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Taxonomy - Science topic

Explore the latest questions and answers in Taxonomy, and find Taxonomy experts.
Questions related to Taxonomy
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I have FASTQ files for metagenomic analysis of the 18S rRNA gene, and I began to analyze them using DADA2 in R, following the tutorial at DADA2 Tutorial(https://benjjneb.github.io/dada2/tutorial.html). However, I stopped at the taxonomy assignment step due to my laptop overheating, which means the device's performance is insufficient to complete the analysis.
My question is: Is there any way to complete the analysis and obtain the taxonomy results while using my laptop? Or is there an alternative to DADA2 that can yield similar results? I would appreciate your expert opinion.
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You can try run kaiju or kraken for taxonomic assignment. There are some online servers that can do it without the need to run it in your computer.
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Normally, a plant species need to have a scientific name as a prerequisite to be able to publish its newly discovered medicinal properties. However, in my situation, this specific plant has a common name widely known by the locals and lacks a scientific name. I'm curious if the publication of findings on an unidentified plant's medicinal properties is acceptable and justifiable?
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Hello Le; Subir offers good advice. I'd add to that by suggesting that you find a botanist to collaborate with on the project. That way you will produce a good description of the species as well as the medicinal contribution.
Best regards, Jim Des Lauriers
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Dear ResearchGate Community,
As I delve deeper into marine biology, I am particularly interested in expanding my knowledge of the taxonomy, ecology, and physiology of algae, with a focus on macroalgae (seaweeds). Unfortunately, my university does not offer a dedicated course on these topics (Phycology). Therefore, I am seeking to educate myself independently.
Could you kindly recommend essential books, guides, scientific papers, or any other academic resources that would help me gain a thorough understanding of marine algae? Your suggestions would be greatly appreciated.
Thank you in advance for your assistance.
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Marine Algae Biodiversity, Taxonomy, Environmental Assessment and Biotechnology
By Leonel Pereira, Joao Magalhaes Neto 2015
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Hi mates, I'm doing systematic work required for obtaining DNA from species that belong to a chaotic genus. I wonder if it's acceptable to apply an non-destructive extraction on the paratype? (we have more than 6 specimen for each species)
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If your method is non-destructive I don't see any reason not to proceed. Are typotypes available? If you are still nervous, you have some choices available. Best regards, Jim Des Lauriers
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I want field guide for collection of dragonflies and damselflies to study taxonomy of odonates
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There are a few field guides and collection guides available online for Odonates of peninsular and central India:
1. Andrew, Raymond & Subramanian, K.A. & Tiple, Ashish. (2008). A Handbook on Common Odonates of Central India.
2. Emiliyamma, K.G., Radhakrishnan, C. and Jaffer Palot, Muhamed (2005). APictorial Handbook on-Common Dragonflies and Damselflies of Kerala: 1-67. Zoological Survey of India, Kolkata.
3. DuBois, Robert. (2021). Sampling Design Considerations for Surveys of Dragonflies and Damselflies (Odonata) in Wisconsin. 200.
4. Fraser, F.C (1933). The Fauna of British India, including Ceylon and Burma. Odonata.Vols I. Taylor and Francis Ltd., London.
5. Fraser, F.C (1934). The Fauna of British India, including Ceylon and Burma. Odonata.Vols II. Taylor and Francis Ltd., London.
6. Fraser, F.C (1936). The Fauna of British India, including Ceylon and Burma. Odonata.Vols III. Taylor and Francis Ltd., London.
7. Mitra, T. R. (2006). Handbook on Common Indian Dragonflies (Insecta : Odonata): For Nature Lovers and Conservationists. India: Zoological Survey of India.
8. Needham, James G. 1899. Directions for Collecting and Rearing Dragon Flies, Stone Flies, and May Flies. Washington, D.C. Govt. Printing Office. (Bulletin of the United States National Museum, no. 39)
9. Needham, J. G. (1932). A Key to the Dragonflies of India. Records of the Zoological Survey of India, 34(2), 195–228. https://doi.org/10.26515/rzsi/v34/i2/1932/162568
10. Subramanian, K.A. (2005). Damselflies and dragonflies of peninsular India-A field Guide. E-book of the Project Lifescape.
I hope this helps.
Regards,
Meehir
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I need a camera lucida to draw polychaeta's chaetae and other details for taxonomical purposes, but I don't know were I can find one. On the internet I found only some museum piece. I know that I could take photos, but sometimes drawings are more suitable for taxonomic works, specially when details are not in the same focal plane. Is there a chance of getting one suitable with my microscope, that has 45° inclined eyepieces?
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Hi Alessandro
First you have to consider that drawing tubes (works similarly to camera lucida) are usually brand specific and most times even depend on the model (very important if it is to be fit in the body of the scope). On the other hand, you have the old fashion camera lucida that goes on the ocular and should fit regardless of brand (important to check diamater of ocular beforehand to check if it fits). Something very important when using a camera lucida in to the ocular is to ensure that the drawing surface is in the same plane as the camera lucida (usually the head of modern spoces have a 45º angle, so the paper you are drawing on should be at 45º too to avoid distortion). I have recently purchased one on Ebay. You should find some too (look carefully because some are sold as collectible and are way too expesinve.
Hope this helps
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Hi, I'm in Asia and dealing with the local freshwater benthic macroinvertebrates. I want to ask for suggestions on the best taxonomy book for benthic macroinvertebrates (freshwater). Googling around some books include aquatic worms, snails, etc. Thank you.
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Hi thank you for suggestion. I previously using Freshwater macroinvertebrate of jnited staye by Pennack. But hard to get or even buy a legit copy of it.
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Hi everyone,
I've been struggling to identify the family these guys belong to. Does anyone have any ideas?
