Questions tagged [data]
Data refers to a set of observations or measurements obtained for research purposes. Typically, quantitative or qualitative analysis is carried out on them.
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How to download transcripts with certain words in description in the ENSEMBL. description?
I want to download all human tumor transcripts (in FASTA and GTF format) in ENSEMBL and I have a skim on Customize your download and Fetch data programmatically, but none of them mentioned how to ...
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Estimating the diameter of all earths biomass as a sphere
I am working on an educational resource about the relative scales of resources compared to the earth. Attached is an example of the earth compared to various elements contained within, as well as a ...
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Datasets for Genetic Diversity of Species Across Geographical Distribution
I'm carrying out some research on applying machine learning methods to ecology and conservation. I'd like to know: are there some datasets on genetic diversity across geographical positions? ...
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Quantifying species detection probability using sign surveys as a function of distance in known occupied sites
I ran a pilot study to determine the probability of detecting a rare African small carnivore using scat (feces) detection dog surveys to assist with future population monitoring and occupancy surveys. ...
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semantical meaning of positions of letters in genomic sequences
here is a sequence from the human_nontata_promoters.zip dataset that represents a genome.
My question is whether the position in this genome data is consequent. For example, the positional letters at ...
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How do I construct sample-based rarefaction curves if the area (or volume) sampled is not consistent between samples?
My apologies if a similar question has been asked previously but I cannot find an answer.
I have data from multiple zooplankton tows from different study sites and I am trying to construct sample-...
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MTT assay data pre-processing
I was handed MTT assay data, consisting of drug doses and raw OD scores. The drug treatments were performed three separate times, each followed by MTT assay.
I applied some non-linear mixed-level dose-...
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Accessing the recombination map of Drosophila melanogaster
I'm looking for some information on the data of a recombination map of Drosophila melanogaster. In 2012, an extensive study by Comeron et al. appeared saying that they had reconstructed a ...
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DNA as a data storage medium: how many GB can a human genome store?
DNA molecules may be the digital storage medium of the future. I was looking at how much data you could fit if you would synthesize a DNA molecule the size of a human genome.
So DNA base molecules are ...
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What structures does our brain use for a quick indexing of all the data we store in our heads?
What structures does our brain use for a quick indexing of all the data we store in our heads?
From how my brains work (i.e. that I can very quickly recollect something from the past) I would say that ...
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In phospho/pan analysis in Western blots, what is best way to normalise to an internal loading control?
I am analysing the expression of a protein kinase X that is a phosphoprotein through Western blots. I have labelled the membrane for both the phosphorylated form of the protein and also for the total ...
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When analysing phosphoproteins via Western blot, why is total protein level of the target protein recommended as an internal loading control?
I am analysing the expression of a protein kinase via Western blots, and it is a phosphoprotein. I have labelled my membrane with antibodies against the phosphorylated form of the protein (using ...
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Can you use images taken at different exposure times in western blot image analysis?
I am doing Western blot data analysis where I have images from a number of experiments (where the samples in the experiments are biological/technical replicates). For each experiment, I labelled the ...
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Why do you need to calculate the lane normalisation factor when doing western blot data analysis?
I am learning about western blot data quantification from some online resources. I have read about methods to normalise the data.
I have seen in a number of resources, such as this handbook and this ...
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How to select a microscope for deep microscopy? Specifically for Deep Learning/ML model development
I am new to biology and microscopy. I am a data scientist. I am faced with a question on selecting a good microscope that enables automation of scanning the slides. And cellular object detection using ...
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What is the best way from remove background signal from a band when doing Western blot image analysis?
I am doing image analysis of a Western Blot in Image J. I have calculated the total intensity of my protein bands of interest through outlining each band using the rectangle tool in ImageJ, and ...
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Statistician confused about exact SNP data type
I'm from a statistical (not biological) background, and I'm very confused about what exactly is the "data" associated with a SNP. Below, I'll explain things as best I can--please correct me ...
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Microarray experiment validation meaning
I have a quick question: what does microarray experiment validation mean ?
I was reading a paper in which they say that the data of the experiment show that the 3 genes radB, dp1 and dp2 are co-...
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Where can I download a list of all plant species of the world?
Where can I download a complete list or dataset of every plant species in the world?
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Public fermentation/cell cultivation database?
I am wondering if there are any large collections of fermentation or cell cultivation data publicly available.
I am interested in all cell types used within industrial biotech and biopharma, ...
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How to fit simulated with measured data having systematic errors?
Consider a given time series of measured data, i.e. the number of persons tested positive for COVID-19. And consider a simulation - consisting of a model, possibly fed with some parameters estimated a ...
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Available Protein sequence alignment dataset and HMM model
I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to generate noisy copies of the consensus sequence ...
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Analysing bird diversity data across 2 sites and 2 time periods - Ordinal data. Shannon's and Jaccard?
I am looking for the best way to analyse the data below to measure and compare the bird diversity between 3 sites and across 2 time periods - basically are they different from each other and have they ...
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Where are there analyzable signed directed network datasets?
I'm looking for biological datasets with specific properties that are available for me to analyze. Informally put, I have a hammer and I am looking for a nail. That is to say, I have an algorithm and ...
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Where can I find disease diagnosis datasets?
For an epidemiological study, I'm looking for datasets for any kind of vector-borne disease (i.e. West Nile Virus, Malaria, etc.), or any parasites that are dependent on intermediate hosts (i.e. ...
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Where can I find the data on the geographical distribution of the species of Drosophila within various areas of the world?
Let X denote an arbitrary geographic area where drosophilas occur in the wild. I will need the answers to the questions of the following type:
What is the three most occurring species of the ...
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semantic similarity measurement for cell line ontologies
I have a set of cell line pairs and I want to know to what extent the pairs are similar based on their ontologies.
The problem I have is that I have found a Python library called Fastsemsim, but it ...
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High-res / high quality, public domain cell / bacteria images on the web for download
Wondering if there are any high quality, high res images of eukaryotic cells or bacteria on the web available for download (public domain). I found some illustrations which are public domain, they ...
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Database of plant morphology
Wondering if there are any open databases out there that specify the branching and flowering patterns of plant species, similar to algorithmic botany book.
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How to get taxonomic tree data
I am looking for taxonomy data of individual species and their classes something like the following format:
...
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Choosing viruses for influenza vaccine
When scientists choose viruses for the influenza vaccine based on biological and clinical data, what indicates that a certain strain will circulate and likely be dominant in a certain season?
Does a ...
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How specimens are organized in a large biological specimens archive
In a library, (and I'm not totally sure about this, but from experience) books are organized by category/theme into sections, and then they are given a number so that, globally, the numbers are ...
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Examples of striking/pedagogic large dataset analysis in biology
This question belongs in "Cross-Validated" as well as "Biology"
I am looking for example datasets that I could use both for teaching and for my personal training, that would be good examples of very ...
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Difference between NCBI's /genomes and /1000genomes
Wondering what the difference is in the data hosted here:
ftp://ftp-trace.ncbi.nih.gov/1000genomes
ftp://ftp.ncbi.nih.gov/genomes/
Also (sidenote), would be interested to note what the difference ...
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Where can I find hemagglutination inhibition (HI) assay data?
I am looking for hemagglutination inhibition assay data for type A influenza virus. I've checked in databases such as fludb.com, however it seems to only have genetic data. A lot of the time, ...
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Tensile strength of collagen?
Really specific question, but what is the average tensile strength of human collagen, type I? I've tried looking for it online, and either my google-fu skills are weak, or I'm just unlucky. Also, is ...
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Michaelis-Menten equation; how to find the constants from enzyme activity experimental results?
I was wondering what the constants in the Michaelis-Menten equation actually mean in experimental data of enzymes. How do I process the data to find Km and Kcat?
I did an experiment on catalase and ...
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What values to be taken for x-axis and y-axis?
I did a lab on form and function in photosynthesis and I recorded the values of absorption spectrum in spinach chlorophyll extract. I have the following data and I need to draw a graph. I didn't ...
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Is there any data to explore the heterozygosity of the South African lion over the last 18 years?
Background:
I need to find data on the heterozygosity of the south African lion over the last 18 years... and I'm struggling: so far I have found a single data point.
Question:
Where can I find ...
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Why the genome is divided into several chromosomes and not just a single big chromosome?
In many eukaryote species, there are several chromosomes. In humans, for example, there are 23 pairs of chromosomes.
Why are there several chromosomes and not just a join of all chromosomes into a ...
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How much Open Access Data is there in genetics? [closed]
Type of data of interest
I would like to consider
Genetics data (SNP, microsatelites, whole genome sequencing, RFLP, ...)
Genetic - phenotype data (disease-related data, QTL, etc...)
Sequence ...
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Book recommendations: biological data analysis/error
I'm working as an undergrad in a tissue culture lab, and I have the most experience with statistics out of everyone in the lab. However, most of the knowledge I have in statistics is from my math ...
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Which information can be extracted from time course RNA-Seq Data?
So I am very new to the area of biology so I am sorry if this is a stupid question.
I have RNA-Seq data carried out over a span of 100 days and I have gene expression data in the following format. ...
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It is correct to construct tree species-based rarefaction curves for birds?
If I register all the species of birds that uses sp1 tree, then, all the species of birds that use sp2 tree, and so on. With this dataset, I can made a rarefaction curve using "number of tree species" ...
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Stringdb using R Bioconductor package
I need to retreive a large dataset from String-db.
I 'm newbie in R so even with the documentation , I could not get the dataset fron String
How do I do to retreive a network from String 2k to 3k ...
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Don't understand figures in this citizen-science mosquito ID project
The Citizen-based mosquito monitoring system is a Citizen-Science vector tracking project that involves using any of a wide variety of cell phones to capture "sound bites" (sorry!) of ...
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Open access datasets for QTL analysis?
I'm just getting started out learning how to use the QTL package in R studio, and I'm trying to find additional datasets to practice with. I've already worked through the datasets here on the Rqtl ...
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Am I entitled to the latlong coordinates of all specimens used in a species revision paper?
If someone publishes a species revision with distribution maps but without publishing all the data used in the paper itself - or in an attached or linked-to file - are the authors nevertheless ...
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Looking for a database of plant features
To perform some private data science experiments I am looking for accessible information on morphological plant features (tabular information would be best). Crawling the web I found many websites ...
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Personal Genomic Data Samples
a quick question. I am looking for complete personal genomic data of human individuals. The only requirement for the genomic data is that it contains the complete set of SNPs of a human individual. So ...
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