This document discusses statistical and visualization methods for analyzing metagenomic data. It introduces several R/Bioconductor packages for metagenomic analysis, including metagenomeSeq for differential abundance analysis of 16S data and metagenomicFeatures for annotating 16S features. It also describes msd16s example data. Additionally, it discusses the benefits of R/Bioconductor including infrastructure objects, documentation, and reproducibility. Finally, it introduces Metaviz, an interactive browser-based tool for exploring hierarchical metagenomic data through integration and visualization of multiple data sources.
Collections as Data National Forum (Elings)Mary Elings
From May 7-8, the University of Nevada Las Vegas will hold a second Collections as Data national forum. During the forum a group of librarians, technologists, archivists, and disciplinary researchers will gather to share their work with collections as data, reality test project deliverables, and help frame future directions for collections as data work writ large.
The Meta-Barcoding Research And Visualization Environment (mBRAVE) platform presentation from the 7th International Barcode of Life Conference. An overview of the platform, priorities, and features are provided.
Collections as Data National Forum (Elings)Mary Elings
From May 7-8, the University of Nevada Las Vegas will hold a second Collections as Data national forum. During the forum a group of librarians, technologists, archivists, and disciplinary researchers will gather to share their work with collections as data, reality test project deliverables, and help frame future directions for collections as data work writ large.
The Meta-Barcoding Research And Visualization Environment (mBRAVE) platform presentation from the 7th International Barcode of Life Conference. An overview of the platform, priorities, and features are provided.
Context-free data analysis with Transcendental Information Cascades.Markus Luczak-Rösch
In order to discover hidden relationships and patterns in data streams from multiple heterogenous sources, we work on a method for exploratory data analysis. We disregard any system-specific context to generate generic networks of information co-occurrence. These networks allow for more informed sampling and filtering. Case specific context can be added once these networks have been created to support accurate decision making.
Are you talking to me? Researching a scenario for linking objects and publica...Ellen Van Keer
presentation of the workflow designed in the project "bridging knowledge collections", aimed at integrating an institutional repository with the online catalogs of the museum objects and library publications kept in the RMAH
RDAP 15: “This is just for me”: Researchers on their data documentation pract...ASIS&T
Research Data Access and Preservation Summit, 2015
Minneapolis, MN
April 22-23, 2015
Part of "Beyond metadata: Supporting non-standardized documentation to facilitate data reuse"
Sara Mannheimer, Data Management Librarian, Montana State University
These slides present the paper entitled "A linked data model for semantic sensor stream". It does not include all the details, but an effort is made to show the main contribution of the paper.
RDAP 15: Beyond Metadata: Leveraging the “README” to support disciplinary Doc...ASIS&T
Research Data Access and Preservation Summit, 2015
Minneapolis, MN
April 22-23, 2015
Part of “Beyond metadata: Supporting non-standardized documentation to facilitate data reuse”
In the present era, almost every branch of science and technology has become data intensive requiring algorithms for data analysis and techniques for data visualizations. Under this program we will introduce clustering algorithms applicable to multivariate data such as principal component analysis (PCA) and hierarchical clustering, techniques of how to convert multivariate data into networks, network visualization and network clustering. So get modern skills for handling Big Data.
Integrating repositories and eLab notebooks through an open science frameworkrmacneil88
Overviews Jisc's investigation of including electronic lab notebooks in the Research Data Shared Service, and the benefits of Connected ELNs like RSpace
This presentation was given by Lauren Sorensen, Digital Conversion Specialist for the AAPB at the Library of Congress, at the Association of Moving Image Archivists (AMIA) 2014 conference in Savannah, Georgia.
Jung y platon. influencias de platon en jungHemil Mora
REPÚBLICA BOLIVARIANA DE VENEZUELA UNIVERSIDAD YACAMBÚ FACULTAD DE HUMANIDADES
Hemil A Mora Ramos. HEA-131 00457 CI: 21049691 Sección: MB01MOV
Platón. Teoría de la Anámnesis
“Conocer es Recordar”
Son los sentidos los que provocan la anamnesis, el recuerdo, de las ideas, que forman la realidad verdadera. Platón afirma que el alma es inmortal y que ya existía con anterioridad al cuerpo, en otra vida, junto a los dioses, y que allí conocía las ideas. Ahora, al estar el alma encerrada en un cuerpo material, se pone en contacto con la realidad material y recuerda las ideas, pero éstas ya estaban en nosotros. racionalmente.La actividad del sujeto no es creadora, nosotros no producimos realmente los contenidos del saber a cada paso que damos,
en un proceso de conocimiento que lleva desde el desconocimiento hasta dicho saber; dicho contenido, por el contrario, se nos da por razón de la anámnesis, siendo la percepción sólo un inducción que enciende nuestra alma y la incita a hallar el recuerdo de la idea.
lo que conocemos no viene del exterior, del mundo sensible, ni directamente por medio de los sentidos,
sino que empleamos éstos como auxiliares para que nos descubran el verdadero saber, que se desarrolla partiendo de nuestro propio interior. Jung toma de platón la idea de que el conocimiento y aprendizaje no es algo propio sino que es algo que se recuerda. Jung modificó las tesis freudianas y destacó el papel de lo que él llamó el inconsciente colectivo, que generalizaba la concepción freudiana del ello y se abría a una interpretación de índole más mística. Los elementos más importantes que componen el inconsciente colectivo son los llamados "arquetipos“ que constituyen la estructura de la teoría: son disposiciones innatas psíquicas que nos sirven para experimentar y representar el comportamiento y las situaciones humanas básicas. Todos los arquetipos se ven a través de imágenes en sueños y visiones, probablemente por eso Jung tenía un gran interés en la interpretación de los sueños y símbolos como forma de entender los cambios en la psique. El nacimiento, la muerte, el amor, todo está controlado por diferentes arquetipos, siendo el arquetipo más importante el Ser, el centro de la persona psíquica, su integridad.
La conciencia es un lugar o un depósito de los actos psíquicos. El inconsciente colectivo es algo innato de los seres humanos, viene con uno desde el nacimiento y no se puede adquirir de ninguna otra forma: es una biblioteca universal de sabiduría a la que todos tenemos acceso.
Context-free data analysis with Transcendental Information Cascades.Markus Luczak-Rösch
In order to discover hidden relationships and patterns in data streams from multiple heterogenous sources, we work on a method for exploratory data analysis. We disregard any system-specific context to generate generic networks of information co-occurrence. These networks allow for more informed sampling and filtering. Case specific context can be added once these networks have been created to support accurate decision making.
Are you talking to me? Researching a scenario for linking objects and publica...Ellen Van Keer
presentation of the workflow designed in the project "bridging knowledge collections", aimed at integrating an institutional repository with the online catalogs of the museum objects and library publications kept in the RMAH
RDAP 15: “This is just for me”: Researchers on their data documentation pract...ASIS&T
Research Data Access and Preservation Summit, 2015
Minneapolis, MN
April 22-23, 2015
Part of "Beyond metadata: Supporting non-standardized documentation to facilitate data reuse"
Sara Mannheimer, Data Management Librarian, Montana State University
These slides present the paper entitled "A linked data model for semantic sensor stream". It does not include all the details, but an effort is made to show the main contribution of the paper.
RDAP 15: Beyond Metadata: Leveraging the “README” to support disciplinary Doc...ASIS&T
Research Data Access and Preservation Summit, 2015
Minneapolis, MN
April 22-23, 2015
Part of “Beyond metadata: Supporting non-standardized documentation to facilitate data reuse”
In the present era, almost every branch of science and technology has become data intensive requiring algorithms for data analysis and techniques for data visualizations. Under this program we will introduce clustering algorithms applicable to multivariate data such as principal component analysis (PCA) and hierarchical clustering, techniques of how to convert multivariate data into networks, network visualization and network clustering. So get modern skills for handling Big Data.
Integrating repositories and eLab notebooks through an open science frameworkrmacneil88
Overviews Jisc's investigation of including electronic lab notebooks in the Research Data Shared Service, and the benefits of Connected ELNs like RSpace
This presentation was given by Lauren Sorensen, Digital Conversion Specialist for the AAPB at the Library of Congress, at the Association of Moving Image Archivists (AMIA) 2014 conference in Savannah, Georgia.
Jung y platon. influencias de platon en jungHemil Mora
REPÚBLICA BOLIVARIANA DE VENEZUELA UNIVERSIDAD YACAMBÚ FACULTAD DE HUMANIDADES
Hemil A Mora Ramos. HEA-131 00457 CI: 21049691 Sección: MB01MOV
Platón. Teoría de la Anámnesis
“Conocer es Recordar”
Son los sentidos los que provocan la anamnesis, el recuerdo, de las ideas, que forman la realidad verdadera. Platón afirma que el alma es inmortal y que ya existía con anterioridad al cuerpo, en otra vida, junto a los dioses, y que allí conocía las ideas. Ahora, al estar el alma encerrada en un cuerpo material, se pone en contacto con la realidad material y recuerda las ideas, pero éstas ya estaban en nosotros. racionalmente.La actividad del sujeto no es creadora, nosotros no producimos realmente los contenidos del saber a cada paso que damos,
en un proceso de conocimiento que lleva desde el desconocimiento hasta dicho saber; dicho contenido, por el contrario, se nos da por razón de la anámnesis, siendo la percepción sólo un inducción que enciende nuestra alma y la incita a hallar el recuerdo de la idea.
lo que conocemos no viene del exterior, del mundo sensible, ni directamente por medio de los sentidos,
sino que empleamos éstos como auxiliares para que nos descubran el verdadero saber, que se desarrolla partiendo de nuestro propio interior. Jung toma de platón la idea de que el conocimiento y aprendizaje no es algo propio sino que es algo que se recuerda. Jung modificó las tesis freudianas y destacó el papel de lo que él llamó el inconsciente colectivo, que generalizaba la concepción freudiana del ello y se abría a una interpretación de índole más mística. Los elementos más importantes que componen el inconsciente colectivo son los llamados "arquetipos“ que constituyen la estructura de la teoría: son disposiciones innatas psíquicas que nos sirven para experimentar y representar el comportamiento y las situaciones humanas básicas. Todos los arquetipos se ven a través de imágenes en sueños y visiones, probablemente por eso Jung tenía un gran interés en la interpretación de los sueños y símbolos como forma de entender los cambios en la psique. El nacimiento, la muerte, el amor, todo está controlado por diferentes arquetipos, siendo el arquetipo más importante el Ser, el centro de la persona psíquica, su integridad.
La conciencia es un lugar o un depósito de los actos psíquicos. El inconsciente colectivo es algo innato de los seres humanos, viene con uno desde el nacimiento y no se puede adquirir de ninguna otra forma: es una biblioteca universal de sabiduría a la que todos tenemos acceso.
Linked Data Quality Assessment – daQ and Luzzujerdeb
Presentation at the Ontology Engineering Group at UPM related to Linked Data Quality and the work done in the Enterprise Information System Group at Universität Bonn
UNIT - 5: Data Warehousing and Data MiningNandakumar P
UNIT-V
Mining Object, Spatial, Multimedia, Text, and Web Data: Multidimensional Analysis and Descriptive Mining of Complex Data Objects – Spatial Data Mining – Multimedia Data Mining – Text Mining – Mining the World Wide Web.
Maximizing AI Performance with Vector Databases: A Comprehensive GuideBhusan Chettri
In the dynamic realm of artificial intelligence (AI), the role of vector databases is paramount. These specialized databases offer a robust foundation for storing and manipulating high-dimensional data structures, playing a crucial role in various AI applications. In this comprehensive guide, we will
explore the ins and outs of vector databases, their significance in AI, and how they propel innovation
in data management and analysis.
Towards Semantic APIs for Research Data Services (Invited Talk)Anna Fensel
Rapid development of Internet and Web technology is changing the state of the art in communication of knowledge, or results of research activities. Particularly, Semantic technology, linked and open data become key enablers for successful and efficient progress in research. At first, I define the research data service (RDS) and discuss typical current and possible future usage scenarios involving RDS. Further, I discuss the state of the art in the areas of semantic service and data annotation and API construction, as well as infrastructural solutions, applicable for RDS realisation. At last, innovative methods of online dissemination, promotion and efficient communication of research are discussed.
ChemSpider – disseminating data and enabling an abundance of chemistry platformsKen Karapetyan
ChemSpider is one of the chemistry community’s primary public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data to many tens of websites and software applications at this point. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of solutions that it helps to enable. We will also discuss some of the future directions for the project that are envisaged and how we intend to continue expanding the impact for the platform.
Amit Sheth with TK Prasad, "Semantic Technologies for Big Science and Astrophysics", Invited Plenary Presentation, at Earthcube Solar-Terrestrial End-User Workshop, NJIT, Newark, NJ, August 13, 2014.
Like many other fields of Big Science, Astrophysics and Solar Physics deal with the challenges of Big Data, including Volume, Variety, Velocity, and Veracity. There is already significant work on handling volume related challenges, including the use of high performance computing. In this talk, we will mainly focus on other challenges from the perspective of collaborative sharing and reuse of broad variety of data created by multiple stakeholders, large and small, along with tools that offer semantic variants of search, browsing, integration and discovery capabilities. We will borrow examples of tools and capabilities from state of the art work in supporting physicists (including astrophysicists) [1], life sciences [2], material sciences [3], and describe the role of semantics and semantic technologies that make these capabilities possible or easier to realize. This applied and practice oriented talk will complement more vision oriented counterparts [4].
[1] Science Web-based Interactive Semantic Environment: http://sciencewise.info/
[2] NCBO Bioportal: http://bioportal.bioontology.org/ , Kno.e.sis’s work on Semantic Web for Healthcare and Life Sciences: http://knoesis.org/amit/hcls
[3] MaterialWays (a Materials Genome Initiative related project): http://wiki.knoesis.org/index.php/MaterialWays
[4] From Big Data to Smart Data: http://wiki.knoesis.org/index.php/Smart_Data
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13DataDryad
Presentation by Elena Zudilova-Seinstra on Elsevier's work on data and the article of the future and open data given at the Now and Future of Data Publishing Symposium, 22 May 2013, Oxford, UK
(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.
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.
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.
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.
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 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.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
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.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...
Hmp 201512
1. Statistical and Visualization Methods for Metagenomic Analysis
Héctor Corrada Bravo
Center for Bioinformatics and Computational Biology
2. • metagenomeSeq
– 16S differential abundance
– R/Bioconductor infrastructure for
metagenomic assays
– Longitudinal data
• metagenomicFeatures
– Incipient attempt regularizing 16S feature
annotations in R/Bioconductor
– E.g., greengenes13.5MgDb
• msd16s
– Example data, as infrastructure object
3. R/Bioconductor Strengths
• Infrastructure objects
– Interoperability, speed up startup time for method development
• Strict development practices
– Documentation, use cases, vignettes
• Annotation infrastructure
– Again, interoperability across experiments and data types
• Exploratory analysis
• Reproducibility
– Vignettes, Rmarkdown, etc.
• Recently, exploratory and interactive visualization
– Shiny, epiviz
4. Integrative, visual and computational
exploratory analysis of genomic data
• Browser-based
• Interactive
• Integration of data
• Reproducible dissemination
• Communication with R/Bioconductor: epivizr package
software systems to support creative exploratory analysis of large genome-wide datasets...
7. Dynamically extensible: Easily integrate new data sources, data
types and add new visualizations.
Data providers define coordinate
space
8. One interpretation of Big Data is many sources of relevant
contextual data
• Easily access/integrate contextual data
• Driven by exploratory analysis of immediate
data
• Iterative process
• Visual and computational exploration go
hand in hand
9. Visualization design goals
Context
• Integrate and align multiple data sources;
navigate; search
• Connect: brushing
• Encode: map visualization properties to
data on the fly
• Reconfigure: multiple views of the same
data
10. Visualization design goals
Data
• Select and filter: tight-knit integration with
R/Bioconductor
• (current work) filters on visualization
propagate to data environment
Model
• New 'measurements' the result of
modeling; suggested by data context
11. Metagenomic Visualization
• How to effectively navigate large datasets
where features are organized hierarchically?
• Metaviz: browser-based, interactive
exploratory analysis of metagenomic
data
• Connection to R/Bioconductor with
metavizr package
• Built on metagenomeSeq and
metagenomeFeatures infrastructure
12.
13.
14.
15. Metaviz
• Exploration of hierarchically organized
features
• Geared towards 16S for now
– Hierarchical organization relevant to WGS
• Integration is a big part of design
– Framework designed for data integration
16. Acknowledgements
Brianna Lindsey, O. Colin Stine, Owen White, Anup Mahurkar: University of Maryland Baltimore
Jim Nataro: University of Virginia
NIGMS, Genentech
Florin Chelaru
(now @ MIT)
Joseph Paulson
(now @ Harvard)
Mihai Pop
(@ UMD)
