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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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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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1answer
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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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Identifying the time window at which a meteorological factor influences tree growth the most

This is a problem I am encountering in a research project. I have thought of a naive approach to solve it which relies on many assumptions, is not guaranteed to work, and would be tedious and ...
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1answer
92 views

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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1answer
28 views

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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2answers
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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?

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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1answer
176 views

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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2answers
191 views

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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1answer
128 views

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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1answer
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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 mosquitos. These ...
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41 views

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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1answer
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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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2answers
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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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2answers
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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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1answer
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Can the concentration of a kinase be used to identify its substrate?

I'm currently working on a dataset were I'm trying to identify substrates of an kinase in silico, I have a dataset which contains the concentrations every 0h 2h,4h,6h,8h,10h,24h for a lot of proteins ...
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2answers
266 views

User friendly phylogenetic tree editing software

Background: I have Hackett 2009 (from birdtree.org) phylogenetic tree and I need to reorder it according to Prum 2015. I also work only with some species relevant to my project, not the entire tree. ...
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1answer
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Where can I find clinical trial data published in JAMA?

Data in the paper: http://jama.jamanetwork.com/article.aspx?articleid=336799 is cited in the statistical analysis in the book Clinical Trial Data Analysis using R. Can anyone help me find it?
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1answer
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Availability of a database containing the proteins of Vibrio cholerae and their corresponding gene sequences

I wanted a list of all the proteins (amino acid sequences) and their corresponding gene sequences of Vibrio cholerae. I tried to search in patric, but the number of amino acid sequences and gene ...
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Long-Term EMG studies

I am having trouble differentiating onset/offset of muscle activation. Is there anyone in the field has a specific way to set the threshold for both time and magnitude?
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1answer
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Length of anopheles chromosomes?

Where can I find the length of each anopheles chromosome? I've obtained data in which the length of each 2L chromosome for several anopheles is 39101648. I'm looking for an article that gives the ...
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Finding diploid neanderthal alignment data, looking for ambiguity codes

I'm using Neanderthal alignment data from here: http://www.eva.mpg.de/neandertal/draft-neandertal-genome/data.html Specifically, the .bam files. I would like to find alignments for neanderthal ...
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4answers
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How do I effectively visualize data showing change in a lot of samples over two time periods? [closed]

I've tallied the number of glands in a plant this year and last year. My full data set has about 20 plants in it (I've reproduced the data from 10 of the plants here). I want to show that the plants ...
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1answer
45 views

Calling Alterations in Exome Data

What are the main technical differences between accurately calling somatic point mutations vs copy number variation (CNV) in exome data? Side note: would you need other -omic data to accurately infer ...
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1answer
124 views

4DGenome or another comprehensive database of chromatin interactions

I'm searching for the most comprehensive source of chromatin interactions to support enhancer targets (data such like Hi-C, ChIA-PET, IM-PET, 5C, 4C, 3C, etc.) and my question according that could be ...
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1answer
136 views

How to retrieve logical expression (KO based) for reactions from KEGG?

Whether a module is complete or not can easily be checked by evaluating the Definition entry associated with the module; e.g. in module M00010, it is given by <...
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2answers
631 views

How to find PDB id of an amino acid sequence

Suppose I have an amino acid sequence whose PDB id is unknown. Is there in online server that can find the PDB id of the corresponding amino acid sequence? is there any site that will find the pdb ...
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What model of epistasis best fit the reality?

In theoretical population genetics, it is very common to have to assume a model of epistatic interaction. The two most common models are the additive model and the multiplicative model. Additive ...
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1answer
708 views

where can I find a full list of examples of data types in biology? [closed]

I have no background in biology and I would like to build a collection of the data types in biology. I start searching and reading bout that and found there are 7 data types: 1-Sequences: DNA, RNA, ...
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1answer
122 views

Data on Recombination rate and Gene Positions in Humans

I am looking for estimates of per base pair recombination rate in humans and indication on gene positions. The goal is to be a able to plot recombination rate in the y-axis and position (in bp) along ...
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How do I measure fermentation rate?

I'm doing a lab soon and I need to find a way to measure fermentation rate to a relatively high degree of accuracy without using a specialized sensor. It should ideally be done with easy to find tools ...
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1answer
39 views

How to incorporate intraspecific variation in discrete characters in comparative analyzes?

I'd like to run a multivariate analysis (Pavoine et al. 2011) that aims to disentagle the effect of environmental gradients on traits, considering its autocorrelation with phylogeny and space. It uses ...
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1answer
83 views

Where can I find DNA Sequence data for colon cancer

I am a computer scientist studying pattern recognition, and I am hoping to do some supervised learning on colon cancer. Unfortunately, I'm having a heck of a time finding DNA data in the following ...
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Experimental Analysis: What are possible reasons for this increase in N₂O production?

My professor wanted us to each conduct an experiment for class on something we thought would interesting. My experiment was very simple, but I'm not sure how to interpret my results. (Please note that ...
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How to find name of the gene

Considering the kegg page, this page contains the description of the gene Edwardsiella tarda EIB202: ETAE_0074 . Now this gene has a name given in the page as : wabG. Now considering another gene 1 ...
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Does this recording sound like the pulses emitted by bats?

Out of curiosity, I recorded sounds in an area with lots of bats, hoping to be able to "hear" the bats communicating by lowering the ultrasound to a level down to the frequency which can be heard by a ...
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1answer
208 views

open database of medical images

Does anyone know of an open repository of medical images (e.g., CT scans) organized by disease category? I'm working on some computer vision software that requires a large set of controls from which ...
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1answer
50 views

Bioinformatics - DNA binding, sequence-specific protein data

I am a computer scientist and we are working on protein function prediction algorithms. Right now, we would like to examine protein-DNA binding properties computationaly. For this, we would make use ...
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1answer
101 views

Methylation Data for Erythrocytes (Red Blood Cells)?

Why is it that white blood cells (leukocytes) are highly characterized in DNA methylation pure cell line profiling, but I can't find any profiles of red blood cells (erythrocytes)? Is blood considered ...
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790 views

Online Database for PPG (Photoplethysmography) signals (both Infrared and Red light readings)

I am looking for an online Database for PPG (Photoplethysmography) signals for SPO2 (oximetry) analysis. I have tried several sources but they only have single datasets labelled "PLETH" and not ...
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Do biological phenomena follow Gaussian statistics?

I have recently entered the life sciences (from physics). I am concerned about the use of p values in the life sciences literature. For example, in this article, they test 9 - 12 rats in a control ...
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1answer
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Presence of reaction module in bacteria but not in Eukaryotas (human)

From the statistics page, I found that the Module-M00008 is present only in bacteria and not Eukaryotes. Why so? I noticed that all the compounds necessary or the reaction are present in human body ...
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1answer
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Why is there a compound highlighted in red in a KEGG Module search?

Considering the following module: http://www.kegg.jp/kegg-bin/show_module?M00115+C00003 why is the compound C00003 marked in red?
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What information does the KEGG Module statistics page show?

While browsing through the home page of KEGG Module, I clicked the button named Module statistics. Can someone tell me what does these numbers signify? What are they the statistics of?
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Difference between modules in KEGG Module

The KEGG module M00115 includes a set of reactions while M00542 does not have any; it just shows the list of enzymes. Is the reaction set for M00542 still unknown?
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How to gather life-history traits data on bird species?

I am looking for a data base of life history traits for bird species. Is there such data base? If not, what are your advice on how to collect those data? Is there a handy website that list ...