaningful visualizations on the data.
However, we enter an age where velocity is a key. Not only the velocity of your data is high, but the time to market is shortened. Hence, the time separating the moment you receive a set of data and the time you’ll be able to deliver added value is crucial.
In this talk, we’ll review the legacy Data Science methodologies, what it meant in terms of delivered work and results.
Afterwards, we’ll slightly move towards different concepts, techniques and tools that Data Scientists will have to learn and appropriate in order to accomplish their tasks in the age of Big Data.
The dissertation is closed by exposing the Data Fellas view on a solution to the challenges, specially thanks to the Spark Notebook and the Shar3 product we develop.
Doing for Data what Pubmed did for literature: DATS a model for dataset description datasets indexing and data discovery.
Googleslides [https://goo.gl/cd5KKa] or Slideshare [https://goo.gl/c8DH5N]
Leveraging mesos as the ultimate distributed data science platformAndy Petrella
Keynote at the first @MesosCon #Europe on what was Data Science, what are the new challenge and needs and how we target them in Data Fellas with the Spark Notebook and Shar3
Social Network Analysis Introduction including Data Structure Graph overview. Doug Needham
Social Network Analysis Introduction including Data Structure Graph overview. Given in Cincinnati August 18th 2015 as part of the DataSeed Meetup group.
Getting the most out of your containerized databaseClaus Matzinger
Microservice environments with databases often grow to be a complex architecture behind the scenes to the point where requirements can’t be met. This talk will show how to run a scalable stack with persistent data storage based on Docker and how that will lead to less grey hairs on the Ops team.
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.
Talk at JISC Repositories conference intended for repository managers or research managers on some of the issues involved. Talk had to be originally given unaided because of a technology problem!
This presenations provides an outlook of what we anticipate with the structured data hub: to create linkable datasets, enhance the use of provenance, add quality flags to data, answer new questions and finally, borrow from and provide to public sources such as dbpedia
Spark Summit Europe: Share and analyse genomic data at scaleAndy Petrella
Share and analyse genomic data
at scale with Spark, Adam, Tachyon & the Spark Notebook
Sharp intro to Genomics data
What are the Challenges
Distributed Machine Learning to the rescue
Projects: Distributed teams
Research: Long process
Towards Maximum Share for efficiency
Data Communities - reusable data in and outside your organization.Paul Groth
Description
Data is a critical both to facilitate an organization and as a product. How can you make that data more usable for both internal and external stakeholders? There are a myriad of recommendations, advice, and strictures about what data providers should do to facilitate data (re)use. It can be overwhelming. Based on recent empirical work (analyzing data reuse proxies at scale, understanding data sensemaking and looking at how researchers search for data), I talk about what practices are a good place to start for helping others to reuse your data. I put this in the context of the notion data communities that organizations can use to help foster the use of data both within your organization and externally.
Building collaborative Machine Learning platform for Dataverse network. Lecture by Slava Tykhonov (DANS-KNAW, the Netherlands), DANS seminar series, 29.03.2022
Towards a rebirth of data science (by Data Fellas)Andy Petrella
Nowadays, Data Science is buzzing all over the place.
But what is a, so-called, Data Scientist?
Some will argue that a Data Scientist is a person able to report and present insights in a data set. Others will say that a Data Scientist can handle a high throughput of values and expose them in services. Yet another definition includes the capacity to create meaningful visualizations on the data.
However, we enter an age where velocity is a key. Not only the velocity of your data is high, but the time to market is shortened. Hence, the time separating the moment you receive a set of data and the time you’ll be able to deliver added value is crucial.
In this talk, we’ll review the legacy Data Science methodologies, what it meant in terms of delivered work and results.
Afterwards, we’ll slightly move towards different concepts, techniques and tools that Data Scientists will have to learn and appropriate in order to accomplish their tasks in the age of Big Data.
The dissertation is closed by exposing the Data Fellas view on a solution to the challenges, specially thanks to the Spark Notebook and the Shar3 product we develop.
Doing for Data what Pubmed did for literature: DATS a model for dataset description datasets indexing and data discovery.