Taken from NE Atlantic 2200m depth.
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Yes, Diastylidae unanimously. The pseudorostrum and anterior carapace look very much like Makrokylindrus, but the telson is wrong for that genus.
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books and scientific papers on the morphology, taxonomy and so on of ticks of the suborder Trombidiformes
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Grace Alpizar Thank you very much 🌹
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Recently, people working in faunal research have practice to photomontage when identifying a species (in most cases they are not professional taxon experts), and they make a mirror image of one half and copy it to the first half. However they publish this in quality journals. How correct is that? I've been working in traditional taxonomy for more than 30 years, and often a morphological character can only be presented on one side, or there's an anomaly on the other side, that can lead you down the wrong path.
My question is how correct is this position for traditional taxonomy?
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After having seen what I think are the figures you are referring to, is that such practice should be discouraged and considered data-manipulation, because there is no clear statement in the Materials and methods that it has been done, and why and how. This should especially be treated seriously when describing new taxa. Also, I think you should publish a note on this matter.
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Hi, what way blooms taxonomy will support innovators idea?
Kindly reply to me.
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Respected Professor,
I agreed with your explanation with Bloom taxonomy - cognitive process terms, So higher order thinking stages (evaluate, create) will helpful to innovative wonders.
Can we get the past thought process of scientific people, if we go by revised order of Bloom taxonomy (top to bottom)? By doing so, we can understand their lower order of thinking (remember, understand), which will enrich the pathway of innovation as well as the initial needs of process.
Kindly reply to sir,
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I want to do microbiome analysis using R, for which I have three folders that contain ASV data, metadata i.e. sample data, and taxonomy data for 56 sample studies. I want to read the data in those folders and create a separate phyloseq object for each sample study, then I have to make a merged phyloseq object. The issue I am facing is that while creating a phyloseq object the ASV table is said to be non-numeric. What should I do in such a case?
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# Load necessary libraries
library(phyloseq)
metadata <- "C:/Users/Saesha Verma/OneDrive/Desktop/Analysis/Metadata_table"
asv <- "C:/Users/Saesha Verma/OneDrive/Desktop/Analysis/ASV_table"
taxa <- "C:/Users/Saesha Verma/OneDrive/Desktop/Analysis/Taxa_table"
# Create empty lists to store data
metadata_list <- list()
asv_list <- list()
taxa_list <- list()
# Loop through files in each directory
for (i in 1:56) {
# Construct file paths
metadata_file <- paste0(metadata, "/Study", i, ".csv")
asv_file <- paste0(asv, "/ASVtable.SILVA.16S_", i, ".csv")
taxa_file <- paste0(taxa, "/Taxa_data_", i, ".csv")
# Read files
metadata_list[[i]] <- read.csv(metadata_file, header = TRUE, sep = ",")
asv_list[[i]] <- read.csv(asv_file, header = TRUE, sep = ",")
taxa_list[[i]] <- read.csv(taxa_file, header = TRUE, sep = ",")
# Convert ASV data to numeric, excluding the first column if it's a row name or identifier
asv_list[[i]][, -1] <- lapply(asv_list[[i]][, -1], as.numeric)
}
# Convert specific columns to numeric in metadata (if necessary)
for (i in 1:56) {
if (!is.numeric(metadata_list[[i]][, 1])) {
metadata_list[[i]][, 1] <- as.numeric(as.character(metadata_list[[i]][, 1]))
}
}
# Create empty list to store phyloseq objects
physeq_list <- list()
# Loop through data frames and create phyloseq objects
for (i in 1:56) {
# Ensure the OTU table is a numeric matrix
asv_matrix <- as.matrix(asv_list[[i]][, -1])
rownames(asv_matrix) <- asv_list[[i]][, 1] # Assuming the first column is the row names/identifiers
# Ensure the taxonomy table is a matrix and the row names match the OTU table
taxa_matrix <- as.matrix(taxa_list[[i]])
rownames(taxa_matrix) <- taxa_list[[i]][, 1] # Assuming the first column is the row names/identifiers
# Create phyloseq object
physeq <- phyloseq(
otu_table(asv_matrix, taxa_are_rows = TRUE),
sample_data(metadata_list[[i]]),
tax_table(as.matrix(taxa_list[[i]]))
)
# Assign the phyloseq object to the list
physeq_list[[i]] <- physeq
}
# Name each phyloseq object in the list
names(physeq_list) <- paste0("physeq_", 1:56)
Error in validObject(.Object) : invalid class “phyloseq” object: Component taxa/OTU names do not match. Taxa indices are critical to analysis. Try taxa_names()
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Paleontology/mammalogy/taxonomy colleagues! Does anyone have a complete citation (or, in a perfect world, a PDF) for Nordmann, 1850, the paper in which the Tribe Camelini was named?
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Nicholas; Pardon me! I submitted an answer to a different question.
Sorry, Jim Des Lauriers
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explain its morphology, taxonomy and habitat distributiion
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Fishes graze on marsh?
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I am currently studying Camellia sinensis and am at a loss in the taxonomy of this plant, if anyone knows a detailed taxonomy can help.
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In reading classes work on book content using action verbs of six levels of Bloom s taxonomy and also the technique of Q and A in such classes? As Benjamin Bloom claims that it works well in comprehension and increases students critical thinking.
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Like With Result1D("p1(1)1(1)"), instead of With Result1D(patch sweep 1^"p1(1)1(1)").?!!!
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Last weekend I took a photo of this cave-dwelling snail in a northern peruvian cave (1200 metres above sea level). Could you please help me to identify the Genus and Family? Thank you very much.
