In this tutorial we’ll describe how to create a new ModestR database, how to populate it using taxonomic data stored in a CSV file.
ModestR software can be freely downloaded from http://www.ipez.es/ModestR
24. Creating virtual species with ModestR (Version ModestR 6.4 or higher)modestrsoftware
This tutorial describes how to easily create virtual species and importing them directly in ModestR. Virtual species are a procedure increasingly used in ecology to improve species distribution models. This feature uses the R virtualspecies package from Leroy et al (https://cran.r-project.org/web/packages/virtualspecies/index.html)
25. Phylogenetics trees with ModestRr and bold (Version ModestR 6.5 or higher)modestrsoftware
This tutorial describes how to donwload DNA barcoding data from BOLD to ModestR for any species, and how to use those data to calculate phylogenetic distances and build phylogenetic trees
18. Estimating species composition in one or more regions with KnowBr and Mo...modestrsoftware
In this tutorial we describe how to use ModestR with KnowBR results to estimate species composition by region. Using SDM results for several species and the expected richness estimated by KnowBR, ModestR can determine the most suitable composition of species of a region.
7.- ModestR tools for taxonomy (Version ModestR v5.3 or higher)modestrsoftware
This tutorial describes some tools provided by ModestR to work with taxonomic data. ModestR can use ITIS taxonomic database to explore and export taxonomic data.
It can also use GBIF to check and complete taxonomic data from a list of species.
20. Calculating most probable distribution of a species with Niche of Occurr...modestrsoftware
In this tutorial we describe how to perform species distribution modelling (SDM) with Niche Of Occurrence (NOO) in ModestR. NOO is a new proposed SDM that offers a very good performance and it's easier to perform and understand than other existing SDM's
15. Locating species occupied river basins with ModestR (Version ModestR 5.3...modestrsoftware
In this tutorial we'll explain how to automatically find the river basins that are occupied by a species, using the species known occurences. River basins are very interesting because they can be considered a natural geographical extent for a species.
11.- Calculating species distribution for different periods with ModestR (Ve...modestrsoftware
In this tutorial we’ll describe how to calculate species distribution for different periods. To do that, we’ll use the 3D Niche capability of ModestR, taking time as 3th dimension
24. Creating virtual species with ModestR (Version ModestR 6.4 or higher)modestrsoftware
This tutorial describes how to easily create virtual species and importing them directly in ModestR. Virtual species are a procedure increasingly used in ecology to improve species distribution models. This feature uses the R virtualspecies package from Leroy et al (https://cran.r-project.org/web/packages/virtualspecies/index.html)
25. Phylogenetics trees with ModestRr and bold (Version ModestR 6.5 or higher)modestrsoftware
This tutorial describes how to donwload DNA barcoding data from BOLD to ModestR for any species, and how to use those data to calculate phylogenetic distances and build phylogenetic trees
18. Estimating species composition in one or more regions with KnowBr and Mo...modestrsoftware
In this tutorial we describe how to use ModestR with KnowBR results to estimate species composition by region. Using SDM results for several species and the expected richness estimated by KnowBR, ModestR can determine the most suitable composition of species of a region.
7.- ModestR tools for taxonomy (Version ModestR v5.3 or higher)modestrsoftware
This tutorial describes some tools provided by ModestR to work with taxonomic data. ModestR can use ITIS taxonomic database to explore and export taxonomic data.
It can also use GBIF to check and complete taxonomic data from a list of species.
20. Calculating most probable distribution of a species with Niche of Occurr...modestrsoftware
In this tutorial we describe how to perform species distribution modelling (SDM) with Niche Of Occurrence (NOO) in ModestR. NOO is a new proposed SDM that offers a very good performance and it's easier to perform and understand than other existing SDM's
15. Locating species occupied river basins with ModestR (Version ModestR 5.3...modestrsoftware
In this tutorial we'll explain how to automatically find the river basins that are occupied by a species, using the species known occurences. River basins are very interesting because they can be considered a natural geographical extent for a species.
11.- Calculating species distribution for different periods with ModestR (Ve...modestrsoftware
In this tutorial we’ll describe how to calculate species distribution for different periods. To do that, we’ll use the 3D Niche capability of ModestR, taking time as 3th dimension
7.- ModestR tools for taxonomy (Version ModestR v6.5 or higher)modestrsoftware
This tutorial describes some tools provided by ModestR to work with taxonomic data. ModestR can use ITIS taxonomic database to explore and export taxonomic data.
It can also use GBIF to check and complete taxonomic data from a list of species.
17. An example using ModestR to assess species distribution in different cli...modestrsoftware
In this tutorial we describe how to use ModestR to model species distribution in different climatic change scenarios. To do that, we’ll use the 3D Niche capability of ModestR, taking time as 3th dimension.
21.- Creating virtual species and calculating simple ensemble models with R ...modestrsoftware
In this tutorial we describe two simple scripts in R to generate random virtual species, and to calculate species distribution models (SDM's) using ensemble models.
Those scripts may be useful to test hypotesis, or to work with ModestR or other tools
19. Calculating 3D species distribution in marine habitats with ModestR (Ver...modestrsoftware
In this tutorial we describe how to calculate species distribution along depth (3D) in marine habitats with ModestR. In this way, if you have occurrences with depth information from a species, and environmental/climatic data for different depths (such as those from NOAA or Copernicus), with ModestR you can calculate species distribution in 3D, for each depth where the species is present
4.- How to use data cleaning, EOO estimation and environmental of occurrence ...modestrsoftware
How to use data cleaning, EOO estimation and environmental occurrence features in ModestR.
Describes data cleaning; EOO methods supported in ModestR (convex hull, alpha shape, kernel density); environmental occurrence in ModestR.
12.- Recommendations for marine environments and Economic Exclusive Zones (Ve...modestrsoftware
In this tutorial we’ll give you some tips to work with ModestR in marine environments, different sources of information and how to use the marine Economic Exclusive Zones.
16. Importing different climatic change scenarios from WorldClim to ModestR ...modestrsoftware
In this tutorial we describe how to import different climatic change scenarios from WorldClim to ModestR. This is necessary for example to use the 3D Niche capability of ModestR to model species distribution along those scenarios.
Learn to install and configure open source Technology such as Java, MySQL and BIRT to develop Online Business Intelligence Reports. Presented by Vazi Okhandiar, founder of NR Computer Learning Center. www.nrclc.com
This presentation is a demonstration of how you can use IBM Mashup Center to build a sample American Baseball mashup. This demonstration will use five widgets, two feeds, and a mashup feed.
7.- ModestR tools for taxonomy (Version ModestR v6.5 or higher)modestrsoftware
This tutorial describes some tools provided by ModestR to work with taxonomic data. ModestR can use ITIS taxonomic database to explore and export taxonomic data.
It can also use GBIF to check and complete taxonomic data from a list of species.
17. An example using ModestR to assess species distribution in different cli...modestrsoftware
In this tutorial we describe how to use ModestR to model species distribution in different climatic change scenarios. To do that, we’ll use the 3D Niche capability of ModestR, taking time as 3th dimension.
21.- Creating virtual species and calculating simple ensemble models with R ...modestrsoftware
In this tutorial we describe two simple scripts in R to generate random virtual species, and to calculate species distribution models (SDM's) using ensemble models.
Those scripts may be useful to test hypotesis, or to work with ModestR or other tools
19. Calculating 3D species distribution in marine habitats with ModestR (Ver...modestrsoftware
In this tutorial we describe how to calculate species distribution along depth (3D) in marine habitats with ModestR. In this way, if you have occurrences with depth information from a species, and environmental/climatic data for different depths (such as those from NOAA or Copernicus), with ModestR you can calculate species distribution in 3D, for each depth where the species is present
4.- How to use data cleaning, EOO estimation and environmental of occurrence ...modestrsoftware
How to use data cleaning, EOO estimation and environmental occurrence features in ModestR.
Describes data cleaning; EOO methods supported in ModestR (convex hull, alpha shape, kernel density); environmental occurrence in ModestR.
12.- Recommendations for marine environments and Economic Exclusive Zones (Ve...modestrsoftware
In this tutorial we’ll give you some tips to work with ModestR in marine environments, different sources of information and how to use the marine Economic Exclusive Zones.
16. Importing different climatic change scenarios from WorldClim to ModestR ...modestrsoftware
In this tutorial we describe how to import different climatic change scenarios from WorldClim to ModestR. This is necessary for example to use the 3D Niche capability of ModestR to model species distribution along those scenarios.
Learn to install and configure open source Technology such as Java, MySQL and BIRT to develop Online Business Intelligence Reports. Presented by Vazi Okhandiar, founder of NR Computer Learning Center. www.nrclc.com
This presentation is a demonstration of how you can use IBM Mashup Center to build a sample American Baseball mashup. This demonstration will use five widgets, two feeds, and a mashup feed.
Step by Step Complete Procedure for installation of Moodle on System.
Note: --First of all Please make a folder name e-Content_Backup in your hard
disk and copy all the three DVSs in this folder only. After that make a folder
name moodledata in the above folder and copy all the contents of
moodledata_1, moodledata_2 & moodledata_3 in this folder and delete these
three folders after copying them. (when you will copy these three folders
then a window pop up will come and ask for either copy & replace or merge
the fielder folder. Always choose the merge option.)
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 .
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
(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.
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 pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Nutraceutical market, scope and growth: Herbal drug technology
1. How to create a database (Version ModestR v6.5 or higher)
1. Step by step tutorial:
How to create a
ModestR database
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
2. What do you need for this tutorial:
1. ModestR v.6.5 or higher
software installed
2. Internet connection
3. About 15 minutes
ModestR software can be freely downloaded from http://www.ipez.es/ModestR
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
3. We’ll describe how to create a new
ModestR database, how to populate it
using taxonomic data stored in a CSV
file. Follow the next steps!
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
4. 1. Run ModestR DataManager, go to the File/New Taxonomy database menu option and create a new database called
“MymodestRDatabase”.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Create a new database
5. The next step is creating a new taxonomy in the database. There are two options to do that:
a) Importing a CSV file that contains the taxonomy we want to add to the database.
or
b) Importing a taxonomy range from GBIF Backbone taxonomy.
In the next step of this tutorial we’ll explain the option a).
But you also use the option b) which is explained in the tutorial ModestR tools to work with GBIF and ITIS taxonomy
databases.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
6. 2. Import taxonomy data from a CSV file using the menu Import/Import taxonomy/From CSV file. Select the wanted CSV
file to be imported. For this example, you can download the sample file Ipez.CSV from the ModestR website (see
Help&Doc/Manual and tutorials section).
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
A CSV file with taxonomy data to
be imported. Columns should be:
class, order, family, genus and
species
7. 3. A dialog box will ask you about the format of the CSV file to be imported. Accept defaults if you are using the sample
CSV file provided for this tutorial. If not, adjust the settings according to your CSV file format.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Set importation format settings
(accept defaults if you are using the
sample CSV file provided)
8. 4. Once the importation ended, you will see a taxonomy structure in DataManager:
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Click on any node to expand it
9. Now, let’s suppose you want to
download occurrence data from GBIF
online database for all species of
Callorhinchidae family. Then follow the
next steps!
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
10. 1. Go to Search page on the right panel to easily search for the wanted taxon, just by entering part of its name:
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
1. Go to Search page
2. Write the first letters of the taxon (“Callo”)
3. Search results will appear by levels. Just
click on the wanted taxon to see it selected
in the tree
4. Check this node, to work
just with this branch.
11. 2. Select to import data from GBIF for all the species of the wanted taxon
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
1. Check the “Callorhinchidea”
branch
2. Go to menu “Import” and select the option
“Import presence data for this branch”
3. Then select “From online GBIF database”
12. 3. As a security measure, DataManager will warn you that this operation will modify database contents and therefore
propose you to do a backup. But for this example it is not necessary, so we’ll say “No”.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
For this example, answer
“No” to the message box.
But for real usage, it may be
prudent to answer “Yes” to
make a backup copy of a
database before doing an
important modification
13. 4. You may accept GBIF terms.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
14. 5. Then you’ll have to
set GBIF
importation
options. But for
this example, you
can just indicate
the valid habitats
and accept the
other default
settings.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Note: You may find detailed information
about all options in the ModestR User
Manual available on the ModestR
Website
Remember that you
can obtain a short help
of any option just by
placing the mouse
cursor over the
corresponding
element.
Select valid habitats
for the species. In this
case, just check “Sea”
and click on “Accept”
button
15. 6. Downloading will start automatically. Data for each species will be downloaded and stored in the database. Just wait
for the task to be finished.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Species currently being
downloaded
If a species is considered a
synonyms according to GBIF,
the main species is
automatically found and used
16. 7. When download task is completed, the list of imported species maps is displayed, as well as an importation log that
you can save to a file to keep information about data sources, rights and citations. Here we have downloaded data
for all the species of a whole family. But you can do the same for any taxonomic level, from class to species.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
List of imported species maps
is displayed
You can copy or save the
importation log to keep
information about synonyms
used, data downloaded, and
data sources.
17. 8. You can click on one download species to see it in the tree and open it in MapMaker.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Globe icon aside the species indicates
that this species has a distribution map
stored in the database
1. Click on one species in the
list of downloaded species
(you can also search it in the
Search page or go to it
directly in the tree)
2. In the tree, click with the
right mouse button over the
wanted species to see
contextual menu, and select
Open map in MapMaker
18. 9. MapMaker will be ran and automatically displays the selected species.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Occurrences are shown on the map in
different colors depending on whether
they are located in a valid or an invalid
habitat.
19. 10. Close MapMaker and go back to DataManager. You can filter database records to only see the species that have
distributions maps. This is usually the default filtering when you open DataManager.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Note: remember to verify those settings when
you open DataManager. Some taxons may be
hidden because of those settings , leading to
wrongly think that they are missing.
Only the species with maps will be shown.
Go to “Search page” and check options “Show only
branches with maps” and “Show only species with maps”
20. 11. You can just close DataManager. Data are automatically stored in the database. Remember that the next time you are
running DataManager it will automatically try to open the last database you used, and usually filter species to only
show those which have maps. To permanently change the filters settings go to “Options”-”Preferences” menu. That’s
all for now!
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
1. Go to “Options”-”Preferences” menu
Select both filters
and click on
“Accept” button
21. It was the
Step by step tutorial:
How to create a ModestR database
Thank you for your interest.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/º
You can find this one and other tutorials in
http://www.ipez.es/ModestR
By the ModestR team
Colaborators:
Estefanía Isaza Toro