Googleslides [https://goo.gl/cd5KKa] or Slideshare [https://goo.gl/c8DH5N]
Leveraging mesos as the ultimate distributed data science platformAndy Petrella
Keynote at the first @MesosCon #Europe on what was Data Science, what are the new challenge and needs and how we target them in Data Fellas with the Spark Notebook and Shar3
Social Network Analysis Introduction including Data Structure Graph overview. Doug Needham
Social Network Analysis Introduction including Data Structure Graph overview. Given in Cincinnati August 18th 2015 as part of the DataSeed Meetup group.
Getting the most out of your containerized databaseClaus Matzinger
Microservice environments with databases often grow to be a complex architecture behind the scenes to the point where requirements can’t be met. This talk will show how to run a scalable stack with persistent data storage based on Docker and how that will lead to less grey hairs on the Ops team.
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.
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.
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.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
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.
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...!
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
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 .
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Pcaso: Share and fluidly explore point-cloud data
Nathaniel M. Pearson1, Robert Aboukhalil2, Carmel Dudley3, John Greally4
1New York Genome Center, New York USA; 2Cold Spring Harbor Laboratory, Cold Spring Harbor USA;
3Weizmann Institute of Science, Rehovot Israel; 4Albert Einstein College of Medicine, New York USA
Background
People see and think in too few dimensions to easily grok data with many variates.
Flattening and freezing such data, to view as dots in a plane or box, can reveal some key
patterns, but hide others.
To help plumb many kinds of point-cloud data, in genomics and other fields, we built the
Point cloud analysis stereopticon (Pcaso), a mobile device-friendly way to collaboratively
explore plane-projected (e.g., PCA, MDS, comparative abundance) point clouds.
Distinctively, Pcaso lets users
• post and explore point-cloud datasets as interactive small-multiplots with stable URLs
(e.g., in preprint or publication)
• switch smoothly among orthogonal views, to track how each point shifts relative to others,
among potentially many dimensions
• smoothly zoom, to resolve point clumping
• highlight points by hand, stably colored metaclass (e.g., deme, tissue, platform, sex), or
metadata text search.
These and coming features, elaborated by us and others via CC0-licensed d3+ code, may help
interpret diverse complex, plane- projected datasets.
Pcaso beats paper.
(And the original beats a poster.)
Point your device to pcaso.io/mundo
Using Pcaso
To explore posted data
At the URL for a posted dataset, click any small plot to see it big. Hover on a point in the big plot
to see its metadata. And text search, or click a metaclass, to highlight point(s) by metadata.
To post your own data
At pcaso.io, upload a .csv file, then pick fields to show as axes or metadata, and save. You can
then explore away.
To share your post for others to explore
Share the post’s URL by email, IM, (pre)print text, tweet, carrier pigeon, &c.
What you’ll see
Next features
We hope to soon let users zoom within the main plot, search with autofill, update and/or delete posts, and do other handy
stuff. Please send any thoughts to npearson@nygenome.org – and look soon for source code and updates to Pcaso, along
with other tools, via the budding Open Genomics Visualization Initiative (OGVI).
Anticipated questions
What kinds of data does Pcaso help show? Basically, anything with many numeric dimensions. Could be principal components, of course – but
lots of other data can benefit from smoothly switchable, metadata-responsive planar views. If you’ve got such data, try it out.
What about parallel-coordinate plots? They too can help a lot, by showing many dimensions (especially qualitative or naturally ordered ones) at
once. But dense, criss-crossing point-specific curves can, of course, be hard to follow.
Why not show a 3d box instead of planes? We started with planes that mean something real from underlying data, and that our brains can easily
track when switching axes. (Plus, for data with many axes, a box shows little more of the whole than a plane does.)
But doesn't a stereopticon show 3d images? That’s a stereoscope ;-) Back in steampunk days, stereopticons just let people switch from one slide
to another. We were also inspired by cubists (like Picasso, of course) who splintered complex real-world shapes into many-planar views..
How robust is Pcaso? We’ve started with a beta hosted on a good standard web server, meant first to show key features and spark collaborative
insights and refinement – not (yet) to manage private or versioned data, or stop determined bad actors. Please use Pcaso responsibly.