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The only species of terrestrial snails that resemble your species belong to the Family Polygyridae Pilsbry, 1895, which became a Subfamily by (Bouchet & Rocroi, 2005), also resembles a species of Planorbidae but these are Freshwater snails. The Polygyridae family does not appear to be distributed in Peru, it is certainly a new species belonging to a new genus. The ecosystem from which it comes (in a cave at 1200 m) is undoubtedly interesting, the specimen is albino. I advise you to go and get other specimens and keep me in mind if you want to describe the species. A malacologist, Roberto Ardovini.
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I am looking for a paper (or several) in which the difference between nomenclature and taxonomy has been described in a clear wording.
To me the difference of these concepts is so obvious that I never cared about something written on this.
In my current case the above is connected to resolving a homonymy.
Can someone help me with that?
Thanks
Stefan
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Nomenclature is a part of taxonomy!
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Dear scientific community, does anyone know of a #taxonomy course for #microalgae and #cyanobacteria? I'm eager to continue learning and delving deeper into this fascinating field. Any recommendations would be greatly appreciated. Thank you!
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For Cyanobacteria I would recommend taking a course at The University of South Bohemia at Cesky Budejovice, department of Botany. For freshwater in general you could try https://www.ceh.ac.uk/training/freshwater-phytoplankton-identification. Good luck!
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Morphologically
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Azolla pinnata and Azolla filiculoides are aquatic fern species with distinct morphological differences. Azolla pinnata has deeply lobed leaves with a palmate structure, while Azolla filiculoides have finely divided, feathery leaves. Azolla pinnata is smaller, with smaller individual plants, while Azolla filiculoides is larger with larger floating mats. Pinnata's coloration varies, while filiculoides' is more vibrant. Their growth habits differ.
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MICRO INQUIRY
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In biology and taxonomy, a microinquiry typically refers to a small-scale investigation or study focused on specific aspects of a biological system, often at the microscopic level. It involves detailed examination and analysis of microorganisms, cellular structures, or molecular processes. Microinquiries contribute to our understanding of biological phenomena on a finer scale, aiding in the advancement of knowledge within the field.
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O meu parecer do CNPq produtividade veio assim:
"Vou restringir minha análise à questão "taxonômica" do projeto, já que não me considero apto a opinar na área de Ecologia Aplicada. O projeto sugere que pelo fato de diversas espécies terem sido descritas para as bacias dos rios Grande, Tietê e Paranapanema existe a tendência de que muitas outras possam ser descritas nos próximos anos. Não há no projeto no entanto nenhuma descrição acerca da metodologia empregada na "descoberta" de novas espécies ou sobre a metodologia de descrição das mesmas. Não me parece ser um ponto relevante no projeto proposto."
Se o anônimo não está "... apto a opinar [julgar o projeto] na área de Ecologia Aplicada", que não aceitasse ser o revisor do projeto.
Seria conflito de interesse do revisor com essa tamanha indisposição?
Qual caminho seria mais justo na sua opinião?
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Eu não acho que deveria ser duplo cego. Acho ao contrário. Deveria haver total transparência. O avaliado saber quem o avaliou, e o avaliador saber quem está avaliando. A transparência total é sempre o melhor caminho.
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I have been searching for the internet page on Nomenclator Zoologicus online by uBio but it seems that the link is not working.
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Submit your abstract for the Symposium organised by Ivana Rešetnik and me at the XX International Botanical Congress in Madrid (21-27 July 2024)!
The deadline for abstract submission is November, 30 for oral presentations and February 1, 2024, for posters.
The general link to the congress: https://ibcmadrid2024.com/
Our symposium is the n. 13
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Thank you
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Dear All
Please help me to identify the plant/
Thanks in advance 
Rishad
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The above plant is Aporosa wallichii Hook.f. of Phyllanthaceae family.
Thanks!
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According to Andersson (1990), "The only thing generally agreed upon is that variation in phenetic parameters is not continuous and that character states are not combined randomly". In the same work, he defines species as clusters of individuals in a multidimensional space, where each character marks an axis (and thus a dimension).
However, in practice, when conducting taxonomy at the species level, we frequently encounter intermediate states, hybridizations of characters, etc., which can cause us to question whether the compartmentalization of the total character hyperspace that defines a species is, at least in part, a construct of ours rather than of nature.
So the question I would like to ask is: If biological diversity could be expressed as an n-dimensional mathematical function, what type would it be? Clearly, there are not infinite intermediate states between each species (as a continuous function would seem to require) and there does appear to be empty interstices between the hypervolumes, as Andersson asserts, but do the intermediate characters we find in practice not prevent the function from being entirely discrete?
REFERENCE:
Andersson, L. 1990. The driving force: Species concepts and Ecology. Taxon 39(3): 375-382.
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hi
a very old principle of natural philosophy is that "Natura non facit saltus". More scientifically Darwinian paradigm states that a species always originate from another species through gradual changes. All the biological diversity thus appeared through gradual changes. However, as life is though, most of species are extinct. And this introduces discontinuity, at all the level of biodiversity. Your question can thus be answered only once time scale is given. Cheers
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Hi,
Dear Acarologists and everyone else.
I hope this day will bring you joy, happiness, and success.
I want to get your opinion. Which Software do you use to Illustrate mites or other arthropods? By Illustrate, I mean the usual line drawings in the publication. I use Adobe Illustrator, but I would love to try different options.
So, let me know what you are using or send your recommendations.
Does anyone have experience with AI in this regard? It would be great if we could use it.
Thank you for reading, and I am patiently awaiting your experiences and suggestions.
Regards.
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Dear Jawwad,
Perhaps my approach is a bit old-fashioned - and not the answer you are looking for - but I still prefer to work from a pencil (via camera lucida) and ink these with a pen. The most important benefit of this is that I'm not on a computer during the "ink" phase. So, I can do inking at home and not be anti-social with the family. I might half-watch a movie with the kids, or watch a game of sport. I can do it pretty much anywhere I please providing I have a table and a USB battery pack for the light board - outside, watching birds etc. Any time spent off a computer is good.
After inking, I transfer to Adobe Photoshop, clean the image, add lines if needed, and label. It's then back to the microscope for checking.
If I could not afford Adobe, then I recommend GIMP and, for vector graphics, Inkscape. I haven't used GIMP a great deal, as I've not lost access to Photoshop. I use Inkscape for non illustrative figures but I'm sure it can do scientific illustration. I just find the whole process much slower, less satisfying, and has to be done at my workplace.
There's at least one Acarology-based paper on this topic:
Katya made extraordinary illustrations, so it's a fine technique if you have the technology and patience.
Best wishes,
Owen.
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What would be the correct way of stating that the particular taxon belongs to a species complex, during identification? For example, a gecko that belongs to the Hemidactylus brookii complex. Thank you for the help.
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if the genus gets too large and the species difficult to differentiate I call the genus a 'supergenus' eg, the genus Thyone amongst dendrchiortid holothuroids (please note the apostrophe before and after) but this has no nomenclatural status. If, on the other hand, there are too many different types within a species, which are difficult to separate, I call them cryptic/sibling species, or simply eg. the Thyone fusus complex, using the type species of the genus. Hope this helps.
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In the modern era of technology, many microcontrollers are equipped with multicore processors.
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Yes, Internet of Things (IoT) devices and embedded systems can be classified within Flynn's taxonomy. Flynn's taxonomy is a classification scheme for computer architectures based on the number of instructions and data streams that can be processed simultaneously. The four categories of Flynn's taxonomy are:
  • Single Instruction Single Data (SISD): These architectures process a single instruction on a single data stream at a time. Most traditional personal computers and workstations are SISD architectures.
  • Single Instruction Multiple Data (SIMD): These architectures process a single instruction on multiple data streams at a time. SIMD architectures are well-suited for applications that involve parallel processing, such as image processing and video encoding.
  • Multiple Instruction Single Data (MISD): These architectures process multiple instructions on a single data stream at a time. MISD architectures are rarely used in practice, but they can be useful for applications such as fault tolerance and redundancy.
  • Multiple Instruction Multiple Data (MIMD): These architectures process multiple instructions on multiple data streams at a time. MIMD architectures are the most versatile type of architecture and are used in a wide range of applications, including supercomputers, high-performance computing clusters, and cloud computing platforms.
IoT devices and embedded systems can be classified into all four categories of Flynn's taxonomy. For example, a simple IoT device such as a smart thermostat is typically an SISD architecture. A more complex IoT device such as a self-driving car is likely to be an MIMD architecture.
Here are some examples of IoT devices and embedded systems classified within Flynn's taxonomy:
  • SISD: Smart thermostat, smart light bulb, fitness tracker
  • SIMD: Smart camera, video encoder, image processing accelerator
  • MISD: Fault-tolerant control system, redundant sensor system
  • MIMD: Self-driving car, industrial robot, cloud computing platform
It is important to note that Flynn's taxonomy is a simplified classification scheme and does not capture all of the nuances of modern computer architectures. For example, many modern processors can support both SISD and SIMD instructions. Additionally, some IoT devices and embedded systems may use hybrid architectures that combine elements of multiple categories from Flynn's taxonomy.
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Taxonomy of Brachymeria species
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Hello Varun; I got curious and found this paper that might be of some interest to you. Enjoy it, Jim Des Lauriers
Get access 📷Sexual size dimorphism in parasitoid wasps
Bethia Hurlbutt
Biological Journal of the Linnean Society, Volume 30, Issue 1, January 1987, Pages 63–89, https://doi.org/10.1111/j.1095-8312.1987.tb00290.x
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Hello:
I have a question about the definition of adaptive control, since I´m researching about making a model-free adaptive control system. I will appreciate your help.
The definition I found says that an adaptive control modifies its parameters or structure in order to achieve a performance index. Reading about the subject in different sources I noticed that when they refer to an adaptive controller, it always has a model of the plant and implies an adaptation law which is usually obtained by taking the model and manipulating expressions.
My deduction is that when these sources refers to adaptive control, is about a kind of this instead. Am I right? I will really appreciate your support on this.
Thanks.
Pablo.
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People do many things without adaptive control.
However, at some point, we may understand that the performance may not be what we were looking for. Either the plant parameters were not exactly what we thought, or they might have changed from what they were in the beginning. Moreover, the object of control could be time-varying, nonlinear, etc.
This is what led people to think about “adapting” the control parameter to the actual situation.
A first idea was to only change the main control loop gain. This was called the MIT rule and it worked nicely and was even implemented on a plane that flew nicely…until it crashed. Comes out that working with time-varying control parameters is not the same as fixed parameters.
This made people reluctant to the idea of adaptive control.
Then, some names, such as Prof. Kumpati (Bob) Narendra from Yale, contributed a lot to the theory of stability and also came up with their own idea of adaptive control. This appears in literature as Model Reference Adaptive Control (MRAC) and this is what you usually see in literature.
It requires the plant to behave like some ideal model of the same order and indeed, it tries to modify the parameters of the big plant.
As it happens, by 1980, after some engineering experience, I came to RPI (Rensselaer) for a PhD. The “problem” was that the Professor’s grant was for Large Flexible Structures (LFS). They were not only large plants but also MIMO, so there was not much we could do with the classical MRAC.
They started using another idea, which was called Command Generator Tracking (CGT). You don’t try to make all state variables of the big plant follow all state variables of some big model. Instead, you define some low-order model that only defines the trajectory that you would like your plant output to track. They had some publications, yet the idea was negatively received, so they were almost on their way out. However, the grant forced my advisor to let me “try to do something.”
As I was coming from the industry, I liked this idea of a simplified controller with varying parameters, and I even “felt” that it should work. The plant can be of order 20 or 50 and yet the model and the controller can be of order 5.
What can I say? I ended up with a low-order adaptive controller that managed to control the pretty big LFS. It was interesting that people at JPL liked the idea and even dared to implement it on their large flexible antenna.
After playing with it, I decided to call our approach “Simple Adaptive Control (SAC).”
I won’t make this message a dissertation, but if you write Simple Adaptive Control on Google, you can see quite a bit, of publications from all around the world.
Also, please always feel free to come back with any questions.
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Dear colleagues, especially from India -
Could you please share PDF file of this article: KOMAREKJ,. (1972). Reproduction process and
taxonomy of unicellular endosporine blue-green
algae. In Proceedings of the Symposium on
Taxonomy and Biology of Blue-Green Algae,
pp. 41-47. Edited by T. V. Desikachary. Madras,
India: University of Madras.
I'll appreciate your help very much.
Sincerely, Igor Brown
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You might be able to contact Professor Komárek and request the paper at his webpage: https://www.phycology.cz/people/ji%C5%99%C3%AD-kom%C3%A1rek
or go to https://www.phycology.cz/contact and then press 'People' and you will find his page.
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I recently observed this strange worm in a Northeast Peruvian cave, which seems to catch its prey with hanging strings. Any idea what it is? Thank you very much in advance.
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Thank you very much Owen Seeman . I just saw the photo and I'm pretty sure you're right - thank you very much!
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These ants are closely related to Apis cerana bees in South India.
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From the picture it can be guess that the ant is either Camponotus mitis or Camponotus nicoberensis.
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I have tried to id it but became confused. The crab on the photo looks more like an immature Uca perplexa (as of unbarred leg and lemon yellow color, pattern of dorsal carapace) though having superficial resemblance with Uca triangularis (due to angular spines of carapace).
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Dear ResearchGate community,
I'm currently working with a large dataset of phytoplankton species, and I'm looking for a way to routinely update the taxonomy of these species. Specifically, I'm interested in identifying changes to scientific names, accepted names, synonyms, and higher-level taxonomic classifications.
I've tried using various R packages such as worrms to retrieve taxonomic information from online databases, but I've encountered some challenges with data quality and consistency.
I would appreciate any suggestions or advice on how to efficiently and accurately update the taxonomy of my dataset on a regular basis. Are there any reliable databases or APIs that I should be using, like AlgaeBase? Are there any best practices for handling taxonomic data in R?
Thank you for your help!
Nicolas
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Hi Hana,
You have several ways to proceed. The first one is to use the worrms package (https://docs.ropensci.org/worrms/articles/worrms.html). This package can be a good alternative. The second one, which is a bit more complex, is to request an API key from the administrator of the Algaebase website (https://www.algaebase.org/api/). Afterwards, you will need to create a function in R that allows you to retrieve the information in JSON format and convert it into a dataframe. By the end of the year, I will post on my GitHub the functions that I have created/used to update my data.
Alternatively, you also have https://docs.ropensci.org/taxize/index.html. You can find a lot of information on this website as well: https://www.marinedatascience.co/data/.
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And why for some groups of organisms (for example, for insects) the presence of subgenera in the taxonomy of the group is more typical than for others?
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Hello Alexandra; Among the ants that I study the place of "subgenus" in the taxonomic heirarchy is often referred to as a "species group". Since both terms are not formal parts of the taxonomic nomenclature, which term is used is probably a matter of taste within the group of taxonomists that specialize in that group. Hmmm. Best regards, Jim Des Lauriers
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It uses acronym to compile the taxonomies of electronic dictionaries. Give me that computer scientist a correct definition and a motivation. As a linguist I can give this definition /synthesis for a keyword.
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La comunicazione oggi è in acronimi ed espressa per grafici di algoritmi e....
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I fear that even in my discipline (botanical taxonomy) some people will come up with manuscripts completely written by algorithms in the near future, especially since the whole academic world seems to only revolve around papers and impact factors. There are already way too much papers being published and their metrics have become largely meaningless or at least questionable for a lot of reasons. With the new sophisticated KI-applications, it seems possible, if not likely, that many "scientists" in need of output (early career, temporary employed, people without original thoughts...) will be tempted to let their papers be written at least partially by software. Wouldn´t it be a good idea to force the authors of a scientific paper to clearly state the usage and its extent of such programs in a respective paragraph? There is (at least here in germany) the obligation to make an affidavit statement when submitting a thesis, assuring that it was made without the help of others etc. I have never seen this in the context of publishing a scientific manuscript. Isn´t it time to get something like this into practice? I will be more than happy to make clear that I have written all my papers using my own mind and those of my co-authors only!
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I believe that it would be inevitable, sooner or later, to use AI in scientific articles and other types of science production, such as text or script correction, etc. It would be like using R for statistics…nobody conducts statistics by hand anymore. Furthermore, there are some editorial companies, such as Elsevier, that have already incorporated the use of AI into their author policy. For instance, they ask authors to only use these technologies to improve readability and language, not to replace key researcher tasks, to apply the technology with human oversight and control, and to disclose in their manuscript the use of AI and AI-assisted technologies. Authors are ultimately responsible and accountable for the content of their work. However, up to now using AI seems to be relatively limited or inefficient for certain tasks, since at least according to my experience with the chat of Bing (Microsoft), it is a system relatively limited in finding the most relevant papers in an area, and or for filtering between information produced by a scientific paper (with data evidence) or that is just mentioned on a web page. I believe AI is important for science, as an aid, but that so far it will not replace any mindful researchers. After all, the invention of calculators and of systems such as R did not end mathematics or statistics, respectively. On the contrary, they have helped them
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I have two morphologically similar species that differs molecularly only by 4 bases. Can I synonymmized them? If not, how many base differences can lead to this taxonomic revision? How do I deal with such taxa?
I am looking forward to hear from all experts regarding this unclear situation.
Best Regards
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A paper was published in Taxon sometimes back: Sleepless nights - please do not describe your species based on molecular differences.
I hope this helps.
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I want to do the taxonomy and the phylogeny of the Mycorrhizas (Ectomycorrhizas and Endomycorrhizas). Can you please recommend some necessary publications? Also the effcitive method to obtain the isolates of Mycorrhizas.
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The contagious accomplices in these symbioses are right now positioned in the Zygomycetes in the request Glomnles. Little is had some significant awareness of their variety, particularly at the particular and sub-explicit level. The investigation of variety among arbuscular mycorrhizal growths (AMF) is mostly hampered by the restricted scope of helpful morphological characters and their inconsistent or deficient use in species portrayals. In an endeavor to defeat this issue, sub-atomic methods have been applied. Even though isozymes and DNA arrangement information can recognize growths at any taxonomic level, the species and family idea in the Glomnles are stiH, not distinct, and further work is expected to lay out the degree of ID helpful in investigations of the science and biodiversity of these naturally critical parasites. History Thaxter (1922) gave the basis to the scientific categorization of these organisms, however, their trophic status was not known around then, and both mycorrhizal and non-mycorrhizal parasites were ordered together in one family, Endogone. In 1953, the primary connection was made between 'Endogone' (= Glomus mosseae) spores and the mycorrhizal propensity for growth (Mosse, 1953). This was trailed by the casual portrayal of a few 'spore types'
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This beautiful orchid was recently seen by a friend in the north peruvian Andes (Amazonas). Does anybody know to which family and genus it belongs ?
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I suspect that Utricularia caerulea is found in South America.
Thanks!
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Why is chaetotaxy (of Head and Thorax) given so much importance in taxonomy of flies? Does it bear any evolutionary significance?
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James Des Lauriers, Thank you!
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I do not find clear to which specie the aforementioned organism belongs. On some sites, I read that it references to a group of unclassified species instead ofjust one. I would appreciate if anyone may enlighten me with a taxonomy/phylogenetic approach.
Thanks in advance!
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Hello Juan; Here is a link with a little discussion and some citations. Maybe they will be useful. Best regards, Jim Des Lauriers
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When rever what is waterbird the obvious answer always said that waterbird is a type of bird that lives and depend their live around body of water. But is it just that? Does waterbird itself has special taxonomy like subclass or other? or is it classify by only their morphology?
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You can have any classification you like if it makes sense to you :)
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Recently I took a photo of this cave-dwelling harvestman some 300 meters from the entrance in a northern peruvian cave (1500 metres above sea level). Could you please help me to identify the Genus and Family? Thank you very much.
Greatings from Peru and a happy new year!
Stefan
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Hi Stefan. It is a very troglomorphic and posible troglobite opiliones (endemic from these cave). Including can be a new species. Did you sample?. Please write me (marconisilva@ufla.br) then we can talk a Little more about this amazing animal.
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Taxonomic measurements are critical for formal descriptions of metazoans. However, often these measurements are only provided in a table within the manuscript, losing data from individual specimens in the process, which could be used for morphometric, morphological or other studies.
My question is if anyone knows of an online repository where files (mainly with .xls extension) can be included.
Such a repository that works like ZooBank but with files instead of nomenclatural acts would be extremely useful. When you upload the file, the repository will give you a link to include in the manuscript. This link will be private until the manuscript is published, and then everyone can access the file via the link in the manuscript.
This would provide a very interesting database with individual morphometric data that does not exist for several animal groups.
If you know of such a repository, please let me know.
Thank you in advance.
Best wishes,
Alberto.
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Finally, after an extensive search, and as stated by Miralles et al., (2020), we have not found the aforementioned repository.
Our solution (specific to the study group, in this case, the kinorhynchs) has been to create the database ourselves. For all those interested, the Kinorhyncha Measurement Databse is available at this link: https://sites.google.com/a/meiobenthos.com/laboratory/database/kinorhyncha-measurement-database.
However, we are aware that this is only a specific (and partial) solution for a small group of animals, and the fact that we had to create the database ourselves highlights the need for a global, official and organised repository of taxonomic measurements.
REFERENCES:
Miralles, A., Bruy, T., Wolcott, K., Scherz, M. D., et al. 2020. Repositories for Taxonomic Data: Where We Are and What is Missing. Systematic Biology 69, 6: 1231-1253. https://doi.org/10.1093/sysbio/syaa026.
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What is your opinion on the ongoing discussion regarding the taxonomy of the genus Penaeus?
As someone that is not a taxonomist, when I began working with shrimp I was not aware of it and simply used Litopenaeus because it was the name that I mostly read in recent publications. Today I came upon a recent article published in Aquaculture "Making sense of the taxonomy of the most commercially important shrimps Penaeus Fabricius, 1798 s. l. (Crustacea: Decapoda: Penaeidae), a way forward" that drew my attention to it. There is also an older article by Tim Flegel that deals with this (See below). I am considering using his recommendation of placing the sub-genus in parenthesis, e.g., Penaeus (Litopenaeus) vannamei, because I find his arguments reasonable and what the Yang et al. (2023) study found, but I am concerned because it seems that the use of the sub-genera as genera is very prevalent already.
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I think it is important to consider the ongoing discussion regarding the taxonomy of the genus Penaeus. It is clear that there is a lot of debate surrounding the use of the sub-genus Litopenaeus as a genus, and that there is no consensus on the matter. However, the Yang et al. (2023) study found that the sub-genus Litopenaeus is distinct from Penaeus, and I think it is important to consider this when deciding which taxonomy to use. I also think that Tim Flegel's suggestion of using the sub-genera in parenthesis is reasonable and could help to clarify the taxonomy for people who are not taxonomists. Ultimately, I think it is best to use whichever taxonomy is most accepted and widely used in the scientific community.
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Would you agree its Minuca zacae?
It is from the Eastern Pacific. Coloration is true to living color as the specimen is fresh. Collected on high mangrove area. If there are questions that might help the ID, please let me know.
Thanks in advance for the feedback
Cheers!
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You can identify a fiddler crab species by examining its enlarged claw: the sand fiddler crab's claw is smooth on the underside. If the claw is not smooth on the underside and had red joints, it is a red-jointed fiddler crab. Otherwise, it is a marsh fiddler crab.
Besides mud fiddlers, two other species of fiddler crabs are common along the southeastern Atlantic coast: Uca pugilator, the sand fiddler; and Uca minax, the red-jointed fiddler
Male fiddler crabs are lopsided. Females have two claws of about the same size. Males have one regular size claw and one outsized claw, really outsized.
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At the point we have reached in taxonomy and systematics today, it seems that we are in a situation where details and extremes (in the popular sense) ignore the basics (in the classical sense). Therefore, in a popular sense, we seem to be in a situation (especially by amateur researchers) in which many researchers publish articles without adequate knowledge of the scientific foundations, or even if they do, ignoring these foundations. From this point of view, I think that we should remember the scientific foundations again and know what and how the studies serve.
In this sense, what is taxonomy iessentially and clearly? From what need and how did it arise? What is its main subject and approach? And again, what is systematic essentially and clearly? From what need and how did it arise? What is its main subject and approach?
I think these questions should be answered clearly.
Can a systematic study be done without knowing the taxonomy and a taxonomic study without knowing the systematics? Concisely and clearly, what is a taxonomic study and what does it encompass? What and how does it serve? Also concisely and clearly, what is a systematic study and what does it encompass? What and how does it serve?
I would appreciate if you could share your valuable ideas...
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Good question. The answer have existing at least half of century already. For clear I strongly recommend the brilliant book of Willi Hennig "Phylogenetic Systematics". Please, check it here: http://aracnologia.macn.gov.ar/st/biblio/Hennig%201966%20Phylogenetic%20Systematics.pdf
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Hi, I hope all who are reading, will be fine.
I would like to know more and extend my knowledge about the expert researchers, scientists, and professors, who spent their lives and are spending their precious time exploring mite fauna. Is there any website or internet resource where we can search for names of expert Acarologists? Like in the field of Taxonomy, systematics, genetics, behavior etc.?
I found it difficult to individually search for experts in each field/subject.
Thanking in anticipation.
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I would recommend to look at:
History of Acarology - Google Books
https://books.google.com › books › about › History_of_A...
Bibliographic information ; Title, History of Acarology ; Editor, Vikram Prasad ; Publisher, Indira Publishing House, 1982 ; Length, 472 pages.
and these websites :
DIRECTORY OF ACAROLOGISTS OF THE WORLD 2002
https://www.nhm.ac.uk › hosted_sites › acarology › ica
Specialization: Area of specialization: Ticks and tick-borne diseases. Abou-Awad, Badawi National Research Centre Plant Protection Laboratory, 12311 Dokki, ...
Online directory and list of Acarologists of the World: Join online directory · ICA Directory of Acarologists (2010).
Directory: Society
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Hi everyone, I was wondering about the possibilities of performing numerical taxonomy with SPSS software. I would be very thankful to recieve advice!! For now I have been reading about hierarchical clustering, principal component and discriminant function analysis... Help!!
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you can do it by xlstst to make a hierarchical clustering
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Does anyone have photos of Entomobrya elegans Stach, 1963 and Entomobrya albanica Stach, 1922?
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Dear Antipova, there is a drawing in the original description, see plate XXXIII
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Hello! Between mid-April and throughout June2017 we carried out an extensive sampling to estimate sea urchin settlers through collectors placed on the bottom floor along the Sinis Peninsula (Westcoast of Sardinia , Italy).
We placed 100 collectors at five metres depth, on rocky bottom and Posidonia oceanica meadows, inside and outside the Marine Protected Area of Sinis (according to the method described by Tomas F, Romero J, Turon X, 2004) to evaluate settlement and recruitment of sea urchin Paracentrotus lividus in two contrasting habitats in the Mediterranean (Marine Ecology Progress Series 282: 173-184). Altogether we collected about 500 samples kept at -20 deg. in 70% alcohol. Moreover, we characterized sampling stations calculating habitat and landscape metrics.
However we found many other species of organisms, especially polychaetes, molluscs, crustaceans, other echinoderms, etc.
At the moment we lack resources to perform taxonomic work on these communities.
We are happy to send over the samples to anyone who could be interested. Considering we do have all the environmental data metrics, it would be great to identify biodiversity hot spots in the study area once we have the taxonomic data.
If interested, please contact me at: s.farina@fondazioneimc.it
Cheers!
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It's too late, but I will be interested
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Recently there were published many “comment papers” in valid journals such as Palaeoworld, Geological Journal, Carbonates and Evaporites and ... regarding the larger benthic foraminifera where accurate identifications require a high level of experience and knowledge of their taxonomy, this is the main question who are really the cause of these mistakes and problems?
1- Authors
2- Reviewers
3- Editors
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Peer-review process should commonly discover such obvious mistakes even if the authors are not specialists in taxonomy.
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1. I suggest to prepare the paper devoted the issues of non-financial reporting (institutional approach; non-financial reporting as a source for decision-making; Taxonomy for non-financial reporting, etc.).
2. If someone has an option to publish an article in such a journal, we can prepare an article together. We can also join forces and conduct joint research in this area.
Waiting for response
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I have completed taxonomy assignment of the assembled contig from raw data but I cannot get the relative abundance of the species present. Is there any tool that can do that?
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Hello Ishtiaque,
I have found that Kaiju (taxonomy based on sequence homology) and Metagenomic Intra-species Diversity Analysis System (MIDAS; taxonomy based on curated phylogenetic trees) work terrifically for analyzing relative abundances of taxa with WGS data. These two tools complement each other as well.
Ryan
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This species is encountered in Kokrajhar town of Assam, India. It is thin walled bamboo. As per my knowledge it seems to be Schizostachyum sp. I request the peers to kindly help me identify the same.
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It can not by pic, should be original plant
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I have set of tags per document, and want to create a tree structure of the tags, for example:
Tags:
- Student,
- Instructor,
- Student_profile,
- The_C_Programming_Language_(2nd Edition),
- Head_First_Java
I need to generate a hierarchy as per the attached example image.
Are there Free taxonomy/ontologies which can give Parent words? like
get_parent_word( "Student", "Instructor") = 'People'
get_parent_word("The_C_Programming_Language_(2nd Edition)", "Head_First_Java") = "Book"
is_correct_parent(parent: "Student", child: "Student_profile") = True
I have a corpus of English as well as Technical documents and use Python as the main language. I am exploring WordNet and SUMO Ontology currently, if anyone has used them previously for a similar task or if you know something better I would really appreciate your guidance on this.
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Bahadorreza Ofoghi , thanks for sharing, it looks interesting.
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I can't find a rigid reference defining which is considered computational and which is not and saw some taxonomies including the regression ( isn't this just statistics?)
I am a bit confused and I feel like the term is loosely defined within the literature (at least what I have looked up)
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Hi Omnia,
I believe that is very important to know most specificly the motivation about your ask.
If the motivation is to know how to aplly the "computational methods", i recommend the lectures in articles that use the same methods.
For exemplo in the google schoolar are 85.000 articles with this subject. So, is necessary aplly most criterious to decrease and to define the article's area.
But, i saw that you are a researcher in the social area. In this case, i recommend you see the article in the public encyclopedia in the link below (use the translate):
I know that the wikipedia is not a good reference in the champ universitary, but, when do you want do a first reading i think that is a good option.
I hope hep you,
Caio Serpa.
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What are the most influential ontologies or taxonomies in the behavioral/social sciences? How did they make a difference? What does it mean to be an influential ontology or taxonomy? Citations? Use? Saved lives?
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Oh now I see. Do you mean taxonomies of phenomena in psychology? Of course now I understand that my answer is for the philosophical part and not so much for categories that are used in research on general psychological processes.
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While describing or analyzing species taxonomy, we find some taxonomic changes proposed within thesis that we considered appropriate but, since they have never been published in peer reviewed articles they are not officially accepted.
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Everything that is not published, in terms of scientific information and more in terms of changes or taxonomic proposals, does not exist! You must either publish it yourself and propose it or find the author and publish it together.
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I need help identifying eukaryotic microorganisms found in aquatic samples from a fish farm. Could somebody recommend a source I can use for the taxonomy identification? Or want to take a look at the pictures of my little creatures?
I appreciate any kind of help.
Cheers
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Abhijit, Marc, and Marion thanks for replying and sharing your answers.
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I do not understand what do you mean by taxonomy in it? Is it related to 4IR or the roles of management ?
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We are trying to better understand the taxonomy of liberica and excelsea to find ways to help farmers taking decisions of how to replant different fields and plots of coffee.
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I am not an expert in this field
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I have asked a question, If baboons appear more like us than any other of our primate relatives, is it sane if I think in reconstructing biological taxonomy on a Cultural basis? Now, I want to ask about the meaning which Culture is supposed to be if this taxonomy wants to go further.
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You are most welcome dear Ali A Moursi . Wish you the best always
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If Ardrey suggested that 'because of its terrestrial life the baboon, as I have suggested, pursues an existence more resembling the human than any other of our primate relatives.' is it sane if I think in reconstruct biological taxonomy on Cultural basis?
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A relevant and valuable open-access source (with a very deep list of references) is available on 'eLife': "Insights into the evolution of social systems and species from baboon studies" by Fischer et al. (2019) -- see:
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Soil profile presents a two-dimensional view of the soil body. According to Hartemink (2009), the first depictions of soil profiles were made in the late 1700 long before soil science was established. The soil profile may also be taken as one side of a pedon, the three-dimensional conceptual soil body used as the basic unit of classification in the Soil Taxonomy of USDA. Simonson and Gardner (1960) who proposed the pedon concept compared it to the cell in biological systems. This comparison, however, has been criticized since cells are functional units with real boundaries (cell walls) while pedons have no boundaries since the soil is a continuum. The French pedologist A. Ruellan, past president of the International Union of Soil Sciences, has summarized the criticisms against the pedon concept, as follows: it is not a natural unit of the soil cover but only an abstraction, its morphological lateral limits are artificial, and its genesis is interpreted vertically without looking at the lateral dynamics and relationships (Ruellan, 2002). What is your opinion on this? Which is a better unit or model to use in the study of soils?
References
Simonson, R.W. and D.R. Gardner. 1960. Concepts and function of the pedon. Trans. 7th Intern. Congr. Soil Sci., Vol. 4, Madison, pp: 127-131.
Hartemink, A.E. 2009. The depiction of soil profiles since the late 1700s. Catena 79: 113–127
Ruellan A. 2002. Classification of pedological systems: a challenge for the future of soil science. Trans. 17th World Congr. Soil Science, Bangkok.