Data analysis workflows part 2 2015

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previous: https://github.com/dgrapov/TeachingDemos/blob/master/Demos/Data%20Analysis%20Workflow/report/report.md

Large longitudinal studies may be required to identify
small phenotypic and environmental effects
http://teddy.epi.usf.edu/TEDDY/
TEDDY: The Environmental Determinants of Type 1 Diabetes in the Young
multi-Omic longitudinal study involving > 15,000
samples acquired over 3 yrs
Time
Time
Analytical batch effects can hide smaller
biological effects

Data normalization may require a combination of approaches
Internal standard (ISTD) based normalization may not fully
remove analytical batch effects
Analytical replicate-based normalizations
can be used to estimate and remove
analytical variance
Raw Data Normalized Data
Samples
QCs
LOESS

Omic’ data integration strategies
Biomarker Insights 2015:Suppl. 4 1-6 DOI: 10.4137/BMI.S29511
Empirical
correlation
Network
based
Biochemical
pathway

Pathway analysis

Metabolomic network analysis

MetaMapR: Metabolomic network calculation
http://dgrapov.github.io/MetaMapR/

Omic’ network analysis
http://kwanjeeraw.github.io/grinn/

MappingsNetwork Mapped Network
Grapov D.,American Society of Mass Spectrometry Conference (2013, 2014)
Network Mapping
+ =

DeviumWeb: Data analysis and visualization
https://github.com/dgrapov/DeviumWeb

Questions?
dgrapov@gmail.com
More information:
https://imdevsoftware.wordpress.com/
Software:
https://github.com/dgrapov
Hire me:
createdatasol@gmail.com

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Understanding circumstellar disks is of prime importance in astrophysics, however, their birth process remains poorly constrained due to observational and numerical challenges. Recent numerical works have shown that the small-scale physics, often wrapped into a sub-grid model, play a crucial role in disk formation and evolution. This calls for a combined approach in which both the protostar and circumstellar disk are studied in concert. Aims. We aim to elucidate the small scale physics and constrain sub-grid parameters commonly chosen in the literature by resolving the star-disk interaction. Methods. We carry out a set of very high resolution 3D radiative-hydrodynamics simulations that self-consistently describe the collapse of a turbulent dense molecular cloud core to stellar densities. We study the birth of the protostar, the circumstellar disk, and its early evolution (< 6 yr after protostellar formation). Results. Following the second gravitational collapse, the nascent protostar quickly reaches breakup velocity and sheds its surface material, thus forming a hot (∼ 103 K), dense, and highly flared circumstellar disk. The protostar is embedded within the disk, such that material can flow without crossing any shock fronts. The circumstellar disk mass quickly exceeds that of the protostar, and its kinematics are dominated by self-gravity. Accretion onto the disk is highly anisotropic, and accretion onto the protostar mainly occurs through material that slides on the disk surface. The polar mass flux is negligible in comparison. The radiative behavior also displays a strong anisotropy, as the polar accretion shock is shown to be supercritical whereas its equatorial counterpart is subcritical. We also f ind a remarkable convergence of our results with respect to initial conditions. Conclusions. These results reveal the structure and kinematics in the smallest spatial scales relevant to protostellar and circumstellar disk evolution. They can be used to describe accretion onto regions commonly described by sub-grid models in simulations studying larger scale physics.

Formation of low mass protostars and their circumstellar disks

Formation of low mass protostars and their circumstellar disks

Formation of low mass protostars and their circumstellar disks

Chemistry is the scientific study of matter, its properties, composition, structure, and the changes it undergoes. It's often divided into various sub-disciplines such as organic chemistry, inorganic chemistry, physical chemistry, analytical chemistry, and biochemistry. Chemistry plays a crucial role in understanding the world around us and has applications in various fields such as medicine, materials science, environmental science, and industry.

Chemistry 4th semester series (krishna).pdf

Chemistry 4th semester series (krishna).pdf

Chemistry 4th semester series (krishna).pdf

Sumit Kumar yadav

Forensic Biology & Its biological significance.pdf

Forensic Biology & Its biological significance.pdf

Forensic Biology & Its biological significance.pdf

rohankumarsinghrore1

RecoveringancientrecordsofEarth'smagneticfieldisessentialfordeterminingtheroleofthemagnetosphereinprotectingearlyEarthfromcosmicradiationandatmosphericescape.WepresentpaleomagneticfieldtestshintingthatarecordofEarth's3.7‐billion‐year(Ga)oldmagneticfieldmaybepreservedinthenortheasternIsuaSupracrustalBeltasachemicalremanentmagnetizationacquiredduringamphibolite‐grademetamorphisminthebandedironformation.MultiplepetrologicalandgeochronologicallinesofevidenceindicatethatthenorthernmostpartofIsuahasnotexperiencedmetamorphictemperaturesexceeding380°CsincetheEoarchean,suggestingtherockshavenotbeensignificantlyheatedsincemagnetizationwasacquired.Weuse“pseudo”bakedcontacttests(intrusionsemplaced3.26–3.5Gaago)andafoldtest(folding3.6Gaago)todemonstratethatsomesamplespreserveaca.3.7Garecordofthemagneticfield.Werecoverafieldstrengthof>15μT.ThissuggeststhatEarth'smagneticfieldmayhavebeenweakenoughtoenhanceatmosphericescapeduringtheArchean

PossibleEoarcheanRecordsoftheGeomagneticFieldPreservedintheIsuaSupracrustalBe...

PossibleEoarcheanRecordsoftheGeomagneticFieldPreservedintheIsuaSupracrustalBe...

PossibleEoarcheanRecordsoftheGeomagneticFieldPreservedintheIsuaSupracrustalBe...

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Context. Determining the size distribution of asteroids is key to understanding the collisional history and evolution of the inner Solar System. Aims. We aim to improve our knowledge of the size distribution of small asteroids in the main belt by determining the parallaxes of newly detected asteroids in the Hubble Space Telescope (HST) archive and subsequently their absolute magnitudes and sizes. Methods. Asteroids appear as curved trails in HST images because of the parallax induced by the fast orbital motion of the spacecraft. Taking into account the trajectory of this latter, the parallax effect can be computed to obtain the distance to the asteroids by fitting simulated trajectories to the observed trails. Using distance, we can obtain the absolute magnitude of an object and an estimation of its size assuming an albedo value, along with some boundaries for its orbital parameters. Results. In this work, we analyse a set of 632 serendipitously imaged asteroids found in the ESA HST archive. Images were captured with the ACS/WFC and WFC3/UVIS instruments. A machine learning algorithm (trained with the results of a citizen science project) was used to detect objects in these images as part of a previous study. Our raw data consist of 1031 asteroid trails from unknown objects, not matching any entries in the Minor Planet Center (MPC) database using their coordinates and imaging time. We also found 670 trails from known objects (objects featuring matching entries in the MPC). After an accuracy assessment and filtering process, our analysed HST asteroid set consists of 454 unknown objects and 178 known objects. We obtain a sample dominated by potential main belt objects featuring absolute magnitudes (H) mostly between 15 and 22 mag. The absolute magnitude cumulative distribution logN(H > H0) ∝ αlog(H0) confirms the previously reported slope change for 15 < H < 18, from α ≈ 0.56 to α ≈ 0.26, maintained in our case down to absolute magnitudes of around H ≈ 20, and therefore expanding the previous result by approximately two magnitudes. Conclusions. HST archival observations can be used as an asteroid survey because the telescope pointings are statistically randomly oriented in the sky and cover long periods of time. They allow us to expand the current best samples of astronomical objects at no extra cost in regard to telescope time.

Hubble Asteroid Hunter III. Physical properties of newly found asteroids

Hubble Asteroid Hunter III. Physical properties of newly found asteroids

Hubble Asteroid Hunter III. Physical properties of newly found asteroids

Small size (20-300 nm) / bacteria (size measured in μm) Viral genome – single type of nucleic acid: DNA – dezoxyriboviruses RNA - riboviruses Totally dependant on living cells for all metabolic processes May infect humans, animals, plants, bacteria, fungi,parasites, insects Virion = viral corpuscle = elementary, infectious unit. Only visible by electron microscopy. Laboratory diagnosis of viral infections Methods: • Cytology • Electron microscopy • Cultivation • Detection of viral proteins • Serology • Molecular diagnosis (detection of genetic material i.e. nucleic acids) PPT prepared by Dr. Prince C P

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VIRUSES structure and classification ppt by Dr.Prince C P

VIRUSES structure and classification ppt by Dr.Prince C P

Creating and Analyzing Definitive Screening Designs

Creating and Analyzing Definitive Screening Designs

Creating and Analyzing Definitive Screening Designs

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Zoology 4th semester series (krishna).pdf

Zoology 4th semester series (krishna).pdf

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Bacterial Identification and Classifications

Bacterial Identification and Classifications

Bacterial Identification and Classifications

Formation of low mass protostars and their circumstellar disks

Formation of low mass protostars and their circumstellar disks

Formation of low mass protostars and their circumstellar disks

Chemistry 4th semester series (krishna).pdf

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Chemistry 4th semester series (krishna).pdf

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PossibleEoarcheanRecordsoftheGeomagneticFieldPreservedintheIsuaSupracrustalBe...

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Hubble Asteroid Hunter III. Physical properties of newly found asteroids

Hubble Asteroid Hunter III. Physical properties of newly found asteroids

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VIRUSES structure and classification ppt by Dr.Prince C P

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Creating and Analyzing Definitive Screening Designs

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Zoology 4th semester series (krishna).pdf

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Data analysis workflows part 2 2015

1. Large longitudinal studies may be required to identify small phenotypic and environmental effects http://teddy.epi.usf.edu/TEDDY/ TEDDY: The Environmental Determinants of Type 1 Diabetes in the Young multi-Omic longitudinal study involving > 15,000 samples acquired over 3 yrs Time Time Analytical batch effects can hide smaller biological effects

2. Data normalization may require a combination of approaches Internal standard (ISTD) based normalization may not fully remove analytical batch effects Analytical replicate-based normalizations can be used to estimate and remove analytical variance Raw Data Normalized Data Samples QCs LOESS

3. Omic’ data integration strategies Biomarker Insights 2015:Suppl. 4 1-6 DOI: 10.4137/BMI.S29511 Empirical correlation Network based Biochemical pathway

4. Pathway analysis

5. Metabolomic network analysis

6. MetaMapR: Metabolomic network calculation http://dgrapov.github.io/MetaMapR/

7. Omic’ network analysis http://kwanjeeraw.github.io/grinn/

8. MappingsNetwork Mapped Network Grapov D.,American Society of Mass Spectrometry Conference (2013, 2014) Network Mapping + =

9. DeviumWeb: Data analysis and visualization https://github.com/dgrapov/DeviumWeb

10. Questions? dgrapov@gmail.com More information: https://imdevsoftware.wordpress.com/ Software: https://github.com/dgrapov Hire me: createdatasol@gmail